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MAURICIO, I. L., J. R. STOTHARD, and M. A. MILES. "Leishmania donovanicomplex: genotyping with the ribosomal internal transcribed spacer and the mini-exon." Parasitology 128, no. 3 (March 2004): 263–67. http://dx.doi.org/10.1017/s0031182003004578.
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Intergenic region typing by restriction analysis of the ribosomal internal transcribed spacer (ITS) and mini-exon provide diagnostic markers for someLeishmania. Here, we evaluate restriction analysis of these targets for genotyping and phylogenetic analysis within theLeishmania donovanicomplex (agents of visceral leishmaniasis). Each method was useful for genotyping of bothL. donovanicomplex strains and Old WorldLeishmaniaspecies. The targets produced less robust groups than gp63 intergenic regions, but support the need for re-evaluation of the taxonomy of theL. donovanicomplex.
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Zhuo, Lang, S. L. Sajdak, and R. B. Phillips. "Minimal intraspecific variation in the sequence of the transcribed spacer regions of the ribosomal DNA of lake trout (Salvelinus namaycush)." Genome 37, no. 4 (August 1, 1994): 664–71. http://dx.doi.org/10.1139/g94-094.
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Intraspecific variation in the sequence of the transcribed spacer regions of the ribosomal DNA (rDNA) in lake trout was examined by restriction mapping and sequencing of these regions amplified by the polymerase chain reaction. The length of the first internal transcribed spacer region (ITS-1) was 566 bases and the second internal transcribed spacer region (ITS-2) was 368 bases in lake trout. When the 1.4-kb region including the ITS-1, the 5.8S coding region, and the ITS-2 was amplified from 12 individuals from four populations and digested with eight different enzymes only one intraindividual polymorphism was found that occurred in each population. When the amplified ITS-1 region was sequenced from an additional 10 individuals from five populations, no interindividual variation was found in the sequence. A 6-kb portion of the rDNA repeat unit including 1.6 kb of the 18S coding region, the 5′ external spacer region (5′ ETS), and part of the adjacent intergenic spacer was cloned and a restriction map was prepared for these regions in lake trout. No intraspecific variation was found in the region adjacent to the 18S rDNA, which includes the 5′ ETS, although intraspecific and intraindividual length variation was found in the intergenic spacer region 3–6 kb from the 18S. Sequencing of a 609-b segment of the 5′ ETS adjacent to the 18S coding region revealed the presence of two 41-b repeats. The 198-b sequence between the repeats had some similarity to the 18S coding region of other fishes. Primers were designed for amplification of 559 b of the 5′ ETS using the polymerase chain reaction. No intraspecific variation in this region in lake trout was found when the DNA amplified from this region in 12 individuals from four populations was digested with eight restriction enzymes.Key words: ribosomal DNA, internal transcribed spacer regions, 5′ external spacer region, transcribed spacer, lake trout.
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Dingman, Douglas W. "Paenibacillus larvae 16S–23S rDNA intergenic transcribed spacer (ITS) regions: DNA fingerprinting and characterization." Journal of Invertebrate Pathology 110, no. 3 (July 2012): 352–58. http://dx.doi.org/10.1016/j.jip.2012.03.026.
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McCullough, Michael J., Karl V. Clemons, John H. McCusker, and David A. Stevens. "Intergenic Transcribed Spacer PCR Ribotyping for Differentiation of Saccharomyces Species and Interspecific Hybrids." Journal of Clinical Microbiology 36, no. 4 (1998): 1035–38. http://dx.doi.org/10.1128/jcm.36.4.1035-1038.1998.
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The taxonomy of the genus Saccharomyces has undergone significant changes recently with the use of genotypic rather than phenotypic methods for the identification of strains to the species level. The sequence of rRNA genes has been utilized for the identification of a variety of fungi to the species level. This methodology, applied to species of Saccharomyces, allows unknown Saccharomyces isolates to be assigned to the type strains. It was the aim of the present study to assess whether typing of the intergenic spacer region by using restriction fragment length polymorphisms of PCR products (intergenic transcribed spacer PCR [ITS-PCR] ribotyping) could distinguish among type strains of the 10 accepted species of Saccharomyces and further to assess if this method could distinguish strains that were interspecific hybrids. Cellular DNA, isolated after the lysis of protoplasts, was amplified by PCR using ITS1 and ITS4 primers, purified by liquid chromatography, and digested with restriction endonucleases. Ribotyping patterns using the restriction enzymes MaeI and HaeIII could distinguish all species of Saccharomyces from each other, as well as from Candida glabrata, Candida albicans, and Blastomyces dermatitidis. The only exception to this was the inability to distinguish betweenSaccharomyces bayanus and S. pastorianus(S. carlsbergensis). Furthermore, interspecific hybrids resulting from the mating of sibling species ofSaccharomyces were shown to share the ITS-PCR ribotyping patterns of both parental species. It should now be possible, by this simple PCR-based technique, to accurately identify these strains to the species level, thereby allowing an increase in our understanding of the characteristics required by these interspecific hybrids for their particular ecological niches.
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Luchetti, Andrea, Franca Scanabissi, and Barbara Mantovani. "Molecular characterization of ribosomal intergenic spacer in the tadpole shrimp Triops cancriformis (Crustacea, Branchiopoda, Notostraca)." Genome 49, no. 8 (August 1, 2006): 888–93. http://dx.doi.org/10.1139/g06-047.
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Nuclear ribosomal DNA constitutes a multigene family, with tandemly arranged units linked by an intergenic spacer (IGS), which contains initiation/termination transcription signals and usually tandemly arranged subrepeats. The structure and variability of the IGS region are analyzed here in hermaphroditic and parthenogenetic populations of the "living fossil" Triops cancriformis (Branchiopoda, Notostraca). The results indicate the presence of concerted evolution at the population level for this G+C-rich IGS region as a whole, with the major amount of genetic variability found outside the subrepeat region. The subrepeats region is composed of 3 complete repeats (a, c, d) intermingled with 3 repeat fragments (b, e, f) and unrelated sequences. The most striking datum is the absolute identity of subrepeats (except type d) occupying the same position in different individuals/populations. A putative promoter sequence is present upstream of the 18S rRNA gene, but not in subrepeats, which is at variance with other arthropod IGSs. The absence of a promoter sequence in the subrepeats and subrepeat sequence conservation suggests that this region acts as an enhancer simply by its repetitive nature, as observed in some vertebrates. The putative external transcribed spacer (840 bp) shows hairpin structures, as in yeasts, protozoans, Drosophila, and vertebrates.Key words: concerted evolution, Crustacea, external transcribed spacer, intergenic spacer, ribosomal DNA, subrepeats, Triops cancriformis.
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HAYWARD, Glenys C., Dan J. BLANCHON, and H. Thorsten LUMBSCH. "Molecular data support Ramalina ovalis as a distinct lineage (Ramalinaceae, Ascomycota)." Lichenologist 46, no. 4 (July 2014): 553–61. http://dx.doi.org/10.1017/s0024282913000947.
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AbstractRamalina celastri is a highly variable, widely distributed pan-subtropical lichen species. In Australasia the species had been separated into two subspecies; R. celastri subsp. celastri and R. celastri subsp. ovalis. This study compares morphological variation, substratum preference and sequences of the internal transcribed spacer (ITS) and intergenic spacer (IGS) regions of ribosomal DNA from a range of specimens from New Zealand and one from Australia. Bayesian and ML trees generated using the sequence data form two well-supported clades corresponding to the two previously recognized subspecies. Molecular, morphological and geographical differences support the recognition of R. ovalis at the species rank.
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BAGHERI, ALI, FRANK R. BLATTNER, and REINHARD M. FRITSCH. "Allium gilanense, a new species of Allium sect. Codonoprasum (Amaryllidaceae) from Iran: evidence from morphological and molecular data." Phytotaxa 474, no. 3 (December 3, 2020): 283–92. http://dx.doi.org/10.11646/phytotaxa.474.3.7.
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As a result of recent botanical expeditions to the north of Iran, we describe here a new endemic Allium species from Gilan province named Allium gilanense. Molecular and morphological data indicate that it belongs to Allium sect. Codonoprasum. We provide a morphological description, comparing Allium gilanense with the closest relative taxa A. lenkoranicum and A. paniculatum, the preliminary karyotype of the new species, and molecular phylogenetic data derived from the nuclear ribosomal DNA internal transcribed spacers (ITS) and the chloroplast intergenic spacer trnH-psbA. The chromosome number of the new species is 2n = 16 with 0-3 B chromosomes.
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Friesen, Nikolai, and Ori Fragman-Sapir. "A new Allium species from section Molium from Israel: A. akirense (Amaryllidaceae)." Phytotaxa 173, no. 2 (June 25, 2014): 140. http://dx.doi.org/10.11646/phytotaxa.173.2.4.
