Abstract:
:Small-scale changes in gene order and orientation are common in plant genomes, even across relatively short evolutionary distances. We investigated the association of retrotransposons in and near rice gene pairs with gene pair conservation, inversion, rearrangement, and deletion in sorghum, maize, and Brachypodium. Copia and Gypsy LTR-retrotransposon insertions were found to be primarily associated with reduced frequency of gene pair conservation and an increase in both gene pair rearrangement and gene deletions. SINEs are associated with gene pair rearrangement, while LINEs are associated with gene deletions. Despite being more frequently associated with retrotransposons than convergent and tandem pairs, divergent gene pairs showed the least effects from that association. In contrast, convergent pairs were least frequently associated with retrotransposons yet showed the greatest effects. Insertions between genes were associated with the greatest effects on gene pair arrangement, while insertions flanking gene pairs had significant effects only on divergent pairs.
journal_name
Genomicsjournal_title
Genomicsauthors
Krom N,Ramakrishna Wdoi
10.1016/j.ygeno.2012.02.006subject
Has Abstractpub_date
2012-05-01 00:00:00pages
308-14issue
5eissn
0888-7543issn
1089-8646pii
S0888-7543(12)00045-6journal_volume
99pub_type
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