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

Buell, C. R., McCombie, W. R., Wing, R. A., Yuan, Q., Ouyang, S., Liu, J., Zhu, W., Wang, A., Maiti, R., Haas, B., Wortman, J., Pertea, M., Jones, K. M., Kim, M., Overton, L., Tsitrin, T., Fadrosh, D., Bera, J., Weaver, J., Jin, S., Johri, S., Reardon, M., Webb, K., Hill, J., Moffat, K., Tallon, L., Van Aken, S., Lewis, M., Utterback, T., Feldblyum, T., Zismann, V., Iobst, S., Hsiao, J., De Vazeille, A. R., Salzberg, S. L., White, O., Fraser, C., Yu, Y., Kim, H., Rambo, T., Currie, J., Collura, K., Kernodle-Thompson, S., Wei, F., Kudrna, D., Ammiraju, J. S. S., Luo, M., Goicoechea, J. L., Henry, D., Oates, R., Palmer, M., Pries, G., Saski, C., Simmons, J., Soderlund, C., Nelson, W., De La Bastide, M., Spiegel, L., Nascimento, L., Huang, E., Preston, R., Zutavern, T., Palmer, L., O'Haughnessy, A., Dike, S., Minx, P., Cordum, H., Wilson, R., Jin, W., Lee, H. R., Jiang, J., Jackson, S. (2005) Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. The Rice Chromosome 3 Sequencing Consortium. Genome Research, 15 (9). pp. 1284-1291. ISSN 10889051 (ISSN)

URL: http://www.ncbi.nlm.nih.gov/pubmed/16109971
DOI: 10.1101/gr.3869505

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. ©2005 by Cold Spring Harbor Laboratory Press.

Item Type: Paper
Uncontrolled Keywords: Arabidopsis article cereal chromosome 3 controlled study gene mapping gene sequence genetic analysis genomics grass medical research molecular evolution nonhuman nucleotide sequence plant genetics priority journal rice sequence homology Chromosome Mapping Chromosomes, Artificial, Bacterial Chromosomes, Plant Genes, Plant Minisatellite Repeats Molecular Sequence Data Oryza sativa Physical Chromosome Mapping Poaceae Proteome Species Specificity Zea mays Arabidopsis thaliana Japonica Oryza nivara Triticum aestivum
Subjects: bioinformatics > genomics and proteomics > analysis and processing
bioinformatics > genomics and proteomics > annotation
organism description > plant > Arabidopsis
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosome
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosomes, structure and function > chromosome

organism description > plant
organism description > plant > rice
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > synteny
CSHL Authors:
Communities: CSHL labs > McCombie lab
Depositing User: Matt Covey
Date Deposited: 24 Apr 2013 20:53
Last Modified: 24 Apr 2013 20:53
PMCID: PMC1199543
Related URLs:
URI: http://repository.cshl.edu/id/eprint/28244

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