Extensive pyrosequencing reveals frequent intra-genomic variations of internal transcribed spacer regions of nuclear ribosomal DNA

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dc.contributor.authorSong, J.
dc.contributor.authorShi, L.
dc.contributor.authorLi, D.
dc.contributor.authorSun, Y.
dc.contributor.authorNiu, Y.
dc.contributor.authorChen, Z.
dc.contributor.authorLuo, H.
dc.contributor.authorPang, X.
dc.contributor.authorSun, Z.
dc.contributor.authorLiu, C.
dc.contributor.authorLv, A.
dc.contributor.authorDeng, Y.
dc.contributor.authorLarson-Rabin, Z.
dc.contributor.authorWilkinson, M.
dc.contributor.authorChen, S.
dc.contributor.editorVendramin, G.G.
dc.date.issued2012
dc.description.abstractBACKGROUND: Internal transcribed spacer of nuclear ribosomal DNA (nrDNA) is already one of the most popular phylogenetic and DNA barcoding markers. However, the existence of its multiple copies has complicated such usage and a detailed characterization of intra-genomic variations is critical to address such concerns. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we used sequence-tagged pyrosequencing and genome-wide analyses to characterize intra-genomic variations of internal transcribed spacer 2 (ITS2)regions from 178 plant species. We discovered that mutation of ITS2 is frequent, with a mean of 35 variants per species. And on average, three of the most abundant variants make up 91% of all ITS2 copies. Moreover, we found different congeneric species share identical variants in 13 genera. Interestingly, different species across different genera also share identical variants. In particular, one minor variant of ITS2 in Eleutherococcus giraldii was found identical to the ITS2 major variant of Panax ginseng, both from Araliaceae family. In addition, DNA barcoding gap analysis showed that the intra-genomic distances were markedly smaller than those of the intra-specific or inter-specific variants. When each of 5543 variants were examined for its species discrimination efficiency, a 97% success rate was obtained at the species level. CONCLUSIONS: Identification of identical ITS2 variants across intra-generic or inter-generic species revealed complex species evolutionary history, possibly, horizontal gene transfer and ancestral hybridization. Although intra-genomic multiple variants are frequently found within each genome, the usage of the major variants alone is sufficient for phylogeny construction and species determination in most cases. Furthermore, the inclusion of minor variants further improves the resolution of species identification.
dc.description.statementofresponsibilityJingyuan Song, Linchun Shi, Dezhu Li, Yongzhen Sun, Yunyun Niu, Zhiduan Chen, Hongmei Luo, Xiaohui Pang, Zhiying Sun, Chang Liu, Aiping Lv, Youping Deng, Zachary Larson-Rabin, Mike Wilkinson and Shilin Chen
dc.identifier.citationPLoS One, 2012; 7(8):1-12
dc.identifier.doi10.1371/journal.pone.0043971
dc.identifier.issn1932-6203
dc.identifier.issn1932-6203
dc.identifier.urihttp://hdl.handle.net/2440/73792
dc.language.isoen
dc.publisherPublic Library of Science
dc.rights© 2012 Song et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.source.urihttps://doi.org/10.1371/journal.pone.0043971
dc.subjectCell Nucleus
dc.subjectPlants
dc.subjectDNA, Ribosomal Spacer
dc.subjectReproducibility of Results
dc.subjectSequence Analysis, DNA
dc.subjectEvolution, Molecular
dc.subjectGenome, Plant
dc.subjectGenetic Variation
dc.subjectDNA Barcoding, Taxonomic
dc.titleExtensive pyrosequencing reveals frequent intra-genomic variations of internal transcribed spacer regions of nuclear ribosomal DNA
dc.typeJournal article
pubs.publication-statusPublished

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