Journal articles: 'TrnK intron'

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Nguyen, Sy Dinh, and Hunseung Kang. "Comprehensive analysis of chloroplast intron-containing genes and conserved splice sites in dicot and monocot plants." Science and Technology Development Journal - Natural Sciences 1, T1 (March 31, 2017): 60–68. http://dx.doi.org/10.32508/stdjns.v1it1.435.

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Despite the increasing knowledge on the importance of the intron splicing of chloroplast genes during plant growth and stress responses, identification of intron-containing chloroplast genes and determination of splice sites in chloroplast introns are still lacking. Here, we carried out a comprehensive analysis of the chloroplast genome sequences in important plants and crops, including four dicots (Arabidopsis thaliana, Coffea arabica, Nicotiana tabacum, and Panax schinseng) and four monocots (Musa acuminata, Oryza sativa, Triticum aestivum, and Zea mays). The results showed that both dicot and monocot chloroplast genomes harbor 6 intron-containing tRNAs (trnA, trnG, trnI, trnK, trnL, and trnV) and 10-12 intron-containing mRNAs (atpF, rpl2, rpl16, rps16, ndhA, ndhB, petB, petD, rpoC1, rps12, ycf3, and clpP). Notably, rpoC1 and clpP lacked introns in monocot plants, except M. acuminata. Analysis of the nucleotide sequences of chloroplast introns revealed that the 5’-splice sites, 3’-splice sites, and branch-point sites of the chloroplast introns were highly conserved among dicots and monocots. Notably, the 5’-splice sites and 3’-splice sites of the chloroplast introns were similar to those of the nuclear U12 introns, whereas the branch-point sites of the chloroplast introns were homologous to those of the nuclear U2 introns. Taken together, these results indicated that the chloroplast genomes contained strictly limited intron-containing genes with conserved splice sites, suggesting that splicing of chloroplast introns was important for chloroplast biogenesis and function in both dicot and monocot plants.

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Sun, Jianying, Xiaofeng Dong, Qinghe Cao, Tao Xu, Mingku Zhu, Jian Sun, Tingting Dong, Daifu Ma, Yonghua Han, and Zongyun Li. "A systematic comparison of eight new plastome sequences from Ipomoea L." PeerJ 7 (March 11, 2019): e6563. http://dx.doi.org/10.7717/peerj.6563.

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Background Ipomoea is the largest genus in the family Convolvulaceae. The species in this genus have been widely used in many fields, such as agriculture, nutrition, and medicine. With the development of next-generation sequencing, more than 50 chloroplast genomes of Ipomoea species have been sequenced. However, the repeats and divergence regions in Ipomoea have not been well investigated. In the present study, we sequenced and assembled eight chloroplast genomes from sweet potato’s close wild relatives. By combining these with 32 published chloroplast genomes, we conducted a detailed comparative analysis of a broad range of Ipomoea species. Methods Eight chloroplast genomes were assembled using short DNA sequences generated by next-generation sequencing technology. By combining these chloroplast genomes with 32 other published Ipomoea chloroplast genomes downloaded from GenBank and the Oxford Research Archive, we conducted a comparative analysis of the repeat sequences and divergence regions across the Ipomoea genus. In addition, separate analyses of the Batatas group and Quamoclit group were also performed. Results The eight newly sequenced chloroplast genomes ranged from 161,225 to 161,721 bp in length and displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat (IR) regions (30,798–30,910 bp each) separated by a large single copy (LSC) region (87,575–88,004 bp) and a small single copy (SSC) region (12,018–12,051 bp). The average guanine-cytosine (GC) content was approximately 40.5% in the IR region, 36.1% in the LSC region, 32.2% in the SSC regions, and 37.5% in complete sequence for all the generated plastomes. The eight chloroplast genome sequences from this study included 80 protein-coding genes, four rRNAs (rrn23, rrn16, rrn5, and rrn4.5), and 37 tRNAs. The boundaries of single copy regions and IR regions were highly conserved in the eight chloroplast genomes. In Ipomoea, 57–89 pairs of repetitive sequences and 39–64 simple sequence repeats were found. By conducting a sliding window analysis, we found six relatively high variable regions (ndhA intron, ndhH-ndhF, ndhF-rpl32, rpl32-trnL, rps16-trnQ, and ndhF) in the Ipomoea genus, eight (trnG, rpl32-trnL, ndhA intron, ndhF-rpl32, ndhH-ndhF, ccsA-ndhD, trnG-trnR, and pasA-ycf3) in the Batatas group, and eight (ndhA intron, petN-psbM, rpl32-trnL, trnG-trnR, trnK-rps16, ndhC-trnV, rps16-trnQ, and trnG) in the Quamoclit group. Our maximum-likelihood tree based on whole chloroplast genomes confirmed the phylogenetic topology reported in previous studies. Conclusions The chloroplast genome sequence and structure were highly conserved in the eight newly-sequenced Ipomoea species. Our comparative analysis included a broad range of Ipomoea chloroplast genomes, providing valuable information for Ipomoea species identification and enhancing the understanding of Ipomoea genetic resources.

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Jarret, Robert L. "DNA Barcoding in a Crop Genebank: The Capsicum annuum Species Complex." Open Biology Journal 1, no. 1 (October 28, 2008): 35–42. http://dx.doi.org/10.2174/1874196700801010035.

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Variability within eight cpDNA introns including trnS-trnfM, trnL-trnT, trnH-psbA, trnF-trnL, trnD-trnT, trnCrpoB, rps16 and matK, and the nuclear waxy introns was examined in seven species of Capsicum (C. annuum, C. baccatum, C. chinense, C. frutescens, C. pubescens, C. chacoense and C. rhomboideum) in order to evaluate the feasibility of utilizing these loci for DNA barcoding within the C. annuum complex. Numerous insertions/deletions (indels) and substitutions were detected in all cpDNA introns. However, none was sufficient to differentiate the individual members of the C. annuum complex (C. annuum, C. chinense and C. frutescens). Variation within trnL-trnT, trnF-trnL and trnH-psbA enabled the differentiation of the complex from the other taxa examined. In contrast, single base indels and substitutions within the waxy introns permitted the differentiation of all taxa within the plant materials examined. The use of trnH-psbA or trnL-trnT, and the waxy introns is proposed for barcoding members of the C. annuum complex.

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Liu, Hongshan, Zhihai Su, Shuiqing Yu, Jialin Liu, Xiaojuan Yin, Guowei Zhang, Wei Liu, and Bin Li. "Genome Comparison Reveals Mutation Hotspots in the Chloroplast Genome and Phylogenetic Relationships of Ormosia Species." BioMed Research International 2019 (August 21, 2019): 1–11. http://dx.doi.org/10.1155/2019/7265030.

