The map-based sequence of the rice genome

International Rice Genome Sequencing Project, (2005) The map-based sequence of the rice genome. Nature, 436 (7052). pp. 793-800. ISSN 0028-0836

URL: http://www.ncbi.nlm.nih.gov/pubmed/16100779
DOI: 10.1038/nature03895

Abstract

Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 non-transposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.

Item Type: Paper
Uncontrolled Keywords: Cell Nucleus/genetics Centromere/genetics Chromosomes, Plant/genetics Cloning, Molecular Computational Biology DNA Transposable Elements/genetics Genes, Plant/genetics *Genome, Plant *Genomics International Cooperation Molecular Sequence Data Multigene Family/genetics Organelles/genetics Oryza sativa/*genetics Polymorphism, Genetic/genetics RNA, Untranslated/genetics Sequence Analysis, DNA Tandem Repeat Sequences/genetics
Subjects: bioinformatics > genomics and proteomics > Mapping and Rendering
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
organism description > plant
organism description > plant > rice
CSHL Authors:
Communities: CSHL labs > McCombie lab
Depositing User: Matt Covey
Date Deposited: 08 Jul 2014 20:28
Last Modified: 08 Jul 2014 20:28
Related URLs:
URI: http://repository.cshl.edu/id/eprint/30354

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