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

Hurwitz, B. L., Kudrna, D., Yu, Y., Sebastian, A., Zuccolo, A., Jackson, S. A., Ware, D. H., Wing, R. A., Stein, L. D. (2010) Rice structural variation: A comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. Plant Journal, 63 (6). pp. 990-1003.

URL: https://www.ncbi.nlm.nih.gov/pubmed/20626650
DOI: 10.1111/j.1365-313X.2010.04293.x

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) were randomly located across the chromosomes, and their insertion times corresponded to the date of the A genome radiation. Also, rice-expanded regions contained an over-representation of single-copy genes related to defense factors in the environment. This catalog of confirmed SV in reference to O. sativa provides an entry point for future research in genome evolution, speciation, domestication and novel gene discovery. © 2010 Blackwell Publishing Ltd.

Item Type: Paper
Uncontrolled Keywords: comparative genomics domestication evolution genome Oryza rice
Subjects: organism description > plant > Oryza
bioinformatics > quantitative biology
organism description > plant > rice
CSHL Authors:
Communities: CSHL labs > Jackson lab
CSHL labs > Stein lab
CSHL labs > Ware lab
Depositing User: CSHL Librarian
Date: 2010
Date Deposited: 30 Sep 2011 21:02
Last Modified: 23 Feb 2017 16:55
Related URLs:
URI: http://repository.cshl.edu/id/eprint/15438

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