1. Главная
  2. Ресурсы
  3. Библиотечный поиск
ExtensivePyrosequencingReveals FrequentIntra-GenomicVariations ofInternal TranscribedSpacer Regions ofNuclear Ribosomal DNA Jingyuan SongLinchun ShiLi D2012 год

Extensive Pyrosequencing Reveals Frequent Intra-Genomic Variations of Internal Transcribed Spacer Regions of Nuclear Ribosomal DNA
статья из журнала

Полный текстСтраница публикацииПубликация в OpenAlex
Аннотация: Background 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.
Год издания: 2012
Авторы: Jingyuan Song, Linchun Shi, Li D, Yongzhen Sun, Yunyun Niu, Zhiduan Chen, Hongmei Luo, Xiaohui Pang, Zhiying Sun, Chang Liu, LV Ai-ping, Youping Deng, Zachary Larson‐Rabin, M. J. Wilkinson, Shilin Chen
Издательство: Public Library of Science
Источник: PLoS ONE
Ключевые слова: Ginseng Biological Effects and Applications, Genomics and Phylogenetic Studies, Plant and Fungal Species Descriptions
Другие ссылки: PLoS ONE (PDF)
PLoS ONE (HTML)
DOAJ (DOAJ: Directory of Open Access Journals) (HTML)
Europe PMC (PubMed Central) (PDF)
Europe PMC (PubMed Central) (HTML)
Adelaide Research & Scholarship (AR&S) (University of Adelaide) (PDF)
Adelaide Research & Scholarship (AR&S) (University of Adelaide) (HTML)
PubMed Central (HTML)
INDIGO (University of Illinois at Chicago) (PDF)
INDIGO (University of Illinois at Chicago) (HTML)
PubMed (HTML)