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Journal articles on the topic 'Internal Transcribed Spacer 2'

Author: Grafiati

Published: 4 June 2021

Last updated: 4 February 2022

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1

Wang, Chuan Tang, Xiu Zhen Wang, Yue Yi Tang, Dian Xu Chen, Feng Gao Cui, Jian Cheng Zhang, and Shan Lin Yu. "Phylogeny of Arachis based on internal transcribed spacer sequences." Genetic Resources and Crop Evolution 58, no. 2 (June 9, 2010): 311–19. http://dx.doi.org/10.1007/s10722-010-9576-2.

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2

Voronov, A. S., D. V. Shibalev, A. P. Ryskov, and N. S. Kupriyanova. "Evolutionary divergence of ribosomal internal transcribed spacer 2 in lizards." Molecular Biology 40, no. 1 (January 2006): 37–42. http://dx.doi.org/10.1134/s0026893306010079.

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3

Ji, Lei, Chunju Liu, Li Zhang, Aixin Liu, and Jinfeng Yu. "Variation of rDNA Internal Transcribed Spacer Sequences in Rhizoctonia cerealis." Current Microbiology 74, no. 7 (May 5, 2017): 877–84. http://dx.doi.org/10.1007/s00284-017-1258-2.

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4

Choi, Du Bok, Ji Lu Ding, and Wol-Suk Cha. "Homology search of genus Pleurotus using an internal transcribed spacer region." Korean Journal of Chemical Engineering 24, no. 3 (May 2007): 408–12. http://dx.doi.org/10.1007/s11814-007-0070-2.

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5

Schmiderer, Corinna, Brigitte Lukas, Joana Ruzicka, and Johannes Novak. "What Else Is in Salviae officinalis folium? Comprehensive Species Identification of Plant Raw Material by DNA Metabarcoding." Planta Medica 84, no. 06/07 (November 17, 2017): 428–33. http://dx.doi.org/10.1055/s-0043-121470.

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AbstractQuality control of drugs consists of identifying the raw material to avoid unwanted admixtures or exchange of material as well as looking for abiotic and biotic contaminations. So far, identity and microbial contamination are analyzed by separate processes and separate methods. Species identification by their DNA (“DNA barcoding”) has the potential to supplement existing methods of identification. The introduction of next-generation sequencing methods offers completely new approaches like the identification of whole communities in one analysis, termed “DNA metabarcoding”. Here we present a next-generation sequencing assessment to identify plants and fungi of two commercial sage samples (Salvia officinalis) using the standard DNA barcoding region “internal transcribed spacer” consisting of internal transcribed spacer 1 and internal transcribed spacer 2, respectively. The main species in both samples was identified as S. officinalis. The spectrum of accompanying plant and fungal species, however, was completely different between the samples. Additionally, the composition between internal transcribed spacer 1 and internal transcribed spacer 2 within the samples was different and demonstrated the influence of primer selection and therefore the need for harmonization. This next-generation sequencing approach does not result in quantitative species composition but gives deeper insight into the composition of additional species. Therefore, it would allow for a better knowledge-based risk assessment than any other method available. However, the method is only economically feasible in routine analysis if a high sample throughput can be guaranteed.

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6

Henry, Travis, Peter C. Iwen, and Steven H. Hinrichs. "Identification of Aspergillus Species Using Internal Transcribed Spacer Regions 1 and 2." Journal of Clinical Microbiology 38, no. 4 (2000): 1510–15. http://dx.doi.org/10.1128/jcm.38.4.1510-1515.2000.

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Aspergillus species are the most frequent cause of invasive mold infections in immunocompromised patients. Although over 180 species are found within the genus, 3 species, Aspergillus flavus, A. fumigatus, and A. terreus, account for most cases of invasive aspergillosis (IA), with A. nidulans, A. niger, and A. ustus being rare causes of IA. The ability to distinguish between the various clinically relevant Aspergillus species may have diagnostic value, as certain species are associated with higher mortality and increased virulence and vary in their resistance to antifungal therapy. A method to identify Aspergillus at the species level and differentiate it from other true pathogenic and opportunistic molds was developed using the 18S and 28S rRNA genes for primer binding sites. The contiguous internal transcribed spacer (ITS) region, ITS 1–5.8S–ITS 2, from referenced strains and clinical isolates of aspergilli and other fungi were amplified, sequenced, and compared with non-reference strain sequences in GenBank. ITS amplicons fromAspergillus species ranged in size from 565 to 613 bp. Comparison of reference strains and GenBank sequences demonstrated that both ITS 1 and ITS 2 regions were needed for accurate identification ofAspergillus at the species level. Intraspecies variation among clinical isolates and reference strains was minimal. Sixteen other pathogenic molds demonstrated less than 89% similarity withAspergillus ITS 1 and 2 sequences. A blind study of 11 clinical isolates was performed, and each was correctly identified. Clinical application of this approach may allow for earlier diagnosis and selection of effective antifungal agents for patients with IA.

