Annotation of the rice genome
2007
Ouyang, S. | Zhu, W. | Hamilton, J. | Lin, H.N. | Campbell, M. | Lee, Y.D. | Malek, R.L. | Wang, A.H. | Yuan, Q.P. | Haas, B. | Wortman, J. | Buell, C.R.
A high-quality finished sequence of the rice genome was completed in 2005. However, to maximally use the sequences, quality annotation of the genes and genome features is necessary. The process of annotation is iterative in nature and requires the application and refinement of computational tools coupled with manual curation and evaluation. We are funded by the U.S. National Science Foundation to annotate the rice genome and have constructed pseudomolecules for the 12 Oryza sativa subspecies japonica var. Nipponbare chromosomes, which are publicly available through our project Web site (http://rice.tigr.org). We identified genes, gene models, and other annotation features in the rice genome. We expanded our annotation features to include a rice transcript assembly and its alignment with the rice genome, small noncoding RNAs, simple sequence repeats, as well as single nucleotide polymorphisms ans insertions/deletions based on alignment with the indica subspecies. We updated our Oryza repeat database, which has allowed us to better quantify the repetitive sequences within the rice genome, which total 29% of the genome. To assist users in accessing the genome and our annotation, we expanded the content and functions of our Rice Genome Browser such that it supports 37 annotation tracks and data downloads of the underlying annotation data in various formats.
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