NDLI: Inter-species sequence comparison of Brachypodium reveals how transposon activity corrodes genome colinearity

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Inter-species sequence comparison of Brachypodium reveals how transposon activity corrodes genome colinearity

Content Provider	Scilit
Author	Buchmann, Jan P. Matsumoto, Takashi Stein, Nils Keller, Beat Wicker, Thomas
Copyright Year	2012
Description	Journal: The Plant Journal Intergenic sequences evolve rapidly in plant genomes through a process known as genomic turnover. To investigate the influence of DNA transposons on genomic turnover, we compared 1 Mbp of orthologous genomic sequences from Brachypodium distachyon and Brachypodium sylvaticum. We found that B. distachyon and B. sylvaticum diverged approximately 1.7–2.0 million years ago. Of a total of 219 genes identified on the analyzed sequences, 211 were colinear. However, only 24 transposable elements of a total of 451 were orthologous (i.e. inserted in the common ancestor). We characterized in detail 59 insertions and 60 excisions of DNA transposons in one or other species, which altered 17% of the intergenic space. The DNA transposon excision sites showed complex and highly diagnostic sequence motifs for double‐strand break (DSB) repair. DNA transposon excisions can lead to extensive deletions of hundreds of base pairs of flanking sequence if the DSB is repaired by 'single‐strand annealing', or insertions of up to several hundred base pairs of 'filler DNA' if the DSB is repaired by 'synthesis‐dependent strand annealing'. In some cases, DSBs were repaired by a combination of both methods. We present a model for the evolution of intergenic sequences in which repair of DSBs upon DNA transposon excision is a major factor in the rapid turnover and erosion of intergenic sequences.
Related Links	http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2012.05007.x/pdf
Ending Page	563
Page Count	14
Starting Page	550
e-ISSN	1365313X
DOI	10.1111/j.1365-313x.2012.05007.x
Journal	The Plant Journal
Issue Number	4
Volume Number	71
Language	English
Publisher	Wiley-Blackwell
Publisher Date	2012-06-18
Access Restriction	Open
Subject Keyword	Journal: The Plant Journal Evolutionary Biology Plant Sciences Comparative Genomics Transposable Elements Double‐strand Break Repair Genome Evolution Brachypodium Distachyon Brachypodium Sylvaticum
Content Type	Text
Resource Type	Article

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