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7

Zhao, Li-Li, Shi-Jing Feng, Jie-Yun Tian, An-Zhi Wei, and Tu-Xi Yang. "Internal transcribed spacer 2 (ITS2) barcodes: A useful tool for identifying ChineseZanthoxylum." Applications in Plant Sciences 6, no. 6 (June 2018): e01157. http://dx.doi.org/10.1002/aps3.1157.

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8

van der Sande, Carine A. F. M., Marcel Kwa, Rob W. van Nues, Harm van Heerikhuizen, Hendrik A. Raué, and Rudi J. Planta. "Functional analysis of internal transcribed spacer 2 of Saccharomyces cerevisiae ribosomal DNA." Journal of Molecular Biology 223, no. 4 (February 1992): 899–910. http://dx.doi.org/10.1016/0022-2836(92)90251-e.

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9

Fan, Congzhao, Xiaojin Li, Jun Zhu, Jingyuan Song, and Hui Yao. "Endangered Uyghur Medicinal PlantFerulaIdentification through the Second Internal Transcribed Spacer." Evidence-Based Complementary and Alternative Medicine 2015 (2015): 1–6. http://dx.doi.org/10.1155/2015/479879.

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The medicinal plantFerulahas been widely used in Asian medicine, especially in Uyghur medicine in Xinjiang, China. Given that various substitutes and closely related species have similar morphological characteristics,Ferulais difficult to distinguish based on morphology alone, thereby causing confusion and threatening the safe use ofFerula. In this study, internal transcribed spacer 2 (ITS2) sequences were analyzed and assessed for the accurate identification of two salableFerulaspecies (Ferula sinkiangensisandFerula fukangensis) and eight substitutes or closely related species. Results showed that the sequence length of ITS2 ranged from 451 bp to 45 bp, whereas guanine and cytosine contents (GC) were from 53.6% to 56.2%. A total of 77 variation sites were detected, including 63 base mutations and 14 insertion/deletion mutations. The ITS2 sequence correctly identified 100% of the samples at the species level using the basic local alignment search tool 1 and nearest-distance method. Furthermore, neighbor-joining tree successfully identified the genuine plantsF. sinkiangensisandF. fukangensisfrom their succedaneum and closely related species. These results indicated that ITS2 sequence could be used as a valuable barcode to distinguish Uyghur medicineFerulafrom counterfeits and closely related species. This study may broaden DNA barcoding application in the Uyghur medicinal plant field.

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10

Inglis, Peter, Lorena Mata, Marcos da Silva, Roberto Vieira, Rosa de B. N. Alves, Dijalma Silva, and Vânia Azevedo. "DNA Barcoding for the Identification of Phyllanthus Taxa Used Medicinally in Brazil." Planta Medica 84, no. 17 (June 21, 2018): 1300–1310. http://dx.doi.org/10.1055/a-0644-2688.

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AbstractPlants of the genus Phyllanthus, principally Phyllanthus amarus, Phyllanthus urinaria, Phyllanthus niruri, and Phyllanthus tenellus, are used in Brazilian folk medicine to treat kidney stones as well as other ailments, where the latter two species are listed in the Brazilian Pharmacopeia as quebra-pedra (stone-breaker). However, only P. niruri has been shown to be effective in a clinical setting. Nuclear ribosomal internal transcribed spacer (ITS1 – 5.8S rRNA-ITS2), internal transcribed spacer 2, and chloroplasts rbcL, matK, psbA-trnH, trnL, and trnL-trnF were screened for their potential as DNA barcodes for the identification of 48 Phyllanthus taxa in Brazilian medicinal plant germplasm banks and in “living pharmacies”. The markers were also tested for their ability to validate four commercial herbal teas labelled as quebra-pedra. Using the criterion of high clade posterior probability in Bayesian phylogenetic analysis, the internal transcribed spacer, internal transcribed spacer 2, and chloroplast matK, psbA-trnH, trnL, and trnL-trnF markers all reliably differentiated the four Phyllanthus species, with the internal transcribed spacer and matK possessing the additional advantage that the genus is well represented for these markers in the Genbank database. However, in the case of rbcL, posterior probability for some clades was low and while P. amarus and P. tenellus formed monophyletic groups, P. niruri and P. urinaria accessions could not be reliably distinguished with this marker. Packaged dried quebra-pedra herb from three Brazilian commercial suppliers comprised P. tenellus, but one sample was also found to be mixed with alfalfa (Medicago sativa). An herb marketed as quebra-pedra from a fourth supplier was found to be composed of a mixture of Desmodium barbatum and P. niruri.

