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DNA Research Advance Access first published online on August 6, 2008
This version published online on September 9, 2008
DNA Research, doi:10.1093/dnares/dsn018
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© The Author 2008. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

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

Tingting Lu1,2, Shuliang Yu2,3, Danlin Fan2, Jie Mu2, Yingying Shangguan2, Zixuan Wang4, Yuzo Minobe4, Zhixin Lin1 and Bin Han2,*

1 College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, PR China
2 National Center for Gene Research and Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, PR China
3 School of Life Sciences, Fudan University, Shanghai, PR China
4 Plant Genome Center, 1-25-2 Kan-nondai, Tsukuba, Ibaraki 305-0856, Japan

Received 29 April 2008 ; accepted 9 July 2008.

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.

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

* To whom correspondence should be addressed. Tel. +86 21-64845260. Fax. +86 21-64825775. E-mail: bhan{at}ncgr.ac.cn

Edited by Masahiro Yano

The authors wish to apologise for the following errors: {list errors below}.

1. Page 2, The last sixth line (Line 219): "our 1832 clones..." should be corrected as "our 1888 clones...".

2. Page 3, The first seventh line (Line 231): "MPSS database18" should be cited as "MPSS database13".

3. Page 5, The last tenth line (Line 551): "national center for gene research" should be written as "National Center for Gene Research, CAS".

4. Page 4, Table 1. The first column and the fourth clonename "CT841893" should be replaced of "CT841874".

5. page 6, Table 4. The last third line, the second column. The clonename "CT841912" should be replaced of "CU406778". The last second line, the second column. The clonename "CT841912" should be replaced of "CU861677".


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