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The papilionoid legume genus Ormosia comprises approximately 130 species, which are distributed mostly in the Neotropics, with some species in eastern Asia and northeastern Australia. The taxonomy and evolutionary history remain unclear due to the lack of a robust species-level phylogeny. Chloroplast genomes can provide important information for phylogenetic and population genetic studies. In this study, we determined the complete chloroplast genome sequences of five Ormosia species by Illumina sequencing. The Ormosia chloroplast genomes displayed the typical quadripartite structure of angiosperms, which consisted of a pair of inverted regions separated by a large single-copy region and a small single-copy region. The location and distribution of repeat sequences and microsatellites were determined. Comparative analyses highlighted a wide spectrum of variation, with trnK-rbcL, atpE-trnS-rps4, trnC-petN, trnS-psbZ-trnG, trnP-psaJ-rpl33, and clpP intron being the most variable regions. Phylogenetic analysis revealed that Ormosia is in the Papilionoideae clade and is sister to the Lupinus clade. Overall, this study, which provides Ormosia chloroplast genomic resources and a comparative analysis of Ormosia chloroplast genomes, will be beneficial for the evolutionary study and phylogenetic reconstruction of the genus Ormosia and molecular barcoding in population genetics and will provide insight into the chloroplast genome evolution of legumes.

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CRAWLEY, Sunny S., and Khidir W. HILU. "Caryophyllales: Evaluating phylogenetic signal in trnK intron versus matK." Journal of Systematics and Evolution 50, no. 5 (July 11, 2012): 387–410. http://dx.doi.org/10.1111/j.1759-6831.2012.00197.x.

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Peterson, Paul M., Isidoro Sánchez Vega, Konstantin Romaschenko, Diego Giraldo-Cañas, and Nancy F. Refulio Rodriguez. "Revision of Muhlenbergia (Poaceae, Chloridoideae, Cynodonteae, Muhlenbergiinae) in Peru: classification, phylogeny, and a new species, M. romaschenkoi." PhytoKeys 114 (December 31, 2018): 123–206. http://dx.doi.org/10.3897/phytokeys.114.28799.

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A taxonomic treatment, phylogeny based on analysis of six DNA sequence markers (ITS, ndhA intron, rpl32-trnL, rps3, rps16 intron and rps16-trnK) and classification of Muhlenbergia for Peru is given. Seventeen species and one presumed hybrid are recognised. Muhlenbergiaromaschenkoisp. nov. is newly described from the Río Huallaga Valley, northeast of Huánuco. The type of Podosemumangustatum [≡ Muhlenbergiaangustata] clearly aligns with what we had been referring to as the hybrid between this species and M.rigida. Therefore, we adopt the next available heterotypic name, Muhlenbergiacoerulea, for what we had been calling M.angustata and change the hybrid designation to M.coerulea × M.rigida. Lectotypes are designated for Epicampescoerulea Griseb., Muhlenbergiaaffinis Trin., Muhlenbergiaberlandieri Trin., Muhlenbergiabeyrichiana Kunth, Muhlenbergiaelegansvar.atroviolacea Kuntze, Muhlenbergiaelegansvar.subviridis Kuntze and Muhlenbergiaphragmitoides Griseb.

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Liu, Mi-Li, Wei-Bing Fan, Ning Wang, Peng-Bin Dong, Ting-Ting Zhang, Ming Yue, and Zhong-Hu Li. "Evolutionary Analysis of Plastid Genomes of Seven Lonicera L. Species: Implications for Sequence Divergence and Phylogenetic Relationships." International Journal of Molecular Sciences 19, no. 12 (December 14, 2018): 4039. http://dx.doi.org/10.3390/ijms19124039.

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Plant plastomes play crucial roles in species evolution and phylogenetic reconstruction studies due to being maternally inherited and due to the moderate evolutionary rate of genomes. However, patterns of sequence divergence and molecular evolution of the plastid genomes in the horticulturally- and economically-important Lonicera L. species are poorly understood. In this study, we collected the complete plastomes of seven Lonicera species and determined the various repeat sequence variations and protein sequence evolution by comparative genomic analysis. A total of 498 repeats were identified in plastid genomes, which included tandem (130), dispersed (277), and palindromic (91) types of repeat variations. Simple sequence repeat (SSR) elements analysis indicated the enriched SSRs in seven genomes to be mononucleotides, followed by tetra-nucleotides, dinucleotides, tri-nucleotides, hex-nucleotides, and penta-nucleotides. We identified 18 divergence hotspot regions (rps15, rps16, rps18, rpl23, psaJ, infA, ycf1, trnN-GUU-ndhF, rpoC2-rpoC1, rbcL-psaI, trnI-CAU-ycf2, psbZ-trnG-UCC, trnK-UUU-rps16, infA-rps8, rpl14-rpl16, trnV-GAC-rrn16, trnL-UAA intron, and rps12-clpP) that could be used as the potential molecular genetic markers for the further study of population genetics and phylogenetic evolution of Lonicera species. We found that a large number of repeat sequences were distributed in the divergence hotspots of plastid genomes. Interestingly, 16 genes were determined under positive selection, which included four genes for the subunits of ribosome proteins (rps7, rpl2, rpl16, and rpl22), three genes for the subunits of photosystem proteins (psaJ, psbC, and ycf4), three NADH oxidoreductase genes (ndhB, ndhH, and ndhK), two subunits of ATP genes (atpA and atpB), and four other genes (infA, rbcL, ycf1, and ycf2). Phylogenetic analysis based on the whole plastome demonstrated that the seven Lonicera species form a highly-supported monophyletic clade. The availability of these plastid genomes provides important genetic information for further species identification and biological research on Lonicera.

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Hausner, Georg, Robert Olson, Dawn Simon, Ian Johnson, Erin R. Sanders, Kenneth G. Karol, Richard M. McCourt, and Steven Zimmerly. "Origin and Evolution of the Chloroplast trnK (matK) Intron: A Model for Evolution of Group II Intron RNA Structures." Molecular Biology and Evolution 23, no. 2 (November 2, 2005): 380–91. http://dx.doi.org/10.1093/molbev/msj047.

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Donoghue, Michael J., Bruce G. Baldwin, Jianhua Li, and Richard C. Winkworth. "Viburnum Phylogeny Based on Chloroplast trnK Intron and Nuclear Ribosomal ITS DNA Sequences." Systematic Botany 29, no. 1 (January 1, 2004): 188–98. http://dx.doi.org/10.1600/036364404772974095.

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Wilson, Carol A. "Phylogeny of Iris based on chloroplast matK gene and trnK intron sequence data." Molecular Phylogenetics and Evolution 33, no. 2 (November 2004): 402–12. http://dx.doi.org/10.1016/j.ympev.2004.06.013.

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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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Meimberg, Harald, Stefan Thalhammer, Andreas Brachmann, and Günther Heubl. "Comparative analysis of a translocated copy of the trnK intron in carnivorous family Nepenthaceae." Molecular Phylogenetics and Evolution 39, no. 2 (May 2006): 478–90. http://dx.doi.org/10.1016/j.ympev.2005.11.023.

