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

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.

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

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