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11

GokulRaj, Kathamuthu, Natesan Sundaresan, Enthai Jagan Ganeshan, Pandi Rajapriya, Johnpaul Muthumary, Jayavel Sridhar, and Mohan Pandi. "Phylogenetic reconstruction of endophytic fungal isolates using internal transcribed spacer 2 (ITS2) region." Bioinformation 10, no. 6 (June 30, 2014): 320–28. http://dx.doi.org/10.6026/97320630010320.

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12

Koetschan, Christian, Thomas Hackl, Tobias Müller, Matthias Wolf, Frank Förster, and Jörg Schultz. "ITS2 Database IV: Interactive taxon sampling for internal transcribed spacer 2 based phylogenies." Molecular Phylogenetics and Evolution 63, no. 3 (June 2012): 585–88. http://dx.doi.org/10.1016/j.ympev.2012.01.026.

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13

Markert, S. M., T. Müller, C. Koetschan, T. Friedl, and M. Wolf. "‘Y’Scenedesmus(Chlorophyta, Chlorophyceae): the internal transcribed spacer 2 rRNA secondary structure re-revisited." Plant Biology 14, no. 6 (May 28, 2012): 987–96. http://dx.doi.org/10.1111/j.1438-8677.2012.00576.x.

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14

Rich, S. M., B. M. Rosenthal, S. R. Telford, A. Spielman, D. L. Harti, and F. J. Ayala. "Heterogeneity of the internal transcribed spacer (ITS-2) region within individual deer ticks." Insect Molecular Biology 6, no. 2 (May 1997): 123–29. http://dx.doi.org/10.1111/j.1365-2583.1997.tb00080.x.

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15

Bezzhonova, O. V., and I. I. Goryacheva. "Intragenomic Heterogeneity of rDNA Internal Transcribed Spacer 2 in Anopheles messeae (Diptera: Culicidae)." Journal of Medical Entomology 45, no. 3 (May 1, 2008): 337–41. http://dx.doi.org/10.1093/jmedent/45.3.337.

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16

De Baere, Thierry, Richard Summerbell, Bart Theelen, Teun Boekhout, and Mario Vaneechoutte. "Evaluation of internal transcribed spacer 2-RFLP analysis for the identification of dermatophytes." Journal of Medical Microbiology 59, no. 1 (January 1, 2010): 48–54. http://dx.doi.org/10.1099/jmm.0.013870-0.

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A total of 95 isolates, belonging to 33 species of five dermatophyte genera, i.e. Arthroderma (15 species), Chrysosporium (two), Epidermophyton (one), Microsporum (three) and Trichophyton (12), were studied using internal transcribed spacer 2 (ITS2)-PCR-RFLP analysis (ITS2-RFLP), consisting of amplification of the ITS2 region, restriction digestion with BstUI (CG/CG) and restriction fragment length determination by capillary electrophoresis. ITS2-RFLP analysis proved to be most useful for identification of species of the genera Arthroderma, Chrysosporium and Epidermophyton, but could not distinguish between several Trichophyton species. The identification results are in agreement with established and recent taxonomical insights into the dermatophytes; for example, highly related species also had closely related and sometimes difficult-to-discriminate ITS2-RFLP patterns. In some cases, several ITS2-RFLP groups could be distinguished within species, again mostly in agreement with the taxonomic delineations of subspecies and/or genomovars, confirming the relevance of ITS2-RFLP analysis as an identification technique and as a useful taxonomic approach.

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17

Xin, Tianyi, Hui Yao, Huanhuan Gao, Xinzhu Zhou, Xiaochong Ma, Changqing Xu, Jun Chen, et al. "Super food Lycium barbarum (Solanaceae) traceability via an internal transcribed spacer 2 barcode." Food Research International 54, no. 2 (December 2013): 1699–704. http://dx.doi.org/10.1016/j.foodres.2013.10.007.

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18

Kupriyanova, Natalia, Dmitrii Shibalev, Alexander Voronov, Kirill Netchvolodov, Tatiana Kurako, and Alexei Ryskov. "Vertebrate evolution reflected in the evolution of nuclear ribosomal internal transcribed spacer 2." Gene 508, no. 1 (October 2012): 85–91. http://dx.doi.org/10.1016/j.gene.2012.07.024.