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As part of the phylogenetic revision of the Eurasian representatives of the subgenus Amerallium we have discovered a new Allium species (section Molium) in Israel, related to A. qasyunense. It is described here as Allium akirense, based on living plants and recent herbarium specimens. Independence of the new species is confirmed by morphological and ecological features, and also by molecular ones. To learn more about the phylogenetic relationships within a group of closely related species of section Molium, we used maximum parsimony and Bayesian analyses of combined nuclear (ITS—internal transcribed and ETS—external transcribed spacers of rRNA genes) and chloroplast (rpl32–trnL intergenic spacer) dataset of 7 taxa. Discussion on geographic distribution, conservation status and habitat is provided, as well as an identification key including the closest related species.
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Sutar, Rajeshwari, Joseph K. David, K. Ganesan, Anup K. Ghosh, Sunit Singhi, Arunaloke Chakrabarti, and Anand K. Bachhawat. "Comparison of ITS and IGS1 regions for strain typing of clinical and non-clinical isolates of Pichia anomala." Journal of Medical Microbiology 53, no. 2 (February 1, 2004): 119–23. http://dx.doi.org/10.1099/jmm.0.05436-0.
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Pichia anomala is an emerging nosocomial pathogen and there is a need for methods that distinguish between different P. anomala strains. In the typing of several clinical as well as non-clinical P. anomala strains, the sequence variation of the internal transcribed spacer (ITS) was found to be inadequate for typing purposes. The intergenic spacer 1 (IGS1) region of the rDNA of several P. anomala strains was therefore investigated in detail. The IGS1 region (which varied from 1213 to 1231 bp in length) was interspersed with repeats and had more variation than the ITS regions. Comparative analysis in cases where analysis by the ITS was ambiguous clearly revealed the IGS1 region to be a more discriminatory tool in the typing of P. anomala strains.
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Guo, Zhansheng, Zhen Wang, and Xuguang Hou. "Comparative Analysis of the nrDNA Repeat Unit of Manila Clam Ruditapes philippinarum and Quahog Mercenaria mercenaria." Fishes 6, no. 3 (September 17, 2021): 42. http://dx.doi.org/10.3390/fishes6030042.
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Ruditapes philippinarum and Mercenaria mercenaria are economically important bivalve species. The complete ribosomal DNA (rDNA) unit sequences of R. philippinarum and M. mercenaria, with as-sembled rDNA unit lengths of 12,910 and 12,100 bp, respectively, were obtained in this study for the first time. The rDNA unit structural organisation was similar to that in other eukaryotes, in-cluding the following elements in order: 18S rRNA-internal transcribed spacer 1 (ITS1); 5.8S rRNA-ITS2-28S rRNA-intergenic spacer (IGS) (3′ external transcribed spacer (ETS); non-transcribed spacer (NTS)-5′ ETS). The genetic differences between R. philippinarum and M. mercenaria were mainly attributable to non-coding regions (ITS1, ITS2 and IGS), especially the IGS region. The boundaries of putative 3′ ETS, NTS and 5′ ETS were confirmed. Seven and three sub-repeat fragments were found in R. philippinarum and M. mercenaria, respectively. These frag-ments ranged from 4 to 154 bp in length, and were located at the NTS and 5′ ETS regions. Five and six cytosine–guanine (CpG) islands were detected in R. philippinarum and M. mercenaria, respec-tively, and these covered 85.58% and 79.29% of the entire IGS sequence, respectively. The phylo-genetic tree was constructed based on Veneridae ITS and 18S rRNA sequences using the maxi-mum likelihood (ML) method. The ML tree based on ITS revealed that species within the same genus clearly clustered together with relatively high supporting values, and all the genera were recovered as monophyletic. The phylogenetic analyses using 18S rRNA provided a weaker phy-logenetic signal than ITS.
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O’Sullivan, Audrey C., Gareth J. Sullivan, and Brian McStay. "UBF Binding In Vivo Is Not Restricted to Regulatory Sequences within the Vertebrate Ribosomal DNA Repeat." Molecular and Cellular Biology 22, no. 2 (January 15, 2002): 657–58. http://dx.doi.org/10.1128/mcb.22.2.657-668.2002.
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ABSTRACT The HMG box containing protein UBF binds to the promoter of vertebrate ribosomal repeats and is required for their transcription by RNA polymerase I in vitro. UBF can also bind in vitro to a variety of sequences found across the intergenic spacer in Xenopus and mammalian ribosomal DNA (rDNA) repeats. The high abundance of UBF, its colocalization with rDNA in vivo, and its DNA binding characteristics, suggest that it plays a more generalized structural role over the rDNA repeat. Until now this view has not been supported by any in vivo data. Here, we utilize chromatin immunoprecipitation from a highly enriched nucleolar chromatin fraction to show for the first time that UBF binding in vivo is not restricted to known regulatory sequences but extends across the entire intergenic spacer and transcribed region of Xenopus, human, and mouse rDNA repeats. These results are consistent with a structural role for UBF at active nucleolar organizer regions in addition to its recognized role in stable transcription complex formation at the promoter.
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Daffonchio, Daniele, Ameur Cherif, Lorenzo Brusetti, Aurora Rizzi, Diego Mora, Abdellatif Boudabous, and Sara Borin. "Nature of Polymorphisms in 16S-23S rRNA Gene Intergenic Transcribed Spacer Fingerprinting of Bacillus and Related Genera." Applied and Environmental Microbiology 69, no. 9 (September 2003): 5128–37. http://dx.doi.org/10.1128/aem.69.9.5128-5137.2003.
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ABSTRACT The intergenic transcribed spacers (ITS) between the 16S and 23S rRNA genetic loci are frequently used in PCR fingerprinting to discriminate bacterial strains at the species and intraspecies levels. We investigated the molecular nature of polymorphisms in ITS-PCR fingerprinting of low-G+C-content spore-forming bacteria belonging to the genera Bacillus, Brevibacillus, Geobacillus, and Paenibacillus. We found that besides the polymorphisms in the homoduplex fragments amplified by PCR, heteroduplex products formed during PCR between amplicons from different ribosomal operons, with or without tRNA genes in the ITS, contribute to the interstrain variability in ITS-PCR fingerprinting patterns obtained in polyacrylamide-based gel matrices. The heteroduplex nature of the discriminating bands was demonstrated by fragment separation in denaturing polyacrylamide gels, by capillary electrophoresis, and by cloning, sequencing, and recombination of purified short and tRNA gene-containing long ITS. We also found that heteroduplex product formation is enhanced by increasing the number of PCR cycles. Homoduplex-heteroduplex polymorphisms (HHP) in a conserved region, such as the 16S and 23S rRNA gene ITS, allowed discrimination of closely related strains and species undistinguishable by other methods, indicating that ITS-HHP analysis is an easy and reproducible additional tool for strain typing.
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Saadati, Nasim, Maryam Khoshsokhan Mozaffar, Mahboubeh Sherafati, and Shahrokh Kazempour Osaloo. "Pseudoheterocaryum, a new genus segregated from Heterocaryum (Boraginaceae) on the basis of molecular data." Australian Systematic Botany 30, no. 1 (2017): 105. http://dx.doi.org/10.1071/sb16022.
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The phylogeny of Heterocaryum and Suchtelenia was examined using sequence data from the internal transcribed spacer region of the nuclear rDNA (ITS) and plastid trnL intron and trnL–trnF intergenic spacer (trnL–F) regions. Results indicated that Heterocaryum is non-monophyletic because of the inclusion of Suchtelenia calycina (C.A.Mey.) A.DC. Heterocaryum laevigatum (Kar. & Kir.) A.DC. formed a distinct branch sister to S. calycina and remaining Heterocaryum species. Hence, all species of Heterocaryum except H. laevigatum (type species of the genus) are transferred to a new genus, Pseudoheterocaryum. Taxonomic descriptions are presented for Pseudoheterocaryum and Heterocaryum, as well as a diagnostic key to the three genera included in the present study.
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Zheng, Xu, Qiao-Cheng Chang, Yan Zhang, Si-Qin Tian, Yan Lou, Hong Duan, Dong-Hui Guo, Chun-Ren Wang, and Xing-Quan Zhu. "Characterization of the Complete Nuclear Ribosomal DNA Sequences ofParamphistomum cervi." Scientific World Journal 2014 (2014): 1–11. http://dx.doi.org/10.1155/2014/751907.
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Sequences of the complete nuclear ribosomal DNA (rDNA) gene from five individualParamphistomum cerviwere determined for the first time. The five complete rDNA sequences, which included the 18S rDNA, the internal transcribed spacer 1 (ITS1), the 5.8S rDNA, the internal transcribed spacer 2 (ITS2), the 28S rDNA, and the intergenic spacer (IGS) regions, had a length range of 8,493–10,221 bp. The lengths of the investigated 18S, ITS1, 5.8S, ITS2, and 28S rDNA sequences, which were 1,994 bp, 1,293 bp, 157 bp, 286 bp, and 4,186 bp, respectively, did not vary. However, the IGS rDNA sequences had a length range of 577–2,305 bp. The 5.8S and ITS-2 rDNA sequences had 100% identity among the five investigated samples, while the identities among the IGS had a range of 53.7–99.8%. A comparative analysis revealed that different types and numbers of repeats were found within each ITS1 and IGS region, which may be related to the length polymorphism of IGS. The phylogenetic position ofP. cerviin Paramphistomatidae was analyzed based on the 18S rDNA sequences. These results will aid in studying the intra- and interspecific variation of the Paramphistomatidae and the systematics and phylogenetics of Digenea.