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Meimberg, H., A. Wistuba, P. Dittrich, and G. Heubl. "Molecular Phylogeny of Nepenthaceae Based on Cladistic Analysis of Plastid trnK Intron Sequence Data." Plant Biology 3, no. 2 (March 2001): 164–75. http://dx.doi.org/10.1055/s-2001-12897.

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Wanke, Stefan, M. Alejandra Jaramillo, Thomas Borsch, Marie-Stéphanie Samain, Dietmar Quandt, and Christoph Neinhuis. "Evolution of Piperales—matK gene and trnK intron sequence data reveal lineage specific resolution contrast." Molecular Phylogenetics and Evolution 42, no. 2 (February 2007): 477–97. http://dx.doi.org/10.1016/j.ympev.2006.07.007.

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Huang, Weihua, Yajuan Zhu, Wenjuan Wu, Xuan Li, Delin Zhang, Ping Yin, and Jirong Huang. "The Pentatricopeptide Repeat Protein SOT5/EMB2279 Is Required for Plastid rpl2 and trnK Intron Splicing." Plant Physiology 177, no. 2 (April 23, 2018): 684–97. http://dx.doi.org/10.1104/pp.18.00406.

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Byrne, M., and M. Hankinson. "Testing the variability of chloroplast sequences for plant phylogeography." Australian Journal of Botany 60, no. 7 (2012): 569. http://dx.doi.org/10.1071/bt12146.

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Phylogeography in plants is hampered by lack of DNA-sequence regions that detect sufficient variation in intra-specific lineages to reveal historical patterns. We tested 13 putatively highly variable non-coding chloroplast regions in six species complexes, from four different angiosperm families, where phylogeographic patterns have previously been identified using restriction fragment length polymorphism analysis of the chloroplast genome. All regions tested amplified in most of the species. The intergenic spacer regions trnQ–rps16, trnS–trnG, psbA–trnH, psbD–trnT and ndhC–trnV were the five most promising regions for phylogeographic analysis in terms of variability, and petB and rpl16 were variable, given the utility of being amplified in a single reaction. The trnQ–rps16 and psbA–trnH intergenic spacer regions and the rpl16 D4-loop intron showed variation between known lineages in all species. The psbA–trnH intergenic spacer that has been suggested as a suitable barcoding gene for plants, generally showed a level of variation similar to that in other variable regions in the species investigated here, suggesting that some caution is required in the use of this region for barcoding applications. The present analysis identified a set of seven chloroplast regions that are a useful basis for informed selection of sequences for assessment of phylogeographic structure in plants.

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Miller, Joseph T., Rose Andrew, and Randall J. Bayer. "Molecular phylogenetics of the Australian acacias of subg. Phyllodineae (Fabaceae: Mimosoideae) based on the trnK intron." Australian Journal of Botany 51, no. 2 (2003): 167. http://dx.doi.org/10.1071/bt01099.

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With over 960 species, Acacia is the largest genus of plants in Australia with all but nine of these species classified as subgenus Phyllodineae. DNA sequences for the chloroplast trnK region were sequenced for over 100 species to test sectional classification and survey species relationships within this subgenus. Only one of the seven recognised sections was found to be monophyletic; however, the close relationship of sect. Botrycephalae to certain racemose, uninerved species of sect. Phyllodineae is confirmed. Support is found for an expanded version of Vassal's Pulchelloidea, with the addition of sect. Lycopodiifoliae and several members of sect. Phyllodineae. These species, while morphologically distinct in adult foliage, possess similar seedling characteristics. The multinerved species are unresolved, indicating a rapid morphological radiation with little chloroplast sequence divergence among these species. The low levels of sequence divergence, large numbers of morphological species groups and the adaptive radiation of the group are discussed.

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Mglinets, A. V. "Phylogenetic relationships of genus Beta species based on the chloroplast trnK (matK) gene intron sequence information." Doklady Biochemistry and Biophysics 420, no. 1 (June 2008): 135–38. http://dx.doi.org/10.1134/s1607672908030101.

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Chaw, Shu-Miaw, Terrence W. Walters, Chien-Chang Chang, Shu-Hsuan Hu, and Shin-Hsiao Chen. "A phylogeny of cycads (Cycadales) inferred from chloroplast matK gene, trnK intron, and nuclear rDNA ITS region." Molecular Phylogenetics and Evolution 37, no. 1 (October 2005): 214–34. http://dx.doi.org/10.1016/j.ympev.2005.01.006.

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Widyatmoko, AYPBC, and Susumu Shiraishi. "Inter- and intraspecific variation of chloroplast mini- and microsatellites DNA in the four closed related Acacia species." Indonesian Journal of Biotechnology 19, no. 1 (December 31, 2015): 1. http://dx.doi.org/10.22146/ijbiotech.8639.

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Mini- and microsatellites of four Acacia species, A. aulacocarpa, A. auriculiformis, A. crassicarpa and A.mangium were investigated on four non-coding regions of cpDNA, the intron of trnL, and the intergenicspacers of trnL - trnP, trnD - trnY, and trnP – trnW. Nine single base substitutions and six informative miniandmicrosatellites were detected in the the four cpDNA non-coding regions. Based on the substitutionsand mini- and microsatellites, ten cpDNA haplotypes (A - J) could be distinguished. Acacia auriculiformispossessed fi ve haplotypes, A. aulacocarpa, four haplotypes, and A. crassicarpa, three haplotypes. All samplesof A. mangium possessed the same haplotype. Mini- and microsatellites recognized in this study can beused for species identifi cation of the four Acacia species. The ten haplotypes could divided the four speciesinto 2 groups, A. aulacocarpa-A.crassicarpa group and A. auriculiformis-A. mangium group. By developing thePCR-based markers based on the sequence information, many experiments can be carried out for the Acaciaimprovement programs.

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Johnson, Douglas A., and Jiro Hattori. "Analysis of a hotspot for deletion formation within the intron of the chloroplast trnI gene." Genome 39, no. 5 (October 1, 1996): 999–1005. http://dx.doi.org/10.1139/g96-124.

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The chloroplast genomes of higher plants encode several tRNA genes that contain highly conserved type II introns. Using primers specific to conserved 5′ and 3′ regions within the introns of the genes trnA (tRNA-ala) and trnI (tRNA-ile) we have PCR amplified parts of these introns from 36 plant species representing a wide range of plant families. Deletions were found in the introns of both tRNA genes. Fourteen species had detectable deletions within the intron of trnI and four species within the intron of trnA. The occurrence of these deletions among the various plant families suggests that the events leading to the formation of these deletions occurred independently many times during the evolution of higher plants. Analysis of the amplified PCR products from the trnI intron suggests that these independent deletions may not be random but appear to fall into two size classes. Several members of each class were cloned and sequenced and the end points of the deletions were mapped. The 3′ ends of all deletions studied terminate within the same short region. The 5′ ends of the deletions map to two different regions, giving rise to the two size classes. These two 5′ deletion endpoint regions show some sequence similarity. Only two of the identified deletions contain directly repeated sequences at the deletion endpoints, a feature associated with homologous recombination. Our results suggest that within the trnI intron, there are preferred sites or "hotspots" for deletion formation involving a novel imprecise recombination mechanism. The significance of these sequences and possible mechanisms for deletion formation are discussed. Key words : chloroplast, intron, deletion, sequence.

