Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza

The Plant Journal : for Cell and Molecular Biology
Bonnie L HurwitzLincoln Stein

Abstract

Rapid progress in comparative genomics among the grasses has revealed similar gene content and order despite exceptional differences in chromosome size and number. Large- and small-scale genomic variations are of particular interest, especially among cultivated and wild species, as they encode rapidly evolving features that may be important in adaptation to particular environments. We present a genome-wide study of intermediate-sized structural variation (SV) among rice (Oryza sativa) and three of its closest relatives in the genus Oryza (Oryza nivara, Oryza rufipogon and Oryza glaberrima). We computationally identified regional expansions, contractions and inversions in the Oryza species genomes relative to O. sativa by combining data from paired-end clone alignments to the O. sativa reference genome and physical maps. A subset of the computational predictions was validated using a new approach for BAC size determination. The result was a confirmed catalog of 674 expansions (25-38 Mb) and 611 (4-19 Mb) contractions, and 140 putative inversions (14-19 Mb) between the three Oryza species and O. sativa. In the expanded regions unique to O. sativa we found enrichment in transposable elements (TEs): long terminal repeats (LTRs) wer...Continue Reading

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Aug 21, 2013·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Taiji KawakatsuFumio Takaiwa
Sep 26, 2013·BMC Genomics·Ping YuXing-Hua Wei
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