The Institute for Genomic Research Osa1 Rice Genome Annotation Database

  • Qiaoping Yuan
    The Institute for Genomic Research, Rockville, Maryland 20850
  • Shu Ouyang
    The Institute for Genomic Research, Rockville, Maryland 20850
  • Aihui Wang
    The Institute for Genomic Research, Rockville, Maryland 20850
  • Wei Zhu
    The Institute for Genomic Research, Rockville, Maryland 20850
  • Rama Maiti
    The Institute for Genomic Research, Rockville, Maryland 20850
  • Haining Lin
    The Institute for Genomic Research, Rockville, Maryland 20850
  • John Hamilton
    The Institute for Genomic Research, Rockville, Maryland 20850
  • Brian Haas
    The Institute for Genomic Research, Rockville, Maryland 20850
  • Razvan Sultana
    The Institute for Genomic Research, Rockville, Maryland 20850
  • Foo Cheung
    The Institute for Genomic Research, Rockville, Maryland 20850
  • Jennifer Wortman
    The Institute for Genomic Research, Rockville, Maryland 20850
  • C. Robin Buell
    The Institute for Genomic Research, Rockville, Maryland 20850

抄録

<jats:title>Abstract</jats:title> <jats:p>We have developed a rice (Oryza sativa) genome annotation database (Osa1) that provides structural and functional annotation for this emerging model species. Using the sequence of O. sativa subsp. japonica cv Nipponbare from the International Rice Genome Sequencing Project, pseudomolecules, or virtual contigs, of the 12 rice chromosomes were constructed. Our most recent release, version 3, represents our third build of the pseudomolecules and is composed of 98% finished sequence. Genes were identified using a series of computational methods developed for Arabidopsis (Arabidopsis thaliana) that were modified for use with the rice genome. In release 3 of our annotation, we identified 57,915 genes, of which 14,196 are related to transposable elements. Of these 43,719 nontransposable element-related genes, 18,545 (42.4%) were annotated with a putative function, 5,777 (13.2%) were annotated as encoding an expressed protein with no known function, and the remaining 19,397 (44.4%) were annotated as encoding a hypothetical protein. Multiple splice forms (5,873) were detected for 2,538 genes, resulting in a total of 61,250 gene models in the rice genome. We incorporated experimental evidence into 18,252 gene models to improve the quality of the structural annotation. A series of functional data types has been annotated for the rice genome that includes alignment with genetic markers, assignment of gene ontologies, identification of flanking sequence tags, alignment with homologs from related species, and syntenic mapping with other cereal species. All structural and functional annotation data are available through interactive search and display windows as well as through download of flat files. To integrate the data with other genome projects, the annotation data are available through a Distributed Annotation System and a Genome Browser. All data can be obtained through the project Web pages at http://rice.tigr.org.</jats:p>

収録刊行物

  • Plant Physiology

    Plant Physiology 138 (1), 18-26, 2005-05-01

    Oxford University Press (OUP)

被引用文献 (3)*注記

もっと見る

詳細情報

問題の指摘

ページトップへ