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19

Prahl, Rosa E., Shahjahan Khan, and Ravinesh C. Deo. "The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces." PLOS ONE 16, no. 6 (June 30, 2021): e0253772. http://dx.doi.org/10.1371/journal.pone.0253772.

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Many fungi require specific growth conditions before they can be identified. Direct environmental DNA sequencing is advantageous, although for some taxa, specific primers need to be used for successful amplification of molecular markers. The internal transcribed spacer region is the preferred DNA barcode for fungi. However, inter- and intra-specific distances in ITS sequences highly vary among some fungal groups; consequently, it is not a solely reliable tool for species delineation. Ampelomyces, mycoparasites of the fungal phytopathogen order Erysiphales, can have ITS genetic differences up to 15%; this may lead to misidentification with other closely related unknown fungi. Indeed, Ampelomyces were initially misidentified as other pycnidial mycoparasites, but subsequent research showed that they differ in pycnidia morphology and culture characteristics. We investigated whether the ITS2 nucleotide content and secondary structure was different between Ampelomyces ITS2 sequences and those unrelated to this genus. To this end, we retrieved all ITS sequences referred to as Ampelomyces from the GenBank database. This analysis revealed that fungal ITS environmental DNA sequences are still being deposited in the database under the name Ampelomyces, but they do not belong to this genus. We also detected variations in the conserved hybridization model of the ITS2 proximal 5.8S and 28S stem from two Ampelomyces strains. Moreover, we suggested for the first time that pseudogenes form in the ITS region of this mycoparasite. A phylogenetic analysis based on ITS2 sequences-structures grouped the environmental sequences of putative Ampelomyces into a different clade from the Ampelomyces-containing clades. Indeed, when conducting ITS2 analysis, resolution of genetic distances between Ampelomyces and those putative Ampelomyces improved. Each clade represented a distinct consensus ITS2 S2, which suggested that different pre-ribosomal RNA (pre-rRNA) processes occur across different lineages. This study recommends the use of ITS2 S2s as an important tool to analyse environmental sequencing and unveiling the underlying evolutionary processes.

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20

Rohimah, S., T. Ratnasari, and M. Su’udi. "DNA barcoding of Thrixspermum longipilosum based on Internal Transcribed Spacer 2 (ITS2) region." IOP Conference Series: Earth and Environmental Science 743, no. 1 (May 1, 2021): 012092. http://dx.doi.org/10.1088/1755-1315/743/1/012092.

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21

Fukunaga, Masahito, Mihe Yabuki, Akiko Hamase, James H. Oliver, Jr., and Minoru Nakao. "MOLECULAR PHYLOGENETIC ANALYSIS OF IXODID TICKS BASED ON THE RIBOSOMAL DNA SPACER, INTERNAL TRANSCRIBED SPACER 2, SEQUENCES." Journal of Parasitology 86, no. 1 (February 2000): 38–43. http://dx.doi.org/10.1645/0022-3395(2000)086[0038:mpaoit]2.0.co;2.

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22

Fukunaga, Masahito, Mihe Yabuki, Akiko Hamase, James H. Oliver, and Minoru Nakao. "Molecular Phylogenetic Analysis of Ixodid Ticks Based on the Ribosomal DNA Spacer, Internal Transcribed Spacer 2, Sequences." Journal of Parasitology 86, no. 1 (February 2000): 38. http://dx.doi.org/10.2307/3284905.

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23

Hinrikson, H. P., S. F. Hurst, T. J. Lott, D. W. Warnock, and C. J. Morrison. "Assessment of Ribosomal Large-Subunit D1-D2, Internal Transcribed Spacer 1, and Internal Transcribed Spacer 2 Regions as Targets for Molecular Identification of Medically Important Aspergillus Species." Journal of Clinical Microbiology 43, no. 5 (May 1, 2005): 2092–103. http://dx.doi.org/10.1128/jcm.43.5.2092-2103.2005.

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24

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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Chaudhry, Asha, Satvinderjeet Kaur, Preety Bhinder, and Bhupinder Barna. "Imidacloprid and thiamethoxam induced mutations in internal transcribed spacer 2 (ITS2) of Anopheles stephensi." Toxicology International 19, no. 2 (2012): 201. http://dx.doi.org/10.4103/0971-6580.97223.

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26

Hung, Yu-Tang, Chaolun Allen Chen, Wen-Jer Wu, Chung-Chi Lin, and Cheng-Jen Shih. "Phylogenetic utility of the ribosomal internal transcribed spacer 2 in Strumigenys spp. (Hymenoptera: Formicidae)." Molecular Phylogenetics and Evolution 32, no. 1 (July 2004): 407–15. http://dx.doi.org/10.1016/j.ympev.2004.03.010.

