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Comparative analysis of genome composition in Triticeae reveals strong variation in transposable element dynamics and nucleotide diversity.
MedLine Citation:
PMID:  23057663     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
A 454 sequencing snapshot was utilised to investigate the genome composition and nucleotide diversity of transposable elements for several Triticeae taxa, including T. aestivum, H. vulgare, H. spontaneum, S. cereale together with relatives of the A, B and D genome donors of wheat, T. urartu (A), Ae. speltoides (S), and Ae. tauschii (D). Additional A genome containing taxa T. monococcum and its wild relative T. boeoticum were also included. The main focus of the analysis was on the genomic composition of transposable elements (TEs) as these make up at least 80% of the overall genome content. Although more than 200 TE families were identified in each species, approximately 50% of the overall genome was comprised of 12-15 TE families. The BARE1 element was the largest contributor to all genomes, contributing more than 10% to the overall genome. We also found that several TE families differ strongly in their abundance between species, indicating that TE families can thrive extremely successfully in one species while going virtually extinct in another. Additionally, nucleotide diversity of BARE1 populations within individual genomes was measured. Interestingly, the nucleotide diversity in the domesticated barley H. vulgare cv. Barke was found to be twice as high as in its wild progenitor H. spontaneum, suggesting that the domesticated barley gained nucleotide diversity from the addition of different genotypes during the domestication and breeding process. In the rye/wheat lineage, sequence diversity of BARE1 elements was generally higher, suggesting that factors such as geographical distribution and mating systems might play a role in intragenomic TE diversity. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.
Authors:
Christopher P Middleton; Nils Stein; Beat Keller; Benjamin Kilian; Thomas Wicker
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-10-12
Journal Detail:
Title:  The Plant journal : for cell and molecular biology     Volume:  -     ISSN:  1365-313X     ISO Abbreviation:  Plant J.     Publication Date:  2012 Oct 
Date Detail:
Created Date:  2012-10-12     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9207397     Medline TA:  Plant J     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Copyright Information:
© 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.
Affiliation:
Institute of Plant Biology, University Zurich, Zollikerstrasse 107, CH-8008, Zurich.
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