Retrotransposon insertion polymorphisms in six rice genes and their evolutionary history.

Journal Article (Journal Article)

Retrotransposons are abundant in higher plant genomes. Although retrotransposons associated with plant genes have been identified, little is known about their evolutionary conservation at the level of species and subspecies. In the present study, we investigated the phylogenetic distribution of long terminal repeat (LTR) retrotransposon, long interspersed nuclear element (LINE) and short interspersed nuclear element (SINE) insertions in six genes in 95 cultivated and wild rice genotypes. These six genes are likely to be functional based on nonsynonymous (Ka) to synonymous (Ks) substitution ratios which were found to be significantly <1. Different conservation patterns of these retrotransposons in genes were observed in cultivated and wild rice species. Four out of seven retrotransposon insertions appear to predate the ancestral Oryza AA genome. Two of these insertions in genes 4 and 5 occurred early in the evolutionary history of Oryza. Two retrotransposon insertions in gene 1 arose after the divergence of Asian cultivated rice from its wild ancestor. Furthermore, the retrotransposon insertion in gene 3 appears to have occurred in the ancestral lineage leading to temperate japonicas. Conservation of retrotransposon insertions in genes in specific groups, species, and lineages might be related to their specific function.

Full Text

Duke Authors

Cited Authors

  • Xu, Z; Ramakrishna, W

Published Date

  • April 15, 2008

Published In

Volume / Issue

  • 412 / 1-2

Start / End Page

  • 50 - 58

PubMed ID

  • 18291601

International Standard Serial Number (ISSN)

  • 0378-1119

Digital Object Identifier (DOI)

  • 10.1016/j.gene.2008.01.012


  • eng

Conference Location

  • Netherlands