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Miller, Joseph T., and Randall J. Bayer. "Molecular phylogenetics of Acacia subgenera Acacia and Aculeiferum (Fabaceae : Mimosoideae), based on the chloroplast matK coding sequence and flanking trnK intron spacer regions." Australian Systematic Botany 16, no. 1 (2003): 27. http://dx.doi.org/10.1071/sb01035.

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The genus Acacia is subdivided into the following three subgenera: subg. Acacia, subg. Aculeiferum and the predominantly Australian subg. Phyllodineae. Morphological and molecular studies have suggested that the tribe Acacieae and genus Acacia are artificial and have a close affinity to the tribe Ingeae. Sequence analysis of the chloroplast trnK intron, including the matK coding region and flanking non-coding regions, were undertaken to examine taxon relationships within Acacia subgenera Acacia and Aculeiferum. Subgenus Acacia is monophyletic while subgenus Aculeiferum is paraphyletic. Within the subgenera, major divisions are found based on biogeography, New World versus African–Asian taxa. These data suggest that characters such as inflorescence and prickle and/or stipule type are polymorphic and homoplasious in cladistic analyses within the subgenera.

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M�ller, K., and T. Borsch. "Phylogenetics of Utricularia (Lentibulariaceae) and molecular evolution of the trnK intron in a lineage with high substitutional rates." Plant Systematics and Evolution 250, no. 1-2 (December 22, 2004): 39–67. http://dx.doi.org/10.1007/s00606-004-0224-1.

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Miller, Joseph T., and Randall J. Bayer. "Molecular phylogenetics of Acacia (Fabaceae: Mimosoideae) based on the chloroplast MATK coding sequence and flanking TRNK intron spacer regions." American Journal of Botany 88, no. 4 (April 2001): 697–705. http://dx.doi.org/10.2307/2657071.

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KOROTKOVA, NADJA, THOMAS BORSCH, and SALVADOR ARIAS. "A phylogenetic framework for the Hylocereeae (Cactaceae) and implications for the circumscription of the genera." Phytotaxa 327, no. 1 (November 3, 2017): 1. http://dx.doi.org/10.11646/phytotaxa.327.1.1.

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The tribe Hylocereeae are represented by mainly Central American-Mexican epiphytic, hemi-epiphytic and climbing cacti. They are popular due to their spectacular nocturnal flowers and have some importance as crops grown for their edible fruits. We present the first comprehensive phylogenetic study of the Hylocereeae sampling 60 out of the 63 currently accepted species and 17 out of 19 infraspecific taxa. Based on four plastid regions (trnK/matK, the rpl16 intron, rps3-rpl16, and trnL-F) we find a highly supported core Hylocereeae clade that also includes Acanthocereus and Peniocereus p.p., while Strophocactus is depicted as polyphyletic and is resolved outside of the Hylocereeae tribe. The clades found within Hylocereeae agree, in general terms, with the currently accepted genera but none of the genera are entirely monophyletic in their current circumscription. A new concept for the Hylocereeae is presented to include the genera Acanthocereus (incl. Peniocereus p.p.), Aporocactus, Disocactus, Epiphyllum, Selenicereus (incl. Hylocereus and Weberocereus p.p.), Pseudorhipsalis, Kimnachia gen. nov., and Weberocereus. New nomenclatural combinations are provided to make these genera monophyletic. The genus Deamia is reinstated for Strophocactus testudo and S. chontalensis, while Strophocactus is newly circumscribed to include S. wittii, Pseudoacanthocereus brasiliensis, and P. sicariguensis. Both genera are excluded from Hylocereeae. A taxonomic synopsis of Hylocereeae is provided.

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Moura, Mónica, Mark A. Carine, Valéry Malécot, Aula Lourenço, Hanno Schaefer, and Luís Silva. "A taxonomic reassessment of Viburnum (Adoxaceae) in the Azores." Phytotaxa 210, no. 1 (May 29, 2015): 4. http://dx.doi.org/10.11646/phytotaxa.210.1.3.

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The taxonomic status of the Azorean endemic Viburnum tinus subsp. subcordatum is reassessed, using morphological characters and new molecular data from the ITS region and the trnK intron. A survey of morphological variation supports the recognition of V. tinus subsp. subcordatum as distinct from V. tinus subsp. tinus and the Canary endemic V. rugosum (formerly known as V. tinus subsp. rigidum) based on leaf shape, the shape of the leaf base and apex, the sub-entire and revolute leaf margins, blistered upper leaf surfaces, trichome density and type, and fruit size. Molecular data also confirm this distinctiveness within section Tinus. Taken together, our morphological and genetic data presented in this paper support the recognition of the Azorean taxon at the species level under the name of Viburnum treleasei. A description of the species is provided and nomenclatural issues relating to the two Macaronesian Viburnum taxa are discussed.

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Peterson, Paul M., Steven P. Sylvester, Konstantin Romaschenko, Robert J. Soreng, Patricia Barberá, Alejandro Quintanar, and Carlos Aedo. "A phylogeny of species near Agrostis supporting the recognition of two new genera, Agrostula and Alpagrostis (Poaceae, Pooideae, Agrostidinae) from Europe." PhytoKeys 167 (November 20, 2020): 57–82. http://dx.doi.org/10.3897/phytokeys.167.55171.

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Based on a molecular DNA phylogeny of three plastid (rpl32-trnK, rps16 intron, and rps16-trnK) and nuclear ITS regions investigating 32 species of Agrostidinae, we describe two new genera, Agrostulagen. nov. with a single species and Alpagrostisgen. nov. with four species; provide support for five species in a monophyletic Podagrostis; and include a small sample of 12 species of a monophyletic Agrostis s.s. (including the type and most species of Neoschischkinia), that separates into two clades corresponding to A. subg. Agrostis and A. subg. Vilfa. Agrostula differs from Agrostis in having leaf blades with pillars of sclerenchyma which are continuous between the adaxial and abaxial surface of the blades, dorsally rounded glumes with blunt to truncate and erose to denticulate apices, florets ½ the length of the glumes, lemmas equally wide as long, widest at (or near) apex, apices broadly truncate, irregularly 5 to 7 denticulate to erose, awnless, anthers longer than the lemmas, and rugose-papillose caryopses. Alpagrostis differs from Agrostis in having geniculate basally inserted awns and truncate lemma apices with lateral veins prolonged from the apex in (2)4 setae. The following eight new combinations are made: Agrostula truncatula, Agrostula truncatula subsp. durieui, Alpagrostis alpina, Alpagrostis alpina var. flavescens, Alpagrostis barceloi, Alpagrostis setacea, Alpagrostis setacea var. flava, and Alpagrostis schleicheri. In addition, we provide a key separating Agrostula and Alpagrostis from Agrostis s.s. and other genera previously considered as synonyms of Agrostis; lectotypify Agrostis alpina Scop., A. schleicheri Jord. & Verl., A. truncatula Parl., and A. truncatula var. durieui Henriq.; and neotypify A. setacea Curtis.

