Journal Article

Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice <i>Oryza rufipogon</i> Griff. W1943

Tingting Lu, Shuliang Yu, Danlin Fan, Jie Mu, Yingying Shangguan, Zixuan Wang, Yuzo Minobe, Zhixin Lin and Bin Han

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 15, issue 5, pages 285-295
Published in print October 2008 | ISSN: 1340-2838
Published online August 2008 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dsn018

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A huge amount of cDNA and EST resources have been developed for cultivated rice species Oryza sativa; however, only few cDNA resources are available for wild rice species. In this study, we isolated and completely sequenced 1888 putative full-length cDNA (FLcDNA) clones from wild rice Oryza rufipogon Griff. W1943 for comparative analysis between wild and cultivated rice species. Two cDNA libraries were constructed from 3-week-old leaf samples under either normal or cold-treated conditions. Homology searching of these cDNA sequences revealed that >96.8% of the wild rice cDNAs were matched to the cultivated rice O. sativa ssp. japonica cv. Nipponbare genome sequence. However, <22% of them were fully matched to the cv. Nipponbare genome sequence. The comparative analysis showed that O. rufipogon W1943 had greater similarity to O. sativa ssp. japonica than to ssp. indica cultivars. In addition, 17 novel rice cDNAs were identified, and 41 putative tissue-specific expression genes were defined through searching the rice massively parallel signature-sequencing database. In conclusion, these FLcDNA clones are a resource for further function verification and could be broadly utilized in rice biological studies.

Keywords: wild rice; Oryza rufipogon; full-length cDNA; transcriptome comparison; tissue-specific expression

Journal Article.  5144 words.  Illustrated.

Subjects: Genetics and Genomics

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