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27

WOLF, M. "Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures." RNA 11, no. 11 (November 1, 2005): 1616–23. http://dx.doi.org/10.1261/rna.2144205.

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28

Wolf, Matthias, and Mark A. Buchheim. "The internal transcribed spacer 2 of Jenufa (Chlorophyta, Chlorophyceae) is extraordinarily long: A hypothesis." Gene 678 (December 2018): 100–104. http://dx.doi.org/10.1016/j.gene.2018.08.019.

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29

JIANG, XIAO-DIE, FANG-RU NAN, JUN-PING LV, QI LIU, SHU-LIAN XIE, JOHN PATRICK KOCIOLEK, and JIA FENG. "Dinobryon taiyuanensis (Chrysophyta, Dinobryaceae), a new freshwater species described from Shanxi province, China." Phytotaxa 404, no. 1 (May 16, 2019): 41. http://dx.doi.org/10.11646/phytotaxa.404.1.4.

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A new freshwater species of Chrysophyceae, Dinobryon taiyuanensis, is described from Linde Lake in Shanxi province, China. This new species is similar to D. sertularia, the type species of the genus, in the shape of the lorica and organization of the colony. The cells have two heterokont flagella surrounded by a lorica and occurred both as free-living, solitary cells or in branched colonies. The lorica of our new species like a bent or S-shaped cone, and shorter than the lorica in D. sertularia. In addition to describing the morphological features of D. taiyuanensis, a phylogenetic analysis based on sequences of the nuclear small subunit ribosomal DNA (SSU rDNA) and internal transcribed spacer (including internal transcribed spacer 1, 5.8S rDNA and internal transcribed spacer 2) placed this alga in single clade with a considerable sequence distance from the other Dinobryon species. Thus, results of both morphological comparisons and phylogenetic analysis based on molecular data suggest this alga as a new species, increasing the total number of recognized freshwater Chrysophyta species in China.

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30

Zeng, J., L. Zhang, X. Fan, H. Q. Zhang, R. W. Yang, and Y. H. Zhou. "Phylogenetic analysis of Kengyilia species based on nuclear ribosomal DNA internal transcribed spacer sequences." Biologia plantarum 52, no. 2 (June 1, 2008): 231–36. http://dx.doi.org/10.1007/s10535-008-0051-2.

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31

Rungpragayphan, Suang, Perayot Pamonsinlapatham, Busaba Powthongchin, Wikanda Prommanee, and Piyaporn Wongakson. "Exploring DNA Barcode Information of Selected Thai Medicinal Plants." Advanced Materials Research 1060 (December 2014): 219–22. http://dx.doi.org/10.4028/www.scientific.net/amr.1060.219.

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DNA barcode is referred to specific ranges, sequences or fragments of DNA used for identification organisms at genus or species levels. There are several plant DNA barcodes which are currently studied, such as ITS (Internal Transcribed Spacer), ITS2 (Internal Transcribed Spacer 2), matK, psbA-trnH, rbcL, trnL-trnF. In this work, ITS, ITS2 and psbA-trnH sequences of many medicinal plants in the “Thai Medicinal Plant DNA Barcode Database” were studied. Total of 163 DNA barcodes from 75 plant families were processed and analysed. ATCG contents, %GC or %CG found, ATG patterns, and alignment patterns were investigated. Also, sequences relationships among families were discussed. This information will be useful for authentication and quality control of herbal medicine.

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Soltanbeiglu, Shadiyeh, Mozaffar Vahedi, Mulood Mohammadi-Bavani, and Ali Reza Chavshin. "Molecular Characterisation of Cytochrome Oxidase I and Internal Transcribed Spacer 2 Fragments of Culiseta longiareolata." Turkish Journal of Parasitology 44, no. 4 (December 2, 2020): 191–96. http://dx.doi.org/10.4274/tpd.galenos.2020.6886.

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33

Silva, William M., and Takako Matsumura-Tundisi. "DNA extraction and ITS2 (internal transcribed spacer 2) gene sequences of some Brazilian freshwater copepods." SIL Proceedings, 1922-2010 29, no. 1 (March 2005): 409–13. http://dx.doi.org/10.1080/03680770.2005.11902044.

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Chao, Li-Lian, Wen-Jer Wu, and Chien-Ming Shih. "Species identification of Ixodes granulatus (Acari: Ixodidae) based on internal transcribed spacer 2 (ITS2) sequences." Experimental and Applied Acarology 54, no. 1 (December 12, 2010): 51–63. http://dx.doi.org/10.1007/s10493-010-9419-z.