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Haider, Nadia, and Imad Nabulsi. "Identification of Bread and Durum Wheats from their Diploid Ancestral Species Based on Chloroplast DNA." Agriculture (Pol'nohospodárstvo) 66, no. 2 (July 1, 2020): 56–66. http://dx.doi.org/10.2478/agri-2020-0006.

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AbstractSpecies that have been identified as the genome donors to cultivated polyploid durum and bread wheats (Triticum durum L. and T. aestivum L., respectively) are potential gene sources for the breeding of these two crops. Therefore, their accurate identification facilitates their use in the improvement of these crops. Based on chloroplast DNA analysis (rpL2 and rps16 introns, psbC-trnS, trnT-L, and trnL-F) using polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (PCR-RFLP), an attempt was made in 2018 (Department of Molecular Biology and Biotechnology/AECS) to identify durum and bread wheats from each of their proposed diploid ancestral species (i.e., T. monococcum, T. urartu, Aegilops speltoides, and Ae. tauschii). The use of two PCR markers (psbC-trnS and trnL-F) and three PCR-RFLP locus-enzyme combinations (rps16 intron-Tru 1I, rpL2 intron-Taq I, and trnT-L-Taq I) allowed the identification of all species involved. Reliable and accurate identification of diploid ancestors of durum and bread wheats using these candidate species-specific cpDNA markers will be useful for wheat breeding programs, in situ and ex situ conservation efforts, verification of seed purity in commercial seed stocks, and ensuring identity and integrity of accessions held within a collection does not change through unwanted gene flow or by genetic drift after regeneration by seed.

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Vogel, Jörg, Thomas Hübschmann, Thomas Börner, and Wolfgang R. Hess. "Splicing and intron-internal RNA editing of trnK-matK transcripts in barley plastids: support for MatK as an essential splice factor." Journal of Molecular Biology 270, no. 2 (July 1997): 179–87. http://dx.doi.org/10.1006/jmbi.1997.1115.

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Rohwer, Jens Gunter, PEDRO LUIS RODRIGUES DE MORAES, BARBARA RUDOLPH, and HENK VAN DER WERFF. "A phylogenetic analysis of the Cryptocarya group (Lauraceae), and relationships of Dahlgrenodendron, Sinopora, Triadodaphne, and Yasunia." Phytotaxa 158, no. 2 (February 3, 2014): 111. http://dx.doi.org/10.11646/phytotaxa.158.2.1.

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A phylogenetic analysis based on nuclear ITS and plastid trnK intron sequences confirms that Dahlgrenodendron, Sinopora, Triadodaphne, and Yasunia are members of the Cryptocarya group, as expected from morphology. Dahlgrenodendron from South Africa is sister to Aspidostemon from Madagascar. Triadodaphne inaequitepala is nested within Endiandra (both from Australasia), and Yasunia from South America is nested among South American Beilschmiedia species. Sinopora is a member of the Beilschmiedia clade, but its precise position is still uncertain. Among large genera of the group, Cryptocarya is clearly monophyletic, and Endiandra appears to be as well, if T. inaequitepala is included. Beilschmiedia is paraphyletic with respect to (at least) Potameia and Yasunia. Most well-supported clades within genera are geographically homogeneous, except a clade including the Chilean Cryptocarya alba and two New Caledonian species. Both Beilschmiedia and Cryptocarya have reached the Americas more than once. Four-locular anthers are plesiomorphic in the Cryptocarya group; two-locular anthers have arisen by fusion of the two pollen sacs of a theca. In the plesiomorphic fruit type, the ovary is completely enclosed in receptacular tissue; a superior fruit, seated free on its pedicel, is a synapomorphy of the Beilschmiedia clade.

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Zhu, Shu, Yanjing Bai, Mayuko Oya, Ken Tanaka, Katsuko Komatsu, Takuro Maruyama, Yukihiro Goda, Takeshi Kawasaki, Masao Fujita, and Toshiro Shibata. "Genetic and chemical diversity of Eleutherococcus senticosus and molecular identification of Siberian ginseng by PCR-RFLP analysis based on chloroplast trnK intron sequence." Food Chemistry 129, no. 4 (December 2011): 1844–50. http://dx.doi.org/10.1016/j.foodchem.2011.05.128.

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32

Choffat, Y., B. Suter, R. Behra, and E. Kubli. "Pseudouridine modification in the tRNA(Tyr) anticodon is dependent on the presence, but independent of the size and sequence, of the intron in eucaryotic tRNA(Tyr) genes." Molecular and Cellular Biology 8, no. 8 (August 1988): 3332–37. http://dx.doi.org/10.1128/mcb.8.8.3332.

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In Saccharomyces cerevisiae, pseudouridine formation in the middle position of the tRNA(Tyr) anticodon (psi 35) is dependent on the presence of the intron in the tRNA(Tyr) gene (Johnson and Abelson, Nature 302:681-687, 1983). Drosophila melanogaster tRNA(Tyr) genes contain introns of three size classes: 20 or 21 base pairs (bp) (six genes), 48 bp (one gene), and 113 bp (one gene). As in yeast, removal of the intron led to loss of psi 35 in the anticodon when transcription was assayed in Xenopus laevis oocytes. All Drosophila intron sizes supported psi 35 formation. The same results were obtained with the homologous X. laevis tRNA(Tyr) genes containing introns of 12 or 13 bp or with a deleted intron. The introns of yeast (Nishikura and DeRobertis, J. Mol. Biol. 145:405-420, 1981), D. melanogaster, and X. laevis tRNA(Tyr) wild-type genes, while they all supported psi 35 synthesis, did not share any consensus sequences. As discussed, these results, taken together, suggest that for appropriate function the psi 35 enzyme in the X. laevis oocyte needs the presence of an unqualified intron in the tRNA gene and a tRNA(Tyr)-like structure in the unprocessed tRNA precursor.

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Choffat, Y., B. Suter, R. Behra, and E. Kubli. "Pseudouridine modification in the tRNA(Tyr) anticodon is dependent on the presence, but independent of the size and sequence, of the intron in eucaryotic tRNA(Tyr) genes." Molecular and Cellular Biology 8, no. 8 (August 1988): 3332–37. http://dx.doi.org/10.1128/mcb.8.8.3332-3337.1988.