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Ryberg, Anna, Crister Olsson, Siv Ahrné, and Hans-Jürg Monstein. "Comparison of (GTG)5-oligonucleotide and ribosomal intergenic transcribed spacer (ITS)-PCR for molecular typing of Klebsiella isolates." Journal of Microbiological Methods 84, no. 2 (February 2011): 183–88. http://dx.doi.org/10.1016/j.mimet.2010.11.019.
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Downie, Stephen R., Deborah S. Katz-Downie, Feng-Jie Sun, and Chang-Shook Lee. "Phylogeny and biogeography of Apiaceae tribe Oenantheae inferred from nuclear rDNA ITS and cpDNA psbI–5′trnK(UUU) sequences, with emphasis on the North American Endemics clade." Botany 86, no. 9 (September 2008): 1039–64. http://dx.doi.org/10.1139/b08-055.
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Intergeneric phylogenetic relationships within Apiaceae tribe Oenantheae were investigated using sequence data from the chloroplast DNA psbI–5′trnK(UUU) and nuclear ribosomal DNA internal transcribed spacer regions. One hundred and thirty-one accessions were examined, representing all 17 genera of the tribe and approximately one-half of its species. The cpDNA region includes four intergenic spacers and the rps16 intron and these noncoding loci were analyzed separately to assess their relative utility for resolving relationships. Separate maximum parsimony analyses of the entire psbI–5′trnK(UUU) and ITS regions, each with and without scored indels, yielded concordant trees. Phylogenies derived from maximum parsimony, Bayesian, or maximum likelihood analyses of combined chloroplast and nuclear DNA sequences for 82 accessions were highly resolved, well supported, and consistent. Among the five noncoding loci examined, the trnQ(UUG)–5′rps16 and 3′rps16–5′trnK(UUU) intergenic spacers are the most variable, with the latter contributing the greatest total number of parsimony informative characters relative to its size. The North American genera Atrema , Cynosciadium , Daucosma , Limnosciadium , Neogoezia , Oxypolis , Ptilimnium , and Trepocarpus ally with the western hemispheric and Australasian genus Lilaeopsis in a strongly supported North American Endemics clade that is a sister group to a clade composed primarily of Old World taxa ( Berula sensu lato, Cryptotaenia , Helosciadium , and Sium ). Oxypolis and Ptilimnium are not monophyletic, with the rachis-leaved members of each comprising a clade separate from their compound-leaved congeners. Dispersal-vicariance analysis suggests that the ancestors of the North American Endemics clade probably originated in Canada and the USA or in a broader ancestral area including Mexico and South America.
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Harasawa, Ryô, David G. Pitcher, Ana S. Ramírez, and Janet M. Bradbury. "A putative transposase gene in the 16S–23S rRNA intergenic spacer region of Mycoplasma imitans." Microbiology 150, no. 4 (April 1, 2004): 1023–29. http://dx.doi.org/10.1099/mic.0.26629-0.
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Examination of the nucleotide sequences of the 16S–23S intergenic transcribed spacer (ITS) region of Mycoplasma imitans and Mycoplasma gallisepticum identified a putative transposase gene located only in the ITS of M. imitans, which can be used as a genetic marker to distinguish these two species. The relative size of the PCR products of the ITS region allowed a clear distinction to be made between strains of M. imitans and M. gallisepticum, both of which could be readily discriminated from the type strains of all the other recognized avian Mycoplasma species. In addition, the putative transposase gene assigned in the ITS of M. imitans was shown to include a sequence homologous to that of the P75 gene of M. gallisepticum. This is believed to be the first description of an insertion element in the rRNA operon region of a mycoplasma species.
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Wang, Siyu, Hongbo Guo, JiaJia Li, Wei Li, Qin Wang, and Xiaodan Yu. "Evaluation of five regions as DNA barcodes for identification of Lepista species (Tricholomataceae, Basidiomycota) from China." PeerJ 7 (July 15, 2019): e7307. http://dx.doi.org/10.7717/peerj.7307.
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Background Distinguishing among species in the genus Lepista is difficult because of their similar morphologies. Methods To identify a suitable DNA barcode for identification of Lepista species, we assessed the following five regions: internal transcribed spacer (ITS), the intergenic spacer (IGS), nuclear ribosomal RNA subunit, mitochondrial small subunit rDNA, and tef1. A total of 134 sequences from 34 samples belong to eight Lepista species were analyzed. The utility of each region as a DNA barcode was assessed based on the success rates of its PCR amplification and sequencing, and on its intra- and inter-specific variations. Results The results indicated that the ITS region could distinguish all species tested. We therefore propose that the ITS region can be used as a DNA barcode for the genus Lepista. In addition, a phylogenetic tree based on the ITS region showed that the tested eight Lepista species, including two unrecognized species, formed eight separate and well-supported clades.
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Bhardwaj, Sonia, Rajeshwari Sutar, Anand K. Bachhawat, Sunit Singhi, and Arunaloke Chakrabarti. "PCR-based identification and strain typing of Pichia anomala using the ribosomal intergenic spacer region IGS1." Journal of Medical Microbiology 56, no. 2 (February 1, 2007): 185–89. http://dx.doi.org/10.1099/jmm.0.46790-0.
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Frequent outbreaks of Pichia anomala fungaemia in paediatric patients have warranted the development of a rapid identification system for this organism. This study describes a specific PCR-based method targeting the rRNA gene intergenic spacer region 1 (IGS1) for rapid identification of Pichia anomala isolates and characterization at the strain level. These methods of species identification and strain typing were used on 106 isolates of Pichia anomala (77 from a previously described outbreak and 29 isolated post-outbreak from the same hospital). Using conventional morphological and biochemical methods, 11 strains isolated during the outbreak were misidentified as P. anomala. blast analysis of sequences of internal transcribed spacer (ITS) regions of rRNA genes confirmed that they were Pichia guilliermondii (eight isolates) and Debaryomyces hansenii (three isolates). Strain typing of Pichia anomala isolates confirmed the previous finding of a point-source outbreak. The results suggest that IGS sequences and their polymorphisms could be exploited for similar typing methods in other organisms.
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Polanco, Carlos, Ana I. González, Álvaro de la Fuente, and Gabriel A. Dover. "Multigene Family of Ribosomal DNA in Drosophila melanogaster Reveals Contrasting Patterns of Homogenization for IGS and ITS Spacer Regions: A Possible Mechanism to Resolve This Paradox." Genetics 149, no. 1 (May 1, 1998): 243–56. http://dx.doi.org/10.1093/genetics/149.1.243.
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Abstract The multigene family of rDNA in Drosophila reveals high levels of within-species homogeneity and between-species diversity. This pattern of mutation distribution is known as concerted evolution and is considered to be due to a variety of genomic mechanisms of turnover (e.g., unequal crossing over and gene conversion) that underpin the process of molecular drive. The dynamics of spread of mutant repeats through a gene family, and ultimately through a sexual population, depends on the differences in rates of turnover within and between chromosomes. Our extensive molecular analysis of the intergenic spacer (IGS) and internal transcribed spacer (ITS) spacer regions within repetitive rDNA units, drawn from the same individuals in 10 natural populations of Drosophila melanogaster collected along a latitudinal cline on the east coast of Australia, indicates a relatively fast rate of X-Y and X-X interchromosomal exchanges of IGS length variants in agreement with a multilineage model of homogenization. In contrast, an X chromosome-restricted 24-bp deletion in the ITS spacers is indicative of the absence of X-Y chromosome exchanges for this region that is part of the same repetitive rDNA units. Hence, a single lineage model of homogenization, coupled to drift and/or selection, seems to be responsible for ITS concerted evolution. A single-stranded exchange mechanism is proposed to resolve this paradox, based on the role of the IGS region in meiotic pairing between X and Y chromosomes in D. melanogaster.
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Jackson, Colin J., Richard C. Barton, and E. Glyn V. Evans. "Species Identification and Strain Differentiation of Dermatophyte Fungi by Analysis of Ribosomal-DNA Intergenic Spacer Regions." Journal of Clinical Microbiology 37, no. 4 (1999): 931–36. http://dx.doi.org/10.1128/jcm.37.4.931-936.1999.
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Restriction fragment length polymorphisms (RFLPs) identified in the ribosomal-DNA (rDNA) repeat were used for molecular strain differentiation of the dermatophyte fungus Trichophyton rubrum. The polymorphisms were detected by hybridization ofEcoRI-digested T. rubrum genomic DNAs with a probe amplified from the small-subunit (18S) rDNA and adjacent internal transcribed spacer (ITS) regions. The rDNA RFLPs mapped to the nontranscribed spacer (NTS) region of the rDNA repeat and appeared similar to those caused by short repetitive sequences in the intergenic spacers of other fungi. Fourteen individual RFLP patterns (DNA types A to N) were recognized among 50 random clinical isolates ofT. rubrum. A majority of strains (19 of 50 [38%]) were characterized by one RFLP pattern (DNA type A), and four types (DNA types A to D) accounted for 78% (39 of 50) of all strains. The remaining types (DNA types E to N) were represented by one or two isolates only. A rapid and simple method was also developed for molecular species identification of dermatophyte fungi. The contiguous ITS and 5.8S rDNA regions were amplified from 17 common dermatophyte species by using the universal primers ITS 1 and ITS 4. Digestion of the amplified ITS products with the restriction endonucleaseMvaI produced unique and easily identifiable fragment patterns for a majority of species. However, some closely related taxon pairs, such as T. rubrum-T. soudanense andT. quinkeanum-T. schoenlenii could not be distinguished. We conclude that RFLP analysis of the NTS and ITS intergenic regions of the rDNA repeat is a valuable technique both for molecular strain differentiation of T. rubrum and for species identification of common dermatophyte fungi.
