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

C Robin Buell, 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, Bruce Weaver, Shaohua Jin, Shivani 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, HeyRan Kim, Teri Rambo, Jennifer Currie, Kristi Collura, Shelly Kernodle-Thompson, Fusheng Wei, Kudrna Kudrna, Jetty Siva S Ammiraju, Meizhong Luo, Jose Luis Goicoechea, Rod A Wing, David Henry, Ryan Oates, Michael Palmer, Gina Pries, Christopher Saski, Jessica Simmons, Carol Soderlund, William Nelson, Melissa de la Bastide, Lori Spiegel, Lidia Nascimento, Emily Huang, Raymond Preston, Theresa Zutavern, Lance Palmer, Andrew O'Shaughnessy, Sujit Dike, W Richard McCombie, Pat Minx, Holly Cordum, Richard Wilson, Weiwei Jin, Hye-Ran Lee, Jiming Jiang, Scott Jackson
Genome Research 2005, 15 (9): 1284-91
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.

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