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In Saccharomyces cerevisiae, pseudouridine formation in the middle position of the tRNA(Tyr) anticodon (psi 35) is dependent on the presence of the intron in the tRNA(Tyr) gene (Johnson and Abelson, Nature 302:681-687, 1983). Drosophila melanogaster tRNA(Tyr) genes contain introns of three size classes: 20 or 21 base pairs (bp) (six genes), 48 bp (one gene), and 113 bp (one gene). As in yeast, removal of the intron led to loss of psi 35 in the anticodon when transcription was assayed in Xenopus laevis oocytes. All Drosophila intron sizes supported psi 35 formation. The same results were obtained with the homologous X. laevis tRNA(Tyr) genes containing introns of 12 or 13 bp or with a deleted intron. The introns of yeast (Nishikura and DeRobertis, J. Mol. Biol. 145:405-420, 1981), D. melanogaster, and X. laevis tRNA(Tyr) wild-type genes, while they all supported psi 35 synthesis, did not share any consensus sequences. As discussed, these results, taken together, suggest that for appropriate function the psi 35 enzyme in the X. laevis oocyte needs the presence of an unqualified intron in the tRNA gene and a tRNA(Tyr)-like structure in the unprocessed tRNA precursor.

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Dkhar, Jeremy, Suman Kumaria, and Pramod Tandon. "Molecular adaptation of the chloroplast matK gene in Nymphaea tetragona, a critically rare and endangered plant of India." Plant Genetic Resources 9, no. 2 (March 16, 2011): 193–96. http://dx.doi.org/10.1017/s1479262111000396.

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Sustainable utilization of plant genetic resources for food and agriculture has been increasingly discussed at both national and international forums. Besides exploitation, conservation of plant genetic resources has become an integral part of these discussions. Conservation aims at maintaining the diversity of living organisms, their habitat and the interrelationship between organisms and their environment. For achieving such goals, appropriate conservation strategies have to be adopted. Determining the genetic makeup of a particular plant species is of critical importance when planning a suitable conservation strategy. In this study, we sequenced the chloroplast trnK intron, matK and rbcL gene aimed at understanding the rarity of Nymphaea tetragona, a critically rare and endangered plant of India found at only one location. We extended our investigation to other Nymphaea species such as N. nouchali, N. pubescens and N. rubra that are commonly available throughout India. Interestingly, matK gene of N. tetragona revealed high number of non-synonymous substitutions. Molecular evolutionary analysis indicated that three of these sites may be under mild selective pressures. Such adaptive changes at the DNA and protein sequence level of matK gene may have been associated with the colonization of N. tetragona, suggesting that it could have migrated from China.

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Chemisquy, M. Amelia, and Osvaldo Morrone. "Phylogenetic analysis of the subtribe Chloraeinae (Orchidaceae): a preliminary approach based on three chloroplast markers." Australian Systematic Botany 23, no. 1 (2010): 38. http://dx.doi.org/10.1071/sb09026.

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The systematic position and relationships between some South American terrestrial orchids, such as Bipinnula Comm. ex Juss., Chloraea Lindl., Gavilea Poepp. and Geoblasta Barb. Rodr., is unclear. These four genera have been grouped in the subtribe Chloraeinae by several authors. Previous phylogenetic studies of the group have included only a few species of Chloraea and Gavilea and not of Bipinnula or Geoblasta. Relationships among these four genera were explored and the monophyly of the subtribe Chloraeinae and the genera Chloraea and Gavilea were tested in this contribution. Molecular phylogenetic analyses were conducted, using the following three chloroplast markers: the matK–trnK intron, the atpB–rbcL spacer and the rpoC1 gene. Sequences were analysed under maximum parsimony and Bayesian inference. In all the analyses, Bipinnula, Chloraea, Gavilea and Geoblasta were grouped in a clade with high support, where Bipinnula, Geoblasta and Gavilea were nested inside Chloraea. Consequently, Chloraea was paraphyletic, whereas Gavilea turned out to be monophyletic with high values of support. The other species of tribe Cranichideae appeared as sister groups of the Chloraeinae. A more exhaustive taxonomic sampling is needed to resolve the systematic placement of the subtribe Chloraeinae and the internal relationships between the genera and species that form it.

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Rudi, Knut, Tonje Fossheim, and Kjetill S. Jakobsen. "Nested Evolution of a tRNALeu(UAA) Group I Intron by both Horizontal Intron Transfer and Recombination of the Entire tRNA Locus." Journal of Bacteriology 184, no. 3 (February 1, 2002): 666–71. http://dx.doi.org/10.1128/jb.184.3.666-671.2002.

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ABSTRACT The origin and evolution of bacterial introns are still controversial issues. Here we present data on the distribution and evolution of a recently discovered divergent tRNALeu(UAA) intron. The intron shows a higher sequence affiliation with introns in tRNAIle(CAU) and tRNAArg(CCU) genes in α- and β-proteobacteria, respectively, than with other cyanobacterial tRNALeu(UAA) group I introns. The divergent tRNALeu(UAA) intron is sporadically distributed both within the Nostoc and the Microcystis radiations. The complete tRNA gene, including flanking regions and intron from Microcystis aeruginosa strain NIVA-CYA 57, was sequenced in order to elucidate the evolutionary pattern of this intron. Phylogenetic reconstruction gave statistical evidence for different phylogenies for the intron and exon sequences, supporting an evolutionary model involving horizontal intron transfer. The distribution of the tRNA gene, its flanking regions, and the introns were addressed by Southern hybridization and PCR amplification. The tRNA gene, including the flanking regions, were absent in the intronless stains but present in the intron-containing strains. This suggests that the sporadic distribution of this intron within the Microcystis genus cannot be attributed to intron mobility but rather to an instability of the entire tRNALeu(UAA) intron-containing genome region. Taken together, the complete data set for the evolution of this intron can best be explained by a model involving a nested evolution of the intron, i.e., wherein the intron has been transferred horizontally (probably through a single or a few events) to a tRNALeu(UAA) gene which is located within a unstable genome region.

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Sedláková, V., P. Sedlák, D. Zeka, J. Domkářová, P. Doležal, and P. Vejl. "Evaluation of variations in plastid DNA non-coding regions in selected species of the genus Solanum." Czech Journal of Genetics and Plant Breeding 53, No. 3 (September 13, 2017): 127–31. http://dx.doi.org/10.17221/76/2015-cjgpb.

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The diversity of three non-coding plastid DNA loci (trnL/trnF spacer, trnV/16SrRNA spacer, trnL/trnL intron) was assessed in 16 Solanum L. species (135 individuals). Polymorphisms were detected by denaturing gradient gel electrophoresis (DGGE) and verified by direct sequencing. No intraspecific diversity and only poor interspecific diversity was detected. Unique S. mochiquense Ochoa specific length polymorphism at the trnL/trnL locus represented by duplication of an 18 bp segment was discovered. The detected DGGE interspecific trnL/trnF locus polymorphism did not specifically associate with single point mutations in the sequence confirmed by sequencing. The DGGE method was found to be a simple and cheap pre-exploring tool for mutation detection in compared DNA regions. Some identified polymorphisms can be used in the management of genetic resources.

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Jiang, Zu Yao, Yan Ling Peng, Xiao Xiao Hu, Yong Feng Zhou, and Jian Quan Liu. "Cytoplasmic DNA variation in and genetic delimitation of Abies nephrolepis and Abies holophylla in northeastern China." Canadian Journal of Forest Research 41, no. 7 (July 2011): 1555–61. http://dx.doi.org/10.1139/x11-069.