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Bezzhonova, O. V., and I. I. Goryacheva. "Intragenomic Heterogeneity of rDNA Internal Transcribed Spacer 2 in Anopheles messeae (Diptera: Culicidae)." Journal of Medical Entomology 45, no. 3 (May 1, 2008): 337–41. http://dx.doi.org/10.1603/0022-2585(2008)45[337:ihorit]2.0.co;2.

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Mahmud, Md Muket, Jayedul Hassan, and KHM Nazmul Hussain Nazir. "Internal transcribed spacer based identification of Aspergillus fumigatus isolated from poultry feed samples." Research in Agriculture Livestock and Fisheries 4, no. 3 (December 29, 2017): 165–71. http://dx.doi.org/10.3329/ralf.v4i3.35093.

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Among over 180 Aspergilli, Aspergillus fumigatus is the most common etiological agent causing invasive mold infection mostly in immunocompromised human and animal. Besides, the fungus is used for various useful purposes. However, for the utilization of A. fumigatus as a useful candidate, accurate identification is crucial. Here, the research work was aimed at identifying A. fumigatus from poultry feed samples using conventional and molecular techniques. Out of 23 feed samples, 2 (8.7%) were found to be positive for A. fumigatus. The internal transcribed spacer 1 (ITS 1) and ITS 2 regions and the 5.8S ribosomal DNA (rDNA) region of the fungus were amplified by polymerase chain reaction. The ITS regions are located between the 18S and 28S rRNA genes, and rRNA gene for 5.8S RNA separates these two ITS regions. The isolated gene has been sequenced and deposited in the GenBank (accession no. KC142152). The gene was 100% similar to other reference species of A. fumigatus, whereas in phylogenetic analysis, a clear distance was found in the cases of other Aspergilli. Based on the unique nature of the ITS1 and ITS2 regions and phylogenetic analysis of the genes, A. fumigatus was correctly identified. The isolated strain could be a good candidate for further studies especially for utilization in the field of biotechnology.Res. Agric. Livest. Fish.4(3): 165-171, December 2017

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LI, GUO-QING, XIAO-FENG XUE, KAI-JUN ZHANG, and XIAO-YUE HONG. "Identification and molecular phylogeny of agriculturally important spider mites (Acari: Tetranychidae) based on mitochondrial and nuclear ribosomal DNA sequences, with an emphasis on Tetranychus." Zootaxa 2647, no. 1 (October 15, 2010): 1. http://dx.doi.org/10.11646/zootaxa.2647.1.1.

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Tetranychid mites are serious agricultural pests. Identification of species in the Tetranychidae is hampered by their close morphological similarities, especially for species within the genus Tetranychus. In this study, we examined the relationships of nine agriculturally important species in the Tetranychidae from China based on mitochondrial (cytochrome c oxidase subunit 1) and nuclear (internal transcribed spacer 1 and 2 of ribosomal RNA gene) sequences. The results confirm the monophyly of the morphologically defined Tetranychus, Panonychus, Amphitetranychus and Petrobia. However the position of Amphitetranychus viennensis within the Tetranychidae needs to be confirmed. The genetic distances between Tetranychus truncatus, T. turkestani and T. urticae that their taxonomy needs revision. In particular, both cytochrome oxidase 1 and the internal transcribed spacers 1 and 2 of rDNA sequences showed large geographical differences within T. cinnabarinus, suggesting the existence of cryptic species within this species.

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Kim, Ok Tae, Kyong Hwan Bang, Dong Su In, Jei Wan Lee, Young Chang Kim, Yoo Soo Shin, Dong Yun Hyun, Sung Sik Lee, Seon Woo Cha, and Nak Sul Seong. "Molecular authentication of ginseng cultivars by comparison of internal transcribed spacer and 5.8S rDNA sequences." Plant Biotechnology Reports 1, no. 3 (July 12, 2007): 163–67. http://dx.doi.org/10.1007/s11816-007-0019-2.

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Lieckfeldt, Elke, Gary J. Samuels, Thomas Börner, and Walter Gams. "Trichoderma koningii: neotypification and Hypocrea teleomorph." Canadian Journal of Botany 76, no. 9 (September 1, 1998): 1507–22. http://dx.doi.org/10.1139/b98-090.