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Dingman, Douglas W. "DNA fingerprinting of Paenibacillus popilliae and Paenibacillus lentimorbus using PCR-amplified 16S–23S rDNA intergenic transcribed spacer (ITS) regions." Journal of Invertebrate Pathology 100, no. 1 (January 2009): 16–21. http://dx.doi.org/10.1016/j.jip.2008.09.006.
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Polanco, Carlos, Ana I. González, and Gabriel A. Dover. "Patterns of Variation in the Intergenic Spacers of Ribosomal DNA in Drosophila melanogaster Support a Model for Genetic Exchanges During X-Y Pairing." Genetics 155, no. 3 (July 1, 2000): 1221–29. http://dx.doi.org/10.1093/genetics/155.3.1221.
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Abstract Detailed analysis of variation in intergenic spacer (IGS) and internal transcribed spacer (ITS) regions of rDNA drawn from natural populations of Drosophila melanogaster has revealed contrasting patterns of homogenization although both spacers are located in the same rDNA unit. On the basis of the role of IGS regions in X-Y chromosome pairing, we proposed a mechanism of single-strand exchanges at the IGS regions, which can explain the different evolutionary trajectories followed by the IGS and the ITS regions. Here, we provide data from the chromosomal distribution of selected IGS length variants, as well as the detailed internal structure of a large number of IGS regions obtained from specific X and Y chromosomes. The variability found in the different internal subrepeat regions of IGS regions isolated from X and Y chromosomes supports the proposed mechanism of genetic exchanges and suggests that only the “240” subrepeats are involved. The presence of a putative site for topoisomerase I at the 5′ end of the 18S rRNA gene would allow for the exchange between X and Y chromosomes of some 240 subrepeats, the promoter, and the ETS region, leaving the rest of the rDNA unit to evolve along separate chromosomal lineages. The phenomenon of localized units (modules) of homogenization has implications for multigene family evolution in general.
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Præsteng, Kirsti E., Roderick I. Mackie, Isaac K. O. Cann, Svein D. Mathiesen, and Monica A. Sundset. "Variations in the 16S–23S rRNA internal transcribed spacer of fibrolytic Butyrivibrio isolates from the reindeer rumen." Canadian Journal of Microbiology 57, no. 7 (July 2011): 617–22. http://dx.doi.org/10.1139/w11-038.
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Strains of Butyrivibrio are principal cellulytic bacteria in the rumen of the High Arctic Svalbard reindeer ( Rangifer tarandus platyrhynchus ). According to phylogenetic analysis based on 16S rRNA gene sequencing, Butyrivibrio can be divided into three subgroups within the Clostridia class of the phylum Firmicutes, but the current phenotypic and genotypic differentiation within the family Lachnospiraceae is insufficient. This current study describes the sequence diversity of the 16S–23S rRNA intergenic transcribed spacer (ITS) region of Butyrivibrio isolates from reindeer. A total of 17 different ITS sequences with sizes between 449 and 784 nt were obtained. Genes encoding tRNAIle and tRNAAla were identified in four of the sequences. Phylogenetic neighbor-joining trees were constructed based on the ITS sequence and compared with a phylogenetic neighbor-joining tree based on 16S rRNA gene sequences previously obtained for the same isolates. These comparisons indicated a better differentiation between strains in the ITS sequence than the 16S rRNA gene based tree. Through this study, a better means for identifying and tracking fibrolytic and potentially probiotic Butyrivibrio strains in reindeer and other ruminants has been provided.
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Torres, R. A., U. Zentgraf, and V. Hemleben. "Species and Genus Specificity of the Intergenic Spacer (IGS) in the Ribosomal RNA Genes of Cucurbitaceae." Zeitschrift für Naturforschung C 44, no. 11-12 (December 1, 1989): 1029–34. http://dx.doi.org/10.1515/znc-1989-11-1224.
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Abstract The use of intergenic spacer (IGS) fragments of plant ribosomal DNA (rDNA) for the differ entiation between genera and species is tested by cross-hybridization experiments with different IGS probes of two Cucurbitaceae, Cucurbita pepo (zucchini) and Cucumis sativus (cucum ber). Hybridization with cloned fragments of different parts of the IGS of ribosomal DNA exhibit a different degree of conservation within and between the Cucurbitaceae genera. In general, Cucur bita species seem to be closer related to each other than the Cucumis species. A repetitive element of the external transcribed spacer (ETS) shows a more genus-specific pattern, reacting only with the respective genera; the region preceding the ETS is conserved between the Cucurbita species but also cross-hybridizes weakly with the Cucumis species. AGC-rich element of the Cucumis sativus IGS (“Cfo-cluster”) is present in small amounts in Cucumis melo (melon) and even less represented in other genera of the Cucurbitaceae.
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Huang, Er-Feng, Gang Yao, Ri-Hong Jiang, Lei-Lei Yang, Wang Xi, Zhong-Shuai Zhang, and Xian-Chun Zhang. "Hoya pyrifolia (Apocynaceae), a new species from south-western Yunnan, China." PhytoKeys 174 (March 12, 2021): 95–106. http://dx.doi.org/10.3897/phytokeys.174.60137.
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Hoya pyrifolia, a new species of Apocynaceae from Yunnan Province, China, is described and illustrated. Results from phylogenetic analyses, based on combined DNA fragments of the nuclear ribosomal external transcribed spacer (ETS), intergeneric transcribed spacer (ITS) and three plastid DNA fragments (matK, psbA-trnH and trnT-trnL), showed that the new species was nested within a clade, including Hoya species distributed in the subtropical foothills of the Himalayas and the Tibet-Sichuan Plateau. Morphologically, the new species can be distinguished from its close relatives by its pyriform and slightly pubescent leaves, as well as the 4-flowered inflorescences.
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Ballarino, Monica, Francesca Pagano, Erika Girardi, Mariangela Morlando, Davide Cacchiarelli, Marcella Marchioni, Nicholas J. Proudfoot, and Irene Bozzoni. "Coupled RNA Processing and Transcription of Intergenic Primary MicroRNAs." Molecular and Cellular Biology 29, no. 20 (August 10, 2009): 5632–38. http://dx.doi.org/10.1128/mcb.00664-09.
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ABSTRACT The first step in microRNA (miRNA) biogenesis occurs in the nucleus and is mediated by the Microprocessor complex containing the RNase III-like enzyme Drosha and its cofactor DGCR8. Here we show that the 5′→3′ exonuclease Xrn2 associates with independently transcribed miRNAs and, in combination with Drosha processing, attenuates transcription in downstream regions. We suggest that, after Drosha cleavage, a torpedo-like mechanism acts on nascent long precursor miRNAs, whereby Xrn2 exonuclease degrades the RNA polymerase II-associated transcripts inducing its release from the template. While involved in primary transcript termination, this attenuation effect does not restrict clustered miRNA expression, which, in the majority of cases, is separated by short spacers. We also show that transcripts originating from a miRNA promoter are retained on the chromatin template and are more efficiently processed than those produced from mRNA or snRNA Pol II-dependent promoters. These data imply that coupling between transcription and processing promotes efficient expression of independently transcribed miRNAs.
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Osorio, Carlos R., Matthew D. Collins, Jesús L. Romalde, and Alicia E. Toranzo. "Variation in 16S-23S rRNA Intergenic Spacer Regions in Photobacterium damselae: a Mosaic-Like Structure." Applied and Environmental Microbiology 71, no. 2 (February 2005): 636–45. http://dx.doi.org/10.1128/aem.71.2.636-645.2005.
