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

doi:10.1101/gr.3869505

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

The Rice Chromosome 3 Sequencing Consortium1,2

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 (∼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.

Footnotes

[Supplemental material is available online at www.genome.org. The chromosome 3 pseudomolecule sequence data from this study has been submitted to GenBank under accession no. DP000009.]
Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.3869505. Article published online before print in August 2005.
↵3 The Institute for Genomic Research, Rockville, Maryland 20850, USA.
↵4 Arizona Genomics Institute (AGI), Department of Plant Sciences and BIO5 Institute, The University of Arizona, Tucson, Arizona 85721, USA.
↵5 Clemson University Genomics Institute (CUGI), Clemson University, Clemson, South Carolina 29634, USA.
↵6 Arizona Genomics Computational Laboratory (AGCoL), Department of Plant Sciences and BIO5 Institute, The University of Arizona, Tucson, Arizona 85721, USA.
↵7 Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, New York 11723, USA.
↵8 Washington University School of Medicine Genome Sequencing Center (WUGSC), St. Louis, Missouri 63108, USA.
↵9 University of Wisconsin, Department of Horticulture, Madison, Wisconsin 53706, USA.
↵10 Purdue University, Department of Agronomy, West Lafayette, Indiana 47907, USA.
↵1 A complete list of authors appears at the end of this manuscript.
↵2 Corresponding authors. C. Robin Buell, E-mail rbuell{at}tigr.org; fax (301) 838-0208. W. Richard McCombie, E-mail mccombie{at}cshl.org; fax (516) 422-4109. Rod A. Wing, E-mail rwing{at}ag.arizona.edu; fax (520) 621-1259.
- Accepted May 17, 2005.
- Received March 3, 2005.
Cold Spring Harbor Laboratory Press