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Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza.
Hurwitz, Bonnie L; Kudrna, Dave; Yu, Yeisoo; Sebastian, Aswathy; Zuccolo, Andrea; Jackson, Scott A; Ware, Doreen; Wing, Rod A; Stein, Lincoln.
Afiliação
  • Hurwitz BL; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
Plant J ; 63(6): 990-1003, 2010 Sep.
Article em En | MEDLINE | ID: mdl-20626650
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.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Oryza Tipo de estudo: Prognostic_studies Idioma: En Revista: Plant J Assunto da revista: BIOLOGIA MOLECULAR / BOTANICA Ano de publicação: 2010 Tipo de documento: Article País de afiliação: Estados Unidos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Oryza Tipo de estudo: Prognostic_studies Idioma: En Revista: Plant J Assunto da revista: BIOLOGIA MOLECULAR / BOTANICA Ano de publicação: 2010 Tipo de documento: Article País de afiliação: Estados Unidos