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ABSTRACT Phenotypically, Photobacterium damselae subsp. piscicida and P. damselae subsp. damselae are easily distinguished. However, their 16S rRNA gene sequences are identical, and attempts to discriminate these two subspecies by molecular tools are hampered by their high level of DNA-DNA similarity. The 16S-23S rRNA internal transcribed spacers (ITS) were sequenced in two strains of Photobacterium damselae subsp. piscicida and two strains of P. damselae subsp. damselae to determine the level of molecular diversity in this DNA region. A total of 17 different ITS variants, ranging from 803 to 296 bp were found, some of which were subspecies or strain specific. The largest ITS contained four tRNA genes (tDNAs) coding for tRNAGlu(UUC), tRNALys(UUU), tRNAVal(UAC), and tRNAAla(GGC). Five amplicons contained tRNAGlu(UUC) combined with two additional tRNA genes, including tRNALys(UUU), tRNAVal(UAC), or tRNAAla(UGC). Five amplicons contained tRNAIle(GAU) and tRNAAla(UGC). Two amplicons contained tRNAGlu(UUC) and tRNAAla(UGC). Two different isoacceptor tRNAAla genes (GGC and UGC anticodons) were found. The five smallest amplicons contained no tRNA genes. The tRNA-gene combinations tRNAGlu(UUC)-tRNAVal(UAC)-tRNAAla(UGC) and tRNAGlu(UUC)-tRNAAla(UGC) have not been previously reported in bacterial ITS regions. The number of copies of the ribosomal operon (rrn) in the P. damselae chromosome ranged from at least 9 to 12. For ITS variants coexisting in two strains of different subspecies or in strains of the same subspecies, nucleotide substitution percentages ranged from 0 to 2%. The main source of variation between ITS variants was due to different combinations of DNA sequence blocks, constituting a mosaic-like structure.
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Sallares, Robert, and Terence A. Brown. "PCR-based analysis of the intergenic spacers of the Nor loci on the A genomes of Triticum diploids and polyploids." Genome 42, no. 1 (February 1, 1999): 116–28. http://dx.doi.org/10.1139/g98-102.
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We present DNA sequence data showing population variation in the intergenic spacer (IGS) regions of the ribosomal DNAs (rDNAs) on the A genomes of 27 diploid and polyploid wheats. PCRs (polymerase chain reactions) specific for the Am genome gave products with five populations of Triticum monococcum but did not give products with AABB or AABBDD wheats. PCRs specific to the Au genome of T. urartu gave products with all the AABB and AABBDD polyploids that were tested, but not with T. monococcum. AAGG tetraploids gave products only with the Au-specific primers, but the AAAAGG hexaploid T. zhukovskyi gave products with both the Au and Am primers. Phylogenetic analysis showed a substantial degree of IGS divergence for both the Am and Au genomes in diploids and polyploids compared with other genomes of Triticum and Aegilops. The rate of evolution of the IGS is much greater than previously reported for the internal transcribed region of the rDNAs but the view that the IGS only gives random noise is rejected, the IGS sequences presented here reflecting the general evolutionary trends affecting the wheat genome as a whole.Key words: wheat, ribosomal DNA, intergenic spacer, polymerase chain reaction.
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Morandi, Stefano, Paola Cremonesi, Milena Povolo, and Milena Brasca. "Enterococcus lactis sp. nov., from Italian raw milk cheeses." International Journal of Systematic and Evolutionary Microbiology 62, Pt_8 (August 1, 2012): 1992–96. http://dx.doi.org/10.1099/ijs.0.030825-0.
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Ten atypical Enterococcus strains were isolated from Italian raw milk cheeses. The 16S rRNA gene, phenylalanyl-tRNA synthase alpha subunit (pheS), RNA polymerase alpha subunit (rpoA) and the 16S–23S rRNA intergenic transcribed spacer (ITS) sequences, randomly amplified polymorphic DNA (RAPD) PCR and the phenotypic properties revealed that the isolates represent a novel enterococcal species. On the basis of 16S rRNA gene sequence analysis, the isolates were closely related to Enterococcus hirae ATCC 8043T, Enterococcus durans CECT 411T and Enterococcus faecium ATCC 19434T, with 98.8, 98.9 and 99.4 % sequence similarity, respectively. On the basis of sequence analysis of the housekeeping gene pheS, the reference strain, BT159T, occupied a position separate from E. faecium LMG 16198. The group of isolates could be easily differentiated from recognized species of the genus Enterococcus by 16S–23S rRNA ITS analysis, RAPD-PCR and phenotypic characteristics. The name Enterococcus lactis sp. nov. is proposed, with BT159T ( = DSM 23655T = LMG 25958T) as the type strain.
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Hussain, Adil, Daniel Potter, Sangtae Kim, Muhammad Q. Hayat, and Syed A. I. Bokhari. "Molecular phylogeny of Artemisia (Asteraceae-Anthemideae) with emphasis on undescribed taxa from Gilgit-Baltistan (Pakistan) based on nrDNA (ITS and ETS) and cpDNA (psbA-trnH) sequences." Plant Ecology and Evolution 152, no. 3 (November 28, 2019): 507–20. http://dx.doi.org/10.5091/plecevo.2019.1583.
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Background – Gilgit-Baltistan, the Northeast region of Pakistan, is well known for its floristic diversity, including members of the genus Artemisia. Artemisia is a large, taxonomically complex genus including ~500 species of both herbs and shrubs. This study was conducted to determine the phylogenetic position of ten undescribed Artemisia taxa from northern Pakistan, using nrDNA internal transcribed spacer (ITS), external transcribed spacer (ETS) and cpDNA intergenic spacer (psbA-trnH) regions.Methods – The phylogenetic relationships of 28 taxa of Artemisia using separate and combined data sets of sequences of three markers (ITS, ETS and psbA-trnH) were analysed with maximum parsimony, maximum likelihood, and Bayesian approaches. Key results – The results resolve northeastern Pakistani Artemisia, which represent five morphologically defined subgenera, into ten major clades. Subgenera Artemisia and Absinthium are shown to be polyphyletic, while Dracunculus, Pacifica and Tridentatae appear monophyletic. All species of subgenus Seriphidium are retrieved in a single clade that also includes annual species from subgenus Artemisia. In the Flora of Pakistan, Seriphidium is described as a separate genus but in this study, Seriphidium fell within the genus Artemisia. In addition, on the basis of phylogenetic analysis, we present evidence that ten as-yet undescribed taxa are present in northeastern Pakistan based on newly recognized three groups (Groups I, II and III) of taxa within the genus Artemisia. One undescribed taxon from group I was placed within the subgenus Dracunculus clade and the remaining nine taxa from groups II and III were placed in the subgenus Absinthium clade. Morphological studies coupled with modern molecular techniques may lead to a new infrageneric classification of the genus Artemisia. It will also clarify and characterize the undescribed taxa reported in this study.
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Nouioui, Imen, Faten Ghodhbane-Gtari, Maria P. Fernandez, Abdellatif Boudabous, Philippe Normand, and Maher Gtari. "Absence of Cospeciation between the UnculturedFrankiaMicrosymbionts and the Disjunct ActinorhizalCoriariaSpecies." BioMed Research International 2014 (2014): 1–9. http://dx.doi.org/10.1155/2014/924235.
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Coriariais an actinorhizal plant that forms root nodules in symbiosis with nitrogen-fixing actinobacteria of the genusFrankia. This symbiotic association has drawn interest because of the disjunct geographical distribution ofCoriariain four separate areas of the world and in the context of evolutionary relationships between host plants and their uncultured microsymbionts. The evolution ofFrankia-Coriariasymbioses was examined from a phylogenetic viewpoint using multiple genetic markers in both bacteria and host-plant partners. Total DNA extracted from root nodules collected from five species:C. myrtifolia,C. arborea,C. nepalensis,C. japonica, andC. microphylla, growing in the Mediterranean area (Morocco and France), New Zealand, Pakistan, Japan, and Mexico, respectively, was used to amplify glnA gene (glutamine synthetase), dnaA gene (chromosome replication initiator), and the nif DK IGS (intergenic spacer between nifD and nifK genes) inFrankiaand the matK gene (chloroplast-encoded maturase K) and the intergenic transcribed spacers (18S rRNA-ITS1-5.8S rRNA-ITS2-28S rRNA) inCoriariaspecies. Phylogenetic reconstruction indicated that the radiations ofFrankiastrains andCoriariaspecies are not congruent. The lack of cospeciation between the two symbiotic partners may be explained by host shift at high taxonomic rank together with wind dispersal and/or survival in nonhost rhizosphere.
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VELMALA, Saara, Leena MYLLYS, Pekka HALONEN, Trevor GOWARD, and Teuvo AHTI. "Molecular data show that Bryoria fremontii and B. tortuosa (Parmeliaceae) are conspecific." Lichenologist 41, no. 3 (May 2009): 231–42. http://dx.doi.org/10.1017/s0024282909008573.
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AbstractBryoria fremontii and B. tortuosa are the only species in the lichenized ascomycete genus Bryoria known to contain the pulvinic acid derivative vulpinic acid. In B. fremontii this yellow pigment is restricted to the soralia and apothecia, while in B. tortuosa it can occur throughout the thallus. The actual amount of vulpinic acid produced by B. tortuosa is rather variable, however, with intermediate specimens bearing both white and yellow pseudocyphellae. We studied the relationship between the two species with parsimony analysis using four DNA regions: 1) the internal transcribed spacers of the nuclear rDNA including the 5.8S region (ITS), 2) partial sequences from the intergenic spacer of the nuclear rDNA (IGS), 3) partial sequences from the small subunit of the mitochondrial rDNA (mtSSU), and 4) partial sequences from the protein-coding glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH). Our phylogenetic analysis revealed that B. fremontii and B. tortuosa must be regarded as conspecific, but allowing for some genetic differentiation between European and North American populations. Bryoria tortuosa is therefore synonymized with B. fremontii.