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A neotype is selected for Trichoderma koningii. The species is characterized by morphological and molecular characters, the latter including polymerase chain reaction (PCR) fingerprinting and restriction fragment length polymorphism (RFLP) analysis and direct sequencing of the variable regions of the rDNA (internal transcribed spacer 1 (ITS-1) and internal transcribed spacer (ITS-2)). The neotype was selected from among four cultures obtained from soil at the type locality. These cultures were compared with a broader collection of Trichoderma strains and anamorphs of Hypocrea that morphologically conform to T. koningii. Comparison was also made with members of Trichoderma sect. Trichoderma and of the Hypocrea schweinitzii complex (Trichoderma sect. Longibrachiatum). According to its ITS sequences, T. koningii is a member of sect. Trichoderma, showing very low variability in comparison with Trichoderma viride and Trichoderma atroviride. We found five additional strains from various geographical regions that are identical to the neotype in morphology and in their sequences. One of them is Hypocrea koningii sp.nov., which we consider to be the teleomorph of T. koningii. PCR fingerprint patterns demonstrate the high genetic similarity of these nine strains. There was only low similarity in molecular characters between T. koningii and the H. schweinitzii complex despite morphological similarities.Key words: Hypocreales, Hypocrea muroiana, Hypocrea rufa, internal transcribed spacer, systematics.

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Shrestha, Sangita, Stephen W. Adkins, Glenn C. Graham, and Donald S. Loch. "Phylogeny of the Sporobolus indicus complex, based on internal transcribed spacer (ITS) sequences." Australian Systematic Botany 16, no. 2 (2003): 165. http://dx.doi.org/10.1071/sb02009.

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The entire internal transcribed spacer (ITS) region, including the 5.8S subunit of the nuclear ribosomal DNA (rDNA), was sequenced by direct double-stranded sequencing of polymerase chain reaction (PCR) amplified fragments. The study included 40 Sporobolus (Family Poaceae, subfamily Chloridoideae) seed collections from 14 putative species (all 11 species from the S. indicus complex and three Australian native species). These sequences, along with those from two out-group species [Pennisetum alopecuroides (L.) Spreng. and Heteropogon contortus (L.) P. Beauv. ex Roemer & Schultes, Poaceae, subfamily Panicoideae], were analysed by the parsimony method (PAUP; version 4.0b4a) to infer phylogenetic relationships among these species. The length of the ITS1, 5.8S subunit and ITS2 region were 222, 164 and 218 base pairs (bp), respectively, in all species of the S. indicus complex, except for the ITS2 region of S. diandrus P.Beauv. individuals, which was 217 bp long. Of the 624 characters included in the analysis, 245 (39.3%) of the 330 variable sites contained potential phylogenetic information. Differences in sequences among the members of the S. pyramidalis P.Beauv., S. natalensis (Steud.) Dur & Schinz and S. jacquemontii Kunth. collections were 0%, while differences ranged from 0 to 2% between these and other species of the complex. Similarly, differences in sequences among collections of S. laxus B.K.Simon, S. sessilis B.K.Simon, S. elongatus R.Br. and S. creber De Nardi were 0%, compared with differences of 1–2% between these four species and the rest of the complex. When comparing S. fertilis (Steud.) Clayton and S. africanus (Poir.) Robyns & Tourney, differences between collections ranged from 0 to 1%. Parsimony analysis grouped all 11 species of the S.�indicus complex together, indicating a monophyletic origin. For the entire data set, pair-wise distances among members of the S. indicus complex varied from 0.00 to 1.58%, compared with a range of 20.08–21.44% among species in the complex and the Australian native species studied. A strict consensus phylogenetic tree separated 11 species of the S. indicus complex into five major clades. The phylogeny, based on ITS sequences, was found to be congruent with an earlier study on the taxonomic relationship of the weedy Sporobolus grasses revealed from random amplified polymorphic DNA (RAPD). However, this cladistic analysis of the complex was not in agreement with that created on past morphological analyses and therefore gives a new insight into the phylogeny of the S.�indicus complex.

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Margutti, P., E. Visconti, P. Mencarini, M. Zolfo, S. Marinaci, E. Tamburrini, A. Siracusano, and E. Ortona. "Typing with internal transcribed spacer regions of Pneumocystis carinii from AIDS patients with recurrent pneumonia." Research in Microbiology 149, no. 8 (September 1998): 595–99. http://dx.doi.org/10.1016/s0923-2508(99)80007-2.

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Güiris-Andrade, D. M., A. Oceguera-Figueroa, D. Osorio-Sarabia, M. E. Pérez-Escobar, M. G. Nieto-López, N. M. Rojas-Hernández, and L. García-Prieto. "Tziminema unachin. gen., n. sp. (Nematoda: Strongylidae: Strongylinae) parasite of Baird's tapirTapirus bairdiifrom Mexico." Journal of Helminthology 92, no. 6 (November 20, 2017): 752–59. http://dx.doi.org/10.1017/s0022149x17001055.

