A Draft Sequence of the Rice Genome