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Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species.

ABSTRACT: Rice (Oryza sativa L.) chromosome 3 is evolutionarily conserved across the cultivated cereals and shares large blocks of synteny with maize and sorghum, which diverged from rice more than 50 million years ago. To begin to completely understand this chromosome, we sequenced, finished, and annotated 36.1 Mb ( approximately 97%) from O. sativa subsp. japonica cv Nipponbare. Annotation features of the chromosome include 5915 genes, of which 913 are related to transposable elements. A putative function could be assigned to 3064 genes, with another 757 genes annotated as expressed, leaving 2094 that encode hypothetical proteins. Similarity searches against the proteome of Arabidopsis thaliana revealed putative homologs for 67% of the chromosome 3 proteins. Further searches of a nonredundant amino acid database, the Pfam domain database, plant Expressed Sequence Tags, and genomic assemblies from sorghum and maize revealed only 853 nontransposable element related proteins from chromosome 3 that lacked similarity to other known sequences. Interestingly, 426 of these have a paralog within the rice genome. A comparative physical map of the wild progenitor species, Oryza nivara, with japonica chromosome 3 revealed a high degree of sequence identity and synteny between these two species, which diverged approximately 10,000 years ago. Although no major rearrangements were detected, the deduced size of the O. nivara chromosome 3 was 21% smaller than that of japonica. Synteny between rice and other cereals using an integrated maize physical map and wheat genetic map was strikingly high, further supporting the use of rice and, in particular, chromosome 3, as a model for comparative studies among the cereals.

SUBMITTER: Buell CR

PROVIDER: S-EPMC1199543 | biostudies-literature | 2005 Sep

REPOSITORIES: biostudies-literature

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Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species.

Buell C Robin CR Yuan Qiaoping Q Ouyang Shu S Liu Jia J Zhu Wei W Wang Aihui A Maiti Rama R Haas Brian B Wortman Jennifer J Pertea Mihaela M Jones Kristine M KM Kim Mary M Overton Larry L Tsitrin Tamara T Fadrosh Douglas D Bera Jayati J Weaver Bruce B Jin Shaohua S Johri Shivani S Reardon Matt M Webb Kristen K Hill Jessica J Moffat Kelly K Tallon Luke L Van Aken Susan S Lewis Matthew M Utterback Teresa T Feldblyum Tamara T Zismann Victoria V Iobst Stacey S Hsiao Joseph J de Vazeille Aymeric R AR Salzberg Steven L SL White Owen O Fraser Claire C Yu Yeisoo Y Kim HeyRan H Rambo Teri T Currie Jennifer J Collura Kristi K Kernodle-Thompson Shelly S Wei Fusheng F Kudrna Kudrna K Ammiraju Jetty Siva S JS Luo Meizhong M Goicoechea Jose Luis JL Wing Rod A RA Henry David D Oates Ryan R Palmer Michael M Pries Gina G Saski Christopher C Simmons Jessica J Soderlund Carol C Nelson William W de la Bastide Melissa M Spiegel Lori L Nascimento Lidia L Huang Emily E Preston Raymond R Zutavern Theresa T Palmer Lance L O'Shaughnessy Andrew A Dike Sujit S McCombie W Richard WR Minx Pat P Cordum Holly H Wilson Richard R Jin Weiwei W Lee Hye-Ran HR Jiang Jiming J Jackson Scott S

Genome research 20050818 9

Rice (Oryza sativa L.) chromosome 3 is evolutionarily conserved across the cultivated cereals and shares large blocks of synteny with maize and sorghum, which diverged from rice more than 50 million years ago. To begin to completely understand this chromosome, we sequenced, finished, and annotated 36.1 Mb ( approximately 97%) from O. sativa subsp. japonica cv Nipponbare. Annotation features of the chromosome include 5915 genes, of which 913 are related to transposable elements. A putative functi ...[more]

PMID: 16109971

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Dataset Information

Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species.

Publications

Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species.

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