Dynamic Oryza genomes: Repetitive DNA sequences as genome modeling agents

Navdeep Gill, Phillip SanMiguel, Braham Deep Singh Dhillon, Brian Abernathy, Hye Ran Kim, Lincoln Stein, Doreen Ware, Rod Wing, Scott A. Jackson

Research output: Contribution to journalArticlepeer-review

10 Scopus citations

Abstract

Repetitive sequences, primarily transposable elements form an indispensable part of eukaryotic genomes. However, little is known about how these sequences originate, evolve and function in context of a genome. In an attempt to address this question, we performed a comparative analysis of repetitive DNA sequences in the genus Oryza, representing ~15 million years of evolution. Both Class I and Class II transposable elements, through their expansion, loss and movement in the genome, were found to influence genome size variation in this genus. We identified 38 LTRretrotransposon families that are present in 1,500 or more copies throughout Oryza, and many are preferentially amplified in specific lineages. The data presented here, besides furthering our understanding of genome organization in the genus Oryza, will aid in the assembly, annotation and analysis of genomic data, as part of the future genome sequencing projects of O. sativa wild relatives.

Original languageEnglish (US)
Pages (from-to)251-269
Number of pages19
JournalRice
Volume3
Issue number4
DOIs
StatePublished - Dec 2010

Keywords

  • Genome size variation
  • LTR-retrotransposons
  • Oryza
  • Repetitive sequences
  • Transposable elements

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Soil Science
  • Plant Science

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