Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species.
Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species.
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DOI：
10.1104/pp.125.3.1166
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发表时间：
2001-03
期刊：
影响因子：
7.4
通讯作者：
Q. Yuan;John Quackenbush;R. Sultana;M. Perțea;S. Salzberg;C. R. Buell
中科院分区：
文献类型：
--
作者：
Q. Yuan;John Quackenbush;R. Sultana;M. Perțea;S. Salzberg;C. R. Buell
水稻（Oryza sativa）是单子叶植物，特别是禾本科植物的模式种。一些属性，如小的基因组大小，二倍体性质，可转化性，以及遗传和分子资源的建立，使其成为植物生物学家易于处理的生物体。估计基因组大小为430 Mb（Arumuganathan和Earle，1991），使用现有技术获得水稻的完整基因组序列是可行的。一项国际努力已经建立，并正在测序O。青花菜利用细菌人工染色体/P1人工染色体鸟枪测序策略，水稻基因组的注释使用基于预测和基于同源性的搜索来识别基因。目前正在开发用于水稻的注释工具，如优化基因预测程序，以提高注释质量。还正在开发资源，以利用水稻基因组序列进行部分基因组项目，如表达序列标签项目，从而最大限度地提高水稻基因组项目的产出。为了给水稻基因组序列提供低水平的注释，我们将所有的水稻细菌人工染色体/P1人工染色体序列与基因组研究所的基因索引进行了比对，基因索引是一组非冗余的转录本，这些转录本是从9个公共植物表达序列标签项目（水稻、小麦、高粱、玉米、大麦、拟南芥、番茄、马铃薯和桶苜蓿）中产生的。此外，我们还使用了基因组研究所基因索引和拟南芥和水稻基因组计划的数据，以确定这九个基因组中推定的直系同源物和旁系同源物。
Rice (Oryza sativa) is a model species for monocotyledonous plants, especially for members in the grass family. Several attributes such as small genome size, diploid nature, transformability, and establishment of genetic and molecular resources make it a tractable organism for plant biologists. With an estimated genome size of 430 Mb (Arumuganathan and Earle, 1991), it is feasible to obtain the complete genome sequence of rice using current technologies. An international effort has been established and is in the process of sequencing O. sativa spp. japonica var "Nipponbare" using a bacterial artificial chromosome/P1 artificial chromosome shotgun sequencing strategy. Annotation of the rice genome is performed using prediction-based and homology-based searches to identify genes. Annotation tools such as optimized gene prediction programs are being developed for rice to improve the quality of annotation. Resources are also being developed to leverage the rice genome sequence to partial genome projects such as expressed sequence tag projects, thereby maximizing the output from the rice genome project. To provide a low level of annotation for rice genomic sequences, we have aligned all rice bacterial artificial chromosome/P1 artificial chromosome sequences with The Institute of Genomic Research Gene Indices that are a set of nonredundant transcripts that are generated from nine public plant expressed sequence tag projects (rice, wheat, sorghum, maize, barley, Arabidopsis, tomato, potato, and barrel medic). In addition, we have used data from The Institute of Genomic Research Gene Indices and the Arabidopsis and Rice Genome Projects to identify putative orthologues and paralogues among these nine genomes.