Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents

Navdeep Gill,Braham Deep Singh Dhillon,Lincoln Stein,Brian Abernathy,Scott A Jackson,Hyeran Kim,Doreen Ware,Phillip Sanmiguel,Rod Wing

doi:10.1007/s12284-010-9054-7

Abstract

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.

Highlights

The genus Oryza, to which cultivated rice belongs, is composed of 23 species (Vaughan et al 2003), including 21 wild and two cultivated species
We investigated the repetitive sequences within the genus Oryza and found association of these elements, the Class I LTR retrotransposons (LTR-RTs) and Class II miniature inverted transposable elements (TEs) (MITEs), with genome size variation
BAC-end sequences (BESs) of 13 Oryza species representing 8–17% (Kim et al 2008) of each of the ten Oryza genome types were analyzed for their repetitive deoxyribonucleic acid (DNA) content

Summary

Introduction

The genus Oryza, to which cultivated rice belongs, is composed of 23 species (Vaughan et al 2003), including 21 wild and two cultivated species. Based on interspecific crossing (Tateoka 1963, 1964), chromosome pairing (Nayar 1973; Li et al 2001) and total genomic DNA hybridization (Aggarwal et al 1997), these species have been divided into ten distinct genome types: six diploid (2n=24) and four. Electronic supplementary material The online version of this article (doi:10.1007/s12284-010-9054-7) contains supplementary material, which is available to authorized users.

Methods

Results

Discussion

Conclusion