Phylogenomics databases for facilitating functional genomics in rice

Jung, Ki-Hong; Cao, Peijian; Sharma, Rita; Jain, Rashmi; Ronald, Pamela C.

doi:10.1186/s12284-015-0060-7

Phylogenomics databases for facilitating functional genomics in rice

Journal Article · Thu Jul 30 00:00:00 EDT 2015 · Rice

DOI:https://doi.org/10.1186/s12284-015-0060-7· OSTI ID:1626753

Jung, Ki-Hong ^[1]; Cao, Peijian ^[2]; Sharma, Rita ^[3]; Jain, Rashmi ^[4]; Ronald, Pamela C. ^[5]

Kyung Hee Univ., Yongin (Korea); DOE/OSTI
Zhengzhou Tobacco Research Institute (China)
Jawaharlal Nehru Univ., School of Life Sciences, New Delhi 110067 (India)
Univ. of California, Davis, CA (United States)
Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Univ. of California, Davis, CA (United States)

The completion of whole genome sequence of rice (Oryza sativa) has significantly accelerated functional genomics studies. Prior to the release of the sequence, only a few genes were assigned a function each year. Since sequencing was completed in 2005, the rate has exponentially increased. As of 2014, 1,021 genes have been described and added to the collection at The Overview of functionally characterized Genes in Rice online database (OGRO). Despite this progress, that number is still very low compared with the total number of genes estimated in the rice genome. One limitation to progress is the presence of functional redundancy among members of the same rice gene family, which covers 51.6 % of all non-transposable element-encoding genes. There remain a significant portion or rice genes that are not functionally redundant, as reflected in the recovery of loss-of-function mutants. To more accurately analyze functional redundancy in the rice genome, we have developed a phylogenomics databases for six large gene families in rice, including those for glycosyltransferases, glycoside hydrolases, kinases, transcription factors, transporters, and cytochrome P450 monooxygenases. In this review, we introduce key features and applications of these databases. We expect that they will serve as a very useful guide in the post-genomics era of research.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1626753

Journal Information:: Rice, Journal Name: Rice Journal Issue: 1 Vol. 8; ISSN 1939-8425

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

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