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Unformatted text preview: The map-based sequence of the rice genome International Rice Genome Sequencing Project* 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. Rice ( Oryza sativa L.) is the most important food crop in the world and feeds over half of the global population. As the first step in a systematic and complete functional characterization of the rice genome, the International Rice Genome Sequencing Project (IRGSP) has generated and analysed a highly accurate finished sequence of the rice genome that is anchored to the genetic map. Our analysis has revealed several salient features of the rice genome: . We provide evidence for a genome size of 389 Mb. This size estimation is , 260 Mb larger than the fully sequenced dicot plant model Arabidopsis thaliana . We generated 370 Mb of finished sequence, representing 95% coverage of the genome and virtually all of the euchromatic regions. . A total of 37,544 non-transposable-element-related protein-cod- ing sequences were detected, compared with , 28,000–29,000 in Arabidopsis , with a lower gene density of one gene per 9.9 kb in rice. A total of 2,859 genes seem to be unique to rice and the other cereals, some of which might differentiate monocot and dicot lineages. . Gene knockouts are useful tools for determining gene function and relating genes to phenotypes. We identified 11,487 Tos17 retro- transposon insertion sites, of which 3,243 are in genes. . Between 0.38 and 0.43% of the nuclear genome contains orga- nellar DNA fragments, representing repeated and ongoing transfer of organellar DNA to the nuclear genome....
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