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Fortina, M. Grazia, G. Ricci, D. Mora, and P. L. Manachini. "Molecular analysis of artisanal Italian cheeses reveals Enterococcus italicus sp. nov." International Journal of Systematic and Evolutionary Microbiology 54, no. 5 (September 1, 2004): 1717–21. http://dx.doi.org/10.1099/ijs.0.63190-0.
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The taxonomic positions of seven atypical Enterococcus strains, isolated from artisanal Italian cheeses, were investigated in a polyphasic study. By using 16S rRNA gene sequencing, DNA–DNA hybridization and intergenic transcribed spacer analysis, as well as by examining the phenotypic properties, the novel isolates were shown to constitute a novel enterococcal species. Their closest relatives are Enterococcus sulfureus and Enterococcus saccharolyticus, having a 16S rRNA gene sequence similarity of 96·7 %. This group of strains can be easily differentiated from the other Enterococcus species by DNA–DNA hybridization and by their phenotypic characteristics: the strains do not grow in 6·5 % NaCl, and they do not produce acid from l-arabinose, melezitose, melibiose, raffinose or ribose. The name Enterococcus italicus sp. nov. is proposed for this species, with strain DSM 15952T (=LMG 22039T) as the type strain.
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Su, X., Y. Zhang, X. Zheng, X. X. Wang, Y. Li, Q. Li, and C. R. Wang. "Characterization of the complete nuclear ribosomal DNA sequences of Eurytrema pancreaticum." Journal of Helminthology 92, no. 4 (June 27, 2017): 484–90. http://dx.doi.org/10.1017/s0022149x17000554.
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AbstractEurytrema pancreaticum is one of the most common trematodes of cattle and sheep, and also infects humans occasionally, causing great economic losses and medical costs. In this study, the sequences of the complete nuclear ribosomal DNA (rDNA) repeat units of five E. pancreaticum individuals were determined for the first time. They were 8306–8310 bp in length, including the small subunit (18S) rDNA, internal transcribed spacer 1 (ITS1), 5.8S rDNA, internal transcribed spacer 2 (ITS2), large subunit (28S) rDNA and intergenic spacer (IGS). There were no length variations in any of the investigated 18S (1996 bp), ITS1 (1103 bp), 5.8S (160 bp), ITS2 (231 bp) or 28S (3669 bp) rDNA sequences, whereas the IGS rDNA sequences of E. pancreaticum had a 4-bp length variation, ranging from 1147 to 1151 bp. The intraspecific variations within E. pancreaticum were 0–0.2% for 18S rDNA, 0–0.5% for ITS1, 0% for 5.8S rDNA and ITS2, 0–0.2% for 28S rDNA and 2.9–20.2% for IGS. There were nine types of repeat sequences in ITS1, two types in 28S rDNA, but none in IGS. A phylogenetic analysis based on the 18S rDNA sequences classified E. pancreaticum in the family Dicrocoeliidae of Plagiorchiata, closely related to the suborder Opisthorchiata. These results provide useful information for the further study of Dicrocoeliidae trematodes.
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Toth, I. K., A. O. Avrova, and L. J. Hyman. "Rapid Identification and Differentiation of the Soft Rot Erwinias by 16S-23S Intergenic Transcribed Spacer-PCR and Restriction Fragment Length Polymorphism Analyses." Applied and Environmental Microbiology 67, no. 9 (September 1, 2001): 4070–76. http://dx.doi.org/10.1128/aem.67.9.4070-4076.2001.
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ABSTRACT Current identification methods for the soft rot erwinias are both imprecise and time-consuming. We have used the 16S-23S rRNA intergenic transcribed spacer (ITS) to aid in their identification. Analysis by ITS-PCR and ITS-restriction fragment length polymorphism was found to be a simple, precise, and rapid method compared to current molecular and phenotypic techniques. The ITS was amplified fromErwinia and other genera using universal PCR primers. After PCR, the banding patterns generated allowed the soft rot erwinias to be differentiated from all other Erwinia and non-Erwinia species and placed into one of three groups (I to III). Group I comprised all Erwinia carotovorasubsp. atroseptica and subsp.betavasculorum isolates. Group II comprised allE. carotovora subsp. carotovora,subsp. odorifera, and subsp. wasabiae andE. cacticida isolates, and group III comprised allE. chrysanthemi isolates. To increase the level of discrimination further, the ITS-PCR products were digested with one of two restriction enzymes. Digestion with CfoI identified E. carotovora subsp.atroseptica and subsp. betavasculorum(group I) and E. chrysanthemi (group III) isolates, while digestion with RsaI identified E. carotovora subsp. wasabiae, subsp. carotovora, and subsp.odorifera/carotovora and E. cacticida isolates (group II). In the latter case, it was necessary to distinguishE. carotovora subsp. odorifera and subsp. carotovora using the α-methyl glucoside test. Sixty suspected soft rot erwinia isolates from Australia were identified as E. carotovora subsp.atroseptica, E. chrysanthemi,E. carotovora subsp. carotovora, and non-soft rot species. Ten “atypical” E. carotovora subsp. atroseptica isolates were identified as E. carotovora subsp.atroseptica, subsp. carotovora, and subsp. betavasculorum and non-soft rot species, and two “atypical” E. carotovora subsp.carotovora isolates were identified as E. carotovora subsp. carotovora and subsp.atroseptica.
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Tokajian, Sima, Siba Al-Medawar, and Fuad Hashwa. "Use of the 16S–23S ribosomal genes spacer region for the molecular typing of sphingomonads." Canadian Journal of Microbiology 54, no. 8 (August 2008): 668–76. http://dx.doi.org/10.1139/w08-054.
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The ability of sphingomonads in drinking water to cause community- and hospital-acquired opportunistic infections has raised the need to establish reproducible identification assays. In this study, a total of 129 isolates recovered from drinking water with yellow- to orange-pigmented colonies were distributed among 10 biotypes on the basis of colony morphology. Polymorphisms, based on the amplification and restriction digestion of the intergenic transcribed spacer (ITS) region within the 10 assigned biotypes and 18 ATCC reference strains, were used to investigate the ability of this approach to differentiate closely related sphingomonads. ITS size, which ranged between 400 and 1100 bp, did not vary enough among the different genera. However, 16 distinct banding patterns within the ATCC reference strains and 9 within the 10 biotypes were obtained through ITS restriction digestion, and the majority of the tested biotypes produced patterns similar to those generated by the ATCC strains. To our knowledge, this study is not only the first comprehensive record of the size of the ITS region in sphingomonads, it is also the first study that describes the use of ITS restriction digestion to subtype those isolates.
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Guo, Zhansheng, Leng Han, Zhenlin Liang, and Xuguang Hou. "Comparative analysis of the ribosomal DNA repeat unit (rDNA) of Perna viridis (Linnaeus, 1758) and Perna canaliculus (Gmelin, 1791)." PeerJ 7 (September 3, 2019): e7644. http://dx.doi.org/10.7717/peerj.7644.
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Perna viridis and P. canaliculus are economically and ecologically important species of shellfish. In this study, the complete ribosomal DNA (rDNA) unit sequences of these species were determined for the first time. The gene order, 18S rRNA–internal transcribed spacer (ITS) 1–5.8S rRNA–ITS2–28S rRNA–intergenic spacer (IGS), was similar to that observed in other eukaryotes. The lengths of the P. viridis and P. canaliculus rDNA sequences ranged from 8,432 to 8,616 bp and from 7,597 to 7,610 bp, respectively, this variability was mainly attributable to the IGS region. The putative transcription termination site and initiation site were confirmed. Perna viridis and P. canaliculus rDNA contained two (length: 93 and 40 bp) and one (length: 131 bp) repeat motifs, respectively. Individual intra-species differences mainly involved the copy number of repeat units. In P. viridis, three cytosine-guanine (CpG) sites with sizes of 440, 1,075 and 537 bp were found to cover nearly the entire IGS sequence, whereas in P. canaliculus, two CpG islands with sizes of 361 and 484 bp were identified. The phylogenetic trees constructed with maximum likelihood and neighbour-joining methods and based on ITS sequences were identical and included three major clusters. Species of the same genus were easily clustered together.
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Sun, Yiqi, Hong Yang, Qiaoyan Zhang, Luping Qin, Pan Li, Joongku Lee, Shichao Chen, Khalid Rahman, Tingguo Kang, and Min Jia. "Genetic diversity and its conservation implications of Vitex rotundifolia (Lamiaceae) populations in East Asia." PeerJ 7 (January 11, 2019): e6194. http://dx.doi.org/10.7717/peerj.6194.