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It has recently been hypothesized that genetic markers experiencing high rates of gene flow would be better suited to differentiate closely related species. We tested this hypothesis by examining genetic variation in the chloroplast (cp) DNA (trnS–trnG and trnL–trnF) and mitochondrial (mt) DNA (nad5 intron 4 and nad7 intron 1) of two fir species, Abies nephrolepis (Trautv.) Maxim. and Abies holophylla Maxim., with overlapping distributions in northeastern China. Two mitotypes were identified; one was common to both species, whereas the other occurred only in A. holophylla. However, four chlorotypes were identified, clustered into two species-specific groups exhibiting distinct mutations; species delimitation using these generated genetic variants was congruent with those obtained by morphological delimitation. Our findings supported the hypotheses that cpDNA, with its high rates of gene flow, is more useful than mtDNA for species delimitation in fir trees. In addition, the low intraspecific diversity observed for both species may result from their repeated range retractions and expansions in response to climatic oscillations in the history.

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Vinícius-Silva, Ronaldo, Lynn G. Clark, Jéferson Nunes Fregonezi, and Ana Paula Santos-Gonçalves. "Morphological evolution and molecular phylogenetics of the Merostachys clade (Poaceae: Bambusoideae: Bambuseae: Arthrostylidiinae) based on multi-locus plastid sequences." Botanical Journal of the Linnean Society 195, no. 1 (September 3, 2020): 53–76. http://dx.doi.org/10.1093/botlinnean/boaa057.

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Abstract Merostachys is a Neotropical woody bamboo genus that occurs in the understory and along forest borders. Our taxonomic studies of its species and morphological analyses have allowed us to recognize morphological groups in the genus. Previous molecular analyses, which included relatively few species, supported Merostachys as monophyletic and sister to Actinocladum or Athroostachys. We here provide a phylogenetic estimation for Merostachys based on a broader taxon sampling and seven plastid markers (one coding: ndhF 3′ end; four intergenic spacers: rps16-trnQ, trnC-rpoB, trnD-trnT and trnT-trnL; and two introns: rpl16 and rps16). We aimed to test the monophyly of the genus, to verify its relationship with other genera of Arthrostylidiinae, mainly Athroostachys and Actinocladum, and to test whether the previously identified morphological groups were congruent with the molecular data. The monophyly of the genus was confirmed, as was its sister relationship with Athroostachys, although alternate hypothesis testing could not reject a sister relationship with Actinocladum. Two well-supported clades in Merostachys were recovered, one of which encompasses a polytomy. These clades did not exhibit consistent morphological synapomorphies and were not congruent with the morphological groups; however, floret surface (shiny vs. dull) was correlated with the two clades. The lack of resolution in Merostachys, as exemplified by the polytomy, can be attributed mainly to incomplete lineage sorting, suggesting a recent radiation in this group.

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Kim, S. C., and N. S. Lee. "Generic delimitation and biogeography of Maianthemum and Smilacina (Ruscaceae sensu lato): preliminary results based on partial 3′ matK gene and trnK 3′ intron sequences of cpDNA." Plant Systematics and Evolution 265, no. 1-2 (April 11, 2007): 1–12. http://dx.doi.org/10.1007/s00606-007-0517-2.

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Murphy, Daniel J., Frank Udovicic, and Pauline Y. Ladiges. "Phylogenetic analysis of Australian Acacia (Leguminosae: Mimosoideae) by using sequence variations of an intron and two intergenic spacers of chloroplast DNA." Australian Systematic Botany 13, no. 5 (2000): 745. http://dx.doi.org/10.1071/sb99027.

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Three regions of chloroplast DNA are assessed for their utility for phylogenetic analysis of Acacia subgenus Phyllodineae: psbA–trnH intergenic spacer, the trnL intron and the trnL–trnF intergenic spacer. There are large differences in the lengths of the psbA–trnH spacer (155–440 bp) and trnL–trnF intergenic spacer (101–422 bp) regions, and large multi-residue indels were coded as multistate characters. Overall information content in these regions is relatively low, but the total evidence tree has 12 nodes resolved, five with jackknife support. By using Parkia timoriana as the outgroup, Acacia subgenus Acacia (A. farnesiana) is basal and Acacia subgenus Aculeiferum (A. senegal) is the sister taxon to subgenus Phyllodineae. Although based on a small sample size, within subgenus Phyllodineae, the results of this study have shown that section Alatae is not monophyletic, section Lycopodiifoliae is monophyletic and Botrycephalae is related to members of section Phyllodineae with racemose inflorescences.

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MAMONTOV, YURIY S., NADEZHDA A. KONSTANTINOVA, and ANNA A. VILNET. "One more species in the genus Jungermannia (Marchantiophyta: Jungermanniaceae)." Bryophyte Diversity and Evolution 40, no. 2 (December 27, 2018): 79. http://dx.doi.org/10.11646/bde.40.2.6.

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Jungermannia afoninae is described from the mountains of South Siberia based on a complex taxonomical approach exploring critical reinvestigation of morphological features and analyses of newly obtained trnL–trnF and trnG-intron cpDNA sequences from six Jungermannia specimens incorporated into a previously published dataset. Description and illustrations of the new species are provided with notes on its differentiation from allied species, ecology and distribution.

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KONSTANTINOVA, NADEZDA A. A., and ANNA A. VILNET. "A new species of the genus Jungermannia (Jungermanniales, Marchantiophyta) from the Caucasus with notes on taxa delimitation and taxonomy of Jungermannia s. str." Phytotaxa 255, no. 3 (April 11, 2016): 227. http://dx.doi.org/10.11646/phytotaxa.255.3.4.

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The new species Jungermannia calcicola Konstant. et Vilnet, is described based on a critical reinvestigation of morphological features and molecular analyses of trnL–trnF and trnG intron cpDNA sequences of forty samples of Jungermannia s. str. The new species is described and illustrated as well as noting its differentiation from allied species and distribution patterns. New data on some taxonomical ambiguities and on the taxa delimitation in the Jungermannia s. str. are discussed.

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ZHANG, WEI, JIAO QIN, RUI YANG, YI YANG, and SHI-BAO ZHANG. "Two new natural hybrids in the genus Pleione (Orchidaceae) from China." Phytotaxa 350, no. 3 (May 23, 2018): 247. http://dx.doi.org/10.11646/phytotaxa.350.3.4.

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Several species in the genus Pleione (Orchidaceae) have same or overlapping geographical distribution in China. In this study, two new natural hybrids, Pleione × baoshanensis and Pleione × maoershanensis, were described and illustrated. The parentage for these two hybrids was confirmed using molecular data from ITS of the nuclear ribosomal, trnT-trnL spacer and trnL-trnF region (trnL intron and trnL-trnF spacer) of the plastid DNA. Pleione × baoshanensis is intermediate between P. albiflora and P. yunnanensis, and characterized by its erose lamellae on the lip. Meanwhile, Pleione × maoershanensis is intermediate between P. hookeriana (P. chunii) and P. pleionoides, and characterized by its deep lacerate lamellae on the lip. For the individuals tested, molecular data suggest that P. albiflora is the maternal parent of Pleione × baoshanensis, and P. hookeriana (P. chunii) is the maternal parent of Pleione × maoershanensis. The history and taxonomic status of P. chunii is also discussed.