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AbstractA new genus and species of nematode,Tziminema unachin. gen., n. sp. is described from the caecum and colon of Baird's tapirTapirus bairdii(Gill, 1865), found dead in the Reserva de la Biósfera El Triunfo, Chiapas State, in the Neotropical realm of Mexico.Tzimineman. gen. differs from the other nine genera included in the Strongylinae by two main characteristics: having 7–9 posteriorly directed tooth-like structures at the anterior end of the buccal capsule, and the external surface of the buccal capsule being heavily striated. Phylogenetic analyses of the DNA sequences of the mitochondrial cytochromecoxidase and nuclear DNA, including a partial sequence of the internal transcribed spacer 1, 5.8S and a partial sequence of the internal transcribed spacer 2 of the new taxon, confirmed its inclusion in Strongylinae and its rank as a new genus.

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Guo, Xiaofan, and Shouming Wang. "Phylogenetic study of Inonotus obliquus (Chaga) based on internal transcribed spacer 2 (ITS2) of ribosomal DNA." European Journal of Horticultural Science 85, no. 6 (December 21, 2020): 387–93. http://dx.doi.org/10.17660/ejhs.2020/85.6.2.

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SCHULTZ, J. "A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota." RNA 11, no. 4 (April 1, 2005): 361–64. http://dx.doi.org/10.1261/rna.7204505.

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Summerbell, R. C., R. A. Haugland, A. Li, and A. K. Gupta. "rRNA Gene Internal Transcribed Spacer 1 and 2 Sequences of Asexual, Anthropophilic Dermatophytes Related toTrichophyton rubrum." Journal of Clinical Microbiology 37, no. 12 (1999): 4005–11. http://dx.doi.org/10.1128/jcm.37.12.4005-4011.1999.

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The ribosomal region spanning the two internal transcribed spacer (ITS) regions and the 5.8S ribosomal DNA region was sequenced for asexual, anthropophilic dermatophyte species with morphological similarity to Trichophyton rubrum, as well as for members of the three previously delineated, related major clades in theT. mentagrophytes complex. Representative isolates ofT. raubitschekii, T. fischeri, and T. kanei were found to have ITS sequences identical to that ofT. rubrum. The ITS sequences of T. soudanenseand T. megninii differed from that of T. rubrumby only a small number of base pairs. Their continued status as species, however, appears to meet criteria outlined in the population genetics-based cohesion species concept of A. R. Templeton. The ITS sequence of T. tonsurans differed from that of the biologically distinct T. equinum by only 1 bp, while the ITS sequence of the recently described species T. krajdeniihad a sequence identical to that of T. mentagrophytesisolates related to the teleomorph Arthroderma vanbreuseghemii.

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Schultz, J., T. Muller, M. Achtziger, P. N. Seibel, T. Dandekar, and M. Wolf. "The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses." Nucleic Acids Research 34, Web Server (July 1, 2006): W704—W707. http://dx.doi.org/10.1093/nar/gkl129.

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Mai, Jeffrey C., and Annette W. Coleman. "The Internal Transcribed Spacer 2 Exhibits a Common Secondary Structure in Green Algae and Flowering Plants." Journal of Molecular Evolution 44, no. 3 (March 1997): 258–71. http://dx.doi.org/10.1007/pl00006143.

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Song, Zhong-kui, Xun-zhang Wang, and Ge-qiu Liang. "Molecular Evolution and Phylogenetic Utility of the Internal Transcribed Spacer 2 (ITS2) in Calyptratae (Diptera: Brachycera)." Journal of Molecular Evolution 67, no. 5 (October 11, 2008): 448–64. http://dx.doi.org/10.1007/s00239-008-9144-y.

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Lott, Timothy J., Brian M. Burns, Rosely Zancope-Oliveira, Cheryl M. Elie, and Errol Reiss. "Sequence Analysis of the Internal Transcribed Spacer 2 (ITS2) from Yeast Species Within the Genus Candida." Current Microbiology 36, no. 2 (February 1, 1998): 63–69. http://dx.doi.org/10.1007/s002849900280.

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50

Yeh, Lee-Chuan C., and John C. Lee. "Structural analysis of the internal transcribed spacer 2 of the precursor ribosomal RNA from Saccharomyces cerevisiae." Journal of Molecular Biology 211, no. 4 (February 1990): 699–712. http://dx.doi.org/10.1016/0022-2836(90)90071-s.

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