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Vitex rotundifolia is an important coastal and medicinal plant, and is recorded in the List of the Important Wild Plants for Conservation in China and Japan. However, an effective conservation strategy is lacking. In the present study, the genetic diversity and population structure were analyzed using phylogeographical methods based on the trnH-psbA and trnG-trnS intergenic spacers of the chloroplast DNA (cpDNA) sequences from 157 individuals from 25 sampling sites for V. rotundifolia and V. trifolia plus the internal transcribed spacer (ITS) of the nuclear ribosomal DNA (nrDNA) sequences of 177 individuals from 27 sampling sites. The results showed that V. rotundifolia and V. trifolia had eight cpDNA and two nrDNA haplotypes, respectively, and the V. rotundifolia has a low level of genetic diversity (haplotype diversity hd,cp = 0.360, hd,nr = 0.440), a more pronounced genetic differentiation among populations (population differentiation at the species level (GST) = 0.201, population differentiation at the allele level (NST) = 0.462), and an insignificantly different phylogeographical structure (NST > GST, P > 0.05). In addition, haplotype network analyses indicated that V. rotundifolia and V. trifolia have distinct haplotypes. Divergence dating based on BEAST software analyses showed that most cpDNA clades diverged in the late Pleistocene era. Demographic analysis indicated that V. rotundifolia underwent a rapid demographic expansion. Some scientific strategies are suggested for resource conservation of V. rotundifolia based on its genetic diversity and population structure.
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Varga, János, Éva Kevei, Beáta Tóth, Zofia Kozakiewicz, and Rolf F. Hoekstra. "Molecular analysis of variability within the toxigenicAspergillus ochraceusspecies." Canadian Journal of Microbiology 46, no. 7 (July 1, 2000): 593–99. http://dx.doi.org/10.1139/w00-031.
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Genetic variability of Aspergillus ochraceus was examined at the DNA level. Based on the HaeIII-BglII generated mitochondrial DNA restriction profiles, most isolates could be classified into two distinct groups. These two groups could also be distinguished by the random amplified polymorphic DNA technique, and with telomeric PCR amplifications. Phylogenetic analysis of sequences of the intergenic transcribed spacer region of some of the strains resulted in a dendrogram with the same topology as that based on mitochondrial DNA and amplified DNA data. None of the isolates with type 2 mtDNA profiles produce ochratoxins. Some strains (e.g., A. ochraceus ICMP 939) displayed strain-specific mitochondrial DNA patterns, and their amplified DNA profiles were also different from all other A. ochraceus strains examined.Key words: Aspergillus ochraceus, phylogenetic analysis, mitochondrial DNA, ITS region.
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Gibbs, Adele K., Frank Udovicic, Andrew N. Drinnan, and Pauline Y. Ladiges. "Phylogeny and classification of Eucalyptus subgenus Eudesmia (Myrtaceae) based on nuclear ribosomal DNA, chloroplast DNA and morphology." Australian Systematic Botany 22, no. 3 (2009): 158. http://dx.doi.org/10.1071/sb08043.
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Phylogenetic analysis of Eucalyptus subgenus Eudesmia is presented on the basis of the following three datasets: sequences of the internal transcribed spacer (ITS) and the external transcribed spacer (ETS) regions from nuclear rDNA, sequences of the psbA–trnH intergenic spacer region from chloroplast DNA, and morphological characters, including stamen bundling, operculum development, seeds and trichomes. Studies of floral development were essential for understanding the morphology of mature flowers and interpretation of synapomorphy and homoplasy. A summary phylogeny was constructed from a maximum parsimony analysis of those nodes coded as characters that had support in the molecular trees together with morphological characters. A revised infra-subgeneric classification is presented on the basis of the summary phylogeny, and compared with classifications of Hill and Johnson (1998) and Brooker (2000). Differences relate to relationships between clades and taxonomic rank (sections, series and subseries) and valid names of Brooker (2000) are conserved where possible. One main clade of 14 species (section Limbatae), many of mallee growth form, was found in all analyses; this clade is distributed in the South-West of Western Australia and adjacent Interzone and desert areas. A second main clade (section Complanatae) occurs in the northern and eastern tropical and subtropical regions of Australia, including Kimberley, Arnhem, Queensland and New South Wales. This section includes E. tetrodonta, previously treated as an isolated taxon in a monotypic section; however, this species is related to E. baileyana, E. similis, E. lirata and series Miniatae. The hypothesised phylogeny provides a framework for further analyses of biogeography and ecology, including functional traits.
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Honnavar, Prasanna, Gandham S. Prasad, Anup Ghosh, Sunil Dogra, Sanjeev Handa, and Shivaprakash M. Rudramurthy. "Malassezia arunalokei sp. nov., a Novel Yeast Species Isolated from Seborrheic Dermatitis Patients and Healthy Individuals from India." Journal of Clinical Microbiology 54, no. 7 (May 4, 2016): 1826–34. http://dx.doi.org/10.1128/jcm.00683-16.
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The majority of species within the genusMalasseziaare lipophilic yeasts that colonize the skin of warm-blooded animals. Two species,Malassezia globosaandMalassezia restricta, are implicated in the causation of seborrheic dermatitis/dandruff (SD/D). During our survey of SD/D cases, we isolated several species ofMalasseziaand noticed vast variations within a few lipid-dependent species. Variations observed in the phenotypic characteristics (colony morphology, absence of catalase activity, growth at 37°C, and precipitation surrounding wells containing Tween 20 or Cremophor EL) suggested the possible presence of a novel species. Sequence divergence observed in the internal transcribed spacer (ITS) region, the D1/D2 domain, and the intergenic spacer 1 (IGS1) region of rDNA and theTEF1gene, PCR-restriction fragment length polymorphism (RFLP) analysis of the ITS2 region, and fluorescent amplified fragment length polymorphism analysis support the existence of a novel species. Based on phenotypic and molecular characterization of these strains, we propose a new species, namely,M. arunalokeisp. nov., and we designate NCCPF 127130 (= MTCC 12054 = CBS 13387) as the type strain.
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Lim, K. Y., K. Skalicka, B. Koukalova, R. A. Volkov, R. Matyasek, V. Hemleben, A. R. Leitch, and A. Kovarik. "Dynamic Changes in the Distribution of a Satellite Homologous to Intergenic 26-18S rDNA Spacer in the Evolution of Nicotiana." Genetics 166, no. 4 (April 1, 2004): 1935–46. http://dx.doi.org/10.1093/genetics/166.4.1935.
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Abstract An ∼135-bp sequence called the A1/A2 repeat was isolated from the transcribed region of the 26-18S rDNA intergenic spacer (IGS) of Nicotiana tomentosiformis. Fluorescence in situ hybridization (FISH) and Southern blot analysis revealed its occurrence as an independent satellite (termed an A1/A2 satellite) outside of rDNA loci in species of Nicotiana section Tomentosae. The chromosomal location, patterns of genomic dispersion, and copy numbers of its tandemly arranged units varied between the species. In more distantly related Nicotiana species the A1/A2 repeats were found only at the nucleolar organizer regions (NOR). There was a trend toward the elimination of the A1/A2 satellite in N. tabacum (tobacco), an allotetraploid with parents closely related to the diploids N. sylvestris and N. tomentosiformis. This process may have already commenced in an S3 generation of synthetic tobacco. Cytosine residues in the IGS were significantly hypomethylated compared with the A1/A2 satellite. There was no clear separation between the IGS and satellite fractions in sequence analysis of individual clones and we found no evidence for CG suppression. Taken together the data indicate a dynamic nature of the A1/A2 repeats in Nicotiana genomes, with evidence for recurrent integration, copy number expansions, and contractions.
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Melanson, R. A., R. S. Sanderlin, A. R. McTaggart, and J. H. Ham. "A Systematic Study Reveals that Xylella fastidiosa Strains from Pecan Are Part of X. fastidiosa subsp. multiplex." Plant Disease 96, no. 8 (August 2012): 1123–34. http://dx.doi.org/10.1094/pdis-09-11-0730-re.
Full textAbstract:
Xylella fastidiosa causes disease in a number of economically important crops, ornamental plants, and shade trees, including grapevine, citrus, oleander, and sycamore. In pecan, X. fastidiosa causes pecan bacterial leaf scorch (PBLS), which leads to defoliation and reduces nut yield. No economically effective treatments are available for PBLS. In order to improve PBLS management practices, it is necessary to determine the subspecies of X. fastidiosa strains that infect pecan so that potential sources of inoculum may be identified. Multiprimer polymerase chain reaction (PCR) and phylogenetic analyses using nucleotide sequence data from the 16S-23S rRNA intergenic transcribed spacer (ITS) region and pglA consistently identified strains of X. fastidiosa isolated from pecan as X. fastidiosa subsp. multiplex. Enterobacterial repetitive intergenic consensus PCR and repetitive extragenic palindromic (REP)-PCR analyses were congruent with phylogenetic analyses. REP-PCR analyses indicated genetic variation within strains of X. fastidiosa from pecan. From these same analyses, X. fastidiosa strains from sycamore, grapevine, and oleander from Louisiana were identified as subsp. multiplex, subsp. fastidiosa, and subsp. sandyi, respectively. This study provides additional information about the host ranges of X. fastidiosa subspecies.
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Hoot, Sara B., W. Carl Taylor, and Nancy S. Napier. "Phylogeny and Biogeography of Isoëtes (Isoëtaceae) Based on Nuclear and Chloroplast DNA Sequence Data." Systematic Botany 31, no. 3 (July 1, 2006): 449–60. http://dx.doi.org/10.1600/036364406778388511.