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Fishbein, Mark, Susan R. Kephart, Mike Wilder, Kate M. Halpin, and Shannon L. Datwyler. "Phylogeny of Camassia (Agavaceae) Inferred from Plastid rpl16 Intron and trnD–trnY–trnE–trnT Intergenic Spacer DNA Sequences: Implications for Species Delimitation." Systematic Botany 35, no. 1 (February 23, 2010): 77–85. http://dx.doi.org/10.1600/036364410790862588.

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Karwowska, U., and Z. Szweykowska-Kulińska. "New intron-containing human tRNA(Leu) genes." Acta Biochimica Polonica 44, no. 4 (December 31, 1997): 791–94. http://dx.doi.org/10.18388/abp.1997_4383.

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Three new human nuclear tRNA(Leu) genes have been isolated and sequenced using the PCR technique. Two of them represent genes containing a CAA anticodon and both contain introns of 22 nucleotides in length but differing in sequence. Intron-containing prolongated anticodon stems can be folded into a secondary structure similar to that of yeast pre-tRNA(Leu). The evolutionary conserved secondary structure suggests the same role of intron sequences in the human and yeast pre-tRNA(Leu) maturation pathway.

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Rudi, Knut, and Kjetill S. Jakobsen. "Complex Evolutionary Patterns of tRNAUAALeu Group I Introns in Cyanobacterial Radiation." Journal of Bacteriology 181, no. 11 (June 1, 1999): 3445–51. http://dx.doi.org/10.1128/jb.181.11.3445-3451.1999.

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ABSTRACT Based on the findings that plastids and cyanobacteria have similar group I introns inserted into tRNAUAA Leu genes, these introns have been suggested to be immobile and of ancient origin. In contrast, recent evidence suggests lateral transfer of cyanobacterial group I introns located in tRNAUAA Leu genes. In light of these new findings, we have readdressed the evolution and lateral transfer of tRNAUAA Leu group I introns in cyanobacteral radiation. We determined the presence of introns in 38 different strains, representing the major cyanobacterial lineages, and characterized the introns in 22 of the strains. Notably, two of these strains have two tRNAUAA Leu genes, with each of these genes interrupted by introns, while three of the strains have both interrupted and uninterrupted genes. Two evolutionary distinct clusters of tRNA genes, with the genes interrupted by introns belonging to two distinct intron clusters, were identified. We also compared 16S rDNA and intron evolution for both closely and distantly related strains. The distribution of the introns in the clustered groups, as defined from 16S rDNA analysis, indicates relatively recent gain and/or loss of the introns in some of these lineages. The comparative analysis also suggests differences in the phylogenetic trees for 16S rDNA and the tRNAUAA Leu group I introns. Taken together, our results show that the evolution of the intron is considerably more complex than previous studies found to be the case. We discuss, based on our results, evolutionary models involving lateral intron transfer and models involving differential loss of the intron.

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Schmidt, Casey A., Joseph D. Giusto, Alicia Bao, Anita K. Hopper, and A. Gregory Matera. "Molecular determinants of metazoan tricRNA biogenesis." Nucleic Acids Research 47, no. 12 (April 29, 2019): 6452–65. http://dx.doi.org/10.1093/nar/gkz311.

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Abstract Mature tRNAs are generated by multiple post-transcriptional processing steps, which can include intron removal. Recently, we discovered a new class of circular non-coding RNAs in metazoans, called tRNA intronic circular (tric)RNAs. To investigate the mechanism of tricRNA biogenesis, we generated constructs that replace native introns of human and fruit fly tRNA genes with the Broccoli fluorescent RNA aptamer. Using these reporters, we identified cis-acting elements required for tricRNA formation in vivo. Disrupting a conserved base pair in the anticodon-intron helix dramatically reduces tricRNA levels. Although the integrity of this base pair is necessary for proper splicing, it is not sufficient. In contrast, strengthening weak bases in the helix also interferes with splicing and tricRNA production. Furthermore, we identified trans-acting factors important for tricRNA biogenesis, including several known tRNA processing enzymes such as the RtcB ligase and components of the TSEN endonuclease complex. Depletion of these factors inhibits Drosophila tRNA intron circularization. Notably, RtcB is missing from fungal genomes and these organisms normally produce linear tRNA introns. Here, we show that in the presence of ectopic RtcB, yeast lacking the tRNA ligase Rlg1/Trl1 are converted into producing tricRNAs. In summary, our work characterizes the major players in eukaryotic tricRNA biogenesis.

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Kjems, Jørgen, Jonna Jensen, Tina Olesen, and Roger A. Garrett. "Comparison of transfer RNA and ribosomal RNA intron splicing in the extreme thermophile and archaebacterium Desulfurococcus mobilis." Canadian Journal of Microbiology 35, no. 1 (January 1, 1989): 210–14. http://dx.doi.org/10.1139/m89-033.

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The structure of the exon–intron boundary was compared for an intron within 23S ribosomal RNA of Desulfurococcus mobilis and a newly discovered intron in tRNAMet from the same organism. The occurrence of a putative common structural feature suggests that intron excision occurs by the same mechanism. The possible recognition of this structural feature by the cleavage enzyme was investigated for the ribosomal RNA intron using RNA substrates exhibiting various exon and intron deletions. The results support the involvement of the structural features in the cleavage process. The evolutionary implications of these results are considered.Key words: archaebacteria, tRNA, ribosomal RNA, introns, intron evolution.

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Li, Zhi-Zhong, Shuang Wu, Chun-Yu Zhou, Yan Liu, Guang-Wan Hu, Samuli Lehtonen, Qing-Feng Wang, and Jin-Ming Chen. "Ottelia fengshanensis, a new bisexual species of Ottelia (Hydrocharitaceae) from southwestern China." PhytoKeys 135 (October 30, 2019): 1–10. http://dx.doi.org/10.3897/phytokeys.135.38531.

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Abstract:

Ottelia fengshanensis, a new species (Hydrocharitaceae) from southwest China is here described and illustrated. Comparing its morphological features to putative close relatives O. guanyangensis, it has 3–4 flowers (vs. 2–5) each spathe, hexagonal-cylindric fruit, white styles (vs. yellow), green leaves (vs. dark green) and fruit tiny winged (vs. winged obviously). Molecular phylogenetic investigation of four DNA sequences (ITS, rbcL, trnK5’ intron and trnS-trnG) and the Poisson Tree Processes model for species delimitation (PTP) analysis, further resolves O. fengshanensis as a new species that is close to O. guanyangensis with distinct support.

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Journal articles on the topic 'TrnK intron'

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