Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. The Rice Chromosome 3 Sequencing Consortium

C. Robin Buell, W. Richard McCombie, Rod A. Wing, Qiaoping Yuan, Shu Ouyang, Jia Liu, Wei Zhu, Aihui Wang, Rama Maiti, Brian Haas, Jennifer Wortman, Mihaela Pertea, Kristine M. Jones, Mary Kim, Larry Overton, Tamara Tsitrin, Douglas Fadrosh, Jayati Bera, Jayati Weaver, Shaohua JinShivani Johri, Matt Reardon, Kristen Webb, Jessica Hill, Kelly Moffat, Luke Tallon, Susan Van Aken, Matthew Lewis, Teresa Utterback, Tamara Feldblyum, Victoria Zismann, Stacey Iobst, Joseph Hsiao, Aymeric R. De Vazeille, Steven L. Salzberg, Owen White, Claire Fraser, Yeisoo Yu, Hey Ran Kim, Teri Rambo, Jennifer Currie, Kristi Collura, Shelly Kernodle-Thompson, Fusheng Wei, David Kudrna, Jetty Siva S. Ammiraju, Meizhong Luo, Jos Luis Goicoechea, David Henry, Ryan Oates, Michael Palmer, Gina Pries, Christopher Saski, Jessica Simmons, Carol Soderlund, Carol Soderlund, Carol Soderlund, William Nelson, Carol Soderlund, Melissa De La Bastide, Lori Spiegel, Lidia Nascimento, Emily Huang, Raymond Preston, Theresa Zutavern, Lance Palmer, Andrew O'haughnessy, Sujit Dike, W. Richard McCombie, Pat Minx, Holly Cordum, Richard Wilson, Weiwei Jin, Hye Ran Lee, Jiming Jiang, Scott Jackson

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60 Scopus citations


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 (∼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 ∼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. ©2005 by Cold Spring Harbor Laboratory Press.
Original languageEnglish (US)
JournalGenome Research
Issue number9
StatePublished - Sep 1 2005
Externally publishedYes

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