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Despite its ancient origins, worldwide distribution, and adaptation to diverse habitats, Isoëtes species have a highly conserved morphology, making it difficult to resolve phylogenetic relationships using morphological characters. In this paper, we report the results from various analyses (maximum parsimony, maximum likelihood, and Bayesian inference) for Isoëtes species from around the world based on nucleotide sequences from the nuclear internal transcribed spacer (ITS) and chloroplast atpB/rbcL intergenic spacer regions. The trees resulting from our analyses of the combined data contain six major well-supported clades (bootstrap ≥ 90%, posterior probabilities 1.00): A clade with possible Gondwanan affinities (I. australis, I. coromandelina, I. panamensis, I. cubana, I. jamaicensis); a South African clade (I. capensis, I. toximontana, I. stellenbossiensis, I. stephansenii); a largely Northern Hemisphere clade (I. nuttallii, I. orcuttii, I. minima, I. dixitei, I. abyssinica, I. olympica, I. longissima, I. velata); an Asian/Australasian clade (I. drummondii, I. gunnii, I. pusilla, I. kirkii, I. muelleri, I. taiwanensis, I. japonica, I. yunguiensis, I. habbemensis); a Mediterranean clade (I. histrix and I. setacea); and a poorly resolved clade consisting of 12 new world species (American species complex). Our results are compared to past classifications and various biogeographical scenarios are explored.
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Chen, Wen, Zeinab Robleh Djama, Michael D. Coffey, Frank N. Martin, Guillaume J. Bilodeau, Lorien Radmer, Geoff Denton, and C. André Lévesque. "Membrane-Based Oligonucleotide Array Developed from Multiple Markers for the Detection of Many Phytophthora Species." Phytopathology® 103, no. 1 (January 2013): 43–54. http://dx.doi.org/10.1094/phyto-04-12-0092-r.
Full textAbstract:
Most Phytophthora spp. are destructive plant pathogens; therefore, effective monitoring and accurate early detection are important means of preventing potential epidemics and outbreaks of diseases. In the current study, a membrane-based oligonucleotide array was developed that can detect Phytophthora spp. reliably using three DNA regions; namely, the internal transcribed spacer (ITS), the 5′ end of cytochrome c oxidase 1 gene (cox1), and the intergenic region between cytochrome c oxidase 2 gene (cox2) and cox1 (cox2-1 spacer). Each sequence data set contained ≈250 sequences representing 98 described and 15 undescribed species of Phytophthora. The array was validated with 143 pure cultures and 35 field samples. Together, nonrejected oligonucleotides from all three markers have the ability to reliably detect 82 described and 8 undescribed Phytophthora spp., including several quarantine or regulated pathogens such as Phytophthora ramorum. Our results showed that a DNA array containing signature oligonucleotides designed from multiple genomic regions provided robustness and redundancy for the detection and differentiation of closely related taxon groups. This array has the potential to be used as a routine diagnostic tool for Phytophthora spp. from complex environmental samples without the need for extensive growth of cultures.
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Hassan, Oliul, Jong Yeob Jeon, Taehyun Chang, Jun Sung Shin, Nam Kwon Oh, and Yong Se Lee. "Molecular and Morphological Characterization of Colletotrichum Species in the Colletotrichum gloeosporioides Complex Associated with Persimmon Anthracnose in South Korea." Plant Disease 102, no. 5 (May 2018): 1015–24. http://dx.doi.org/10.1094/pdis-10-17-1564-re.
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Anthracnose is a major disease of persimmon in the pre- and postharvest phase. Several species of Colletotrichum (Colletotrichum gloeosporioides, C. acutatum, and C. horii) have been reported as causal agents of persimmon anthracnose in South Korea. In this study, a collection of 50 isolates associated with persimmon anthracnose were collected from Sangju (n = 25) and Cheongdo-gun (n = 25), South Korea. The morphological characteristics of all 50 Colletotrichum isolates were similar, and it was difficult to identify the isolates to the species level. A subsample of eight isolates was characterized phylogenetically to ascertain species. BLAST search and phylogenetic analysis of the internal transcribed spacer (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and actin (ACT) genes revealed two species: C. horii as well as a previously unreported persimmon anthracnose causal agent C. siamense. C. siamense isolates were confirmed again by phylogenetic analysis of the ITS, ACT, GAPDH, calmodulin, and Apn2-Mat1-2 intergenic spacer partial mating type genes. Koch’s postulates for C. horii and C. siamense were fulfilled, confirming the pathogenicity of the two species in persimmon fruit. Morphological characteristics (colony morphology and size and shape of conidia and appressoria) from two representative isolates support results of the phylogenetic analysis and match those of previous descriptions of C. horii and C. siamense.
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Coughlan, Patricia, James C. Carolan, Ingrid L. I. Hook, Lisa Kilmartin, and Trevor R. Hodkinson. "Phylogenetics of Taxus Using the Internal Transcribed Spacers of Nuclear Ribosomal DNA and Plastid trnL-F Regions." Horticulturae 6, no. 1 (March 12, 2020): 19. http://dx.doi.org/10.3390/horticulturae6010019.
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Taxus is a genus of trees and shrubs with high value in horticulture and medicine as a source of the anticancer drug paclitaxel. The taxonomy of the group is complex due to the lack of diagnostic morphological characters and the high degree of similarity among species. Taxus has a wide global geographic distribution and some taxonomists recognize only a single species with geographically defined subgroups, whereas others have described several species. To address these differences in taxonomic circumscription, phylogenetic analyses were conducted on DNA sequences using Maximum Likelihood, Bayesian Inference and TCS haplotype networks on single and combined gene regions obtained for the nuclear ribosomal ITS region and the plastid trnL intron and trnL-F intergenic spacer. Evidence is presented for the sister group status of Pseudotaxus to Taxus and the inclusion of Amentotaxus, Austrotaxus, Cephalotaxus and Torreya within Taxaceae. Results are consistent with the taxonomic recognition of nine species: T. baccata, T. brevifolia, T. canadensis, T. cuspidata, T. floridana, T. fuana, T. globosa, T. sumatrana and T. wallichiana, but evidence is found for less species distinction and considerable reticulation within the T. baccata, T. canadensis and T. cuspidata group. We compare the results to known taxonomy, biogeography, present new leaf anatomical data and discuss the origins of the hybrids T. ×media and T. ×hunnewelliana.
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Sadova, Anastasia A., Dmitry Y. Panteleev, and Galina V. Pavlova. "Zooming in: PAGE-Northern Blot Helps to Analyze Anti-Sense Transcripts Originating from Human rIGS under Transcriptional Stress." Non-Coding RNA 7, no. 3 (August 24, 2021): 50. http://dx.doi.org/10.3390/ncrna7030050.
Full textAbstract:
Ribosomal intergenic spacer (rIGS), located between the 45S rRNA coding arrays in humans, is a deep, unexplored source of small and long non-coding RNA molecules transcribed in certain conditions to help a cell generate a stress response, pass through a differentiation state or fine tune the functioning of the nucleolus as a ribosome biogenesis center of the cell. Many of the non-coding transcripts originating from the rIGS are not characterized to date. Here, we confirm the transcriptional activity of the region laying a 2 kb upstream of the rRNA promoter, and demonstrate its altered expression under transcriptional stress, induced by a wide range of known transcription inhibitors. We managed to show an increased variability of anti-sense transcripts in alpha-amanitin treated cells by applying the low-molecular RNA fraction extracted from agarose gel to PAGE-northern. Also, the fractioning of RNA by size using agarose gel slices occurred, being applicable for determining the sizes of target transcripts via RT-PCR.
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Pryor, Barry M., and Themis J. Michailides. "Morphological, Pathogenic, and Molecular Characterization of Alternaria Isolates Associated with Alternaria Late Blight of Pistachio." Phytopathology® 92, no. 4 (April 2002): 406–16. http://dx.doi.org/10.1094/phyto.2002.92.4.406.
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Alternaria isolates were obtained from various pistachio tissues collected in five orchards in California. For all isolates, morphological characteristics of the colony and sporulation apparatus were determined and compared with those of representative isolates of A. alternata, A. tenuissima, A. arborescens, and A. infectoria. A selection of the pistachio isolates and the representative Alternaria isolates were evaluated for pathogenicity to pistachio. Molecular characteristics of these isolates were determined using random amplified polymorphism DNA (RAPD) analysis, polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis of nuclear intergenic spacer rDNA, and sequence analysis of nuclear internal transcribed spacer (ITS) rDNA. Based on morphological characteristics, the pistachio isolates were grouped as identical or very similar to either A. alternata, A. tenuissima, A. arborescens, or A. infectoria. Isolates from the alternata, tenuissima, and arborescens species-groups were pathogenic to pistachio and no significant differences in pathogenicity were observed. Isolates from the infectoria species-group were only weakly pathogenic to pistachio. Based on cluster analysis of RAPD and PCR-RFLP data, three distinct clusters were evident; the infectoria cluster, the arborescens cluster, and a combined alternata/tenuissima cluster. Based on analysis of ITS sequence data, the infectoria species-group was phylogenetically distinct from the other species-groups. Isolates of the alternata, tenuissima, and arborescens species-groups comprised a monophyletic clade in which the three species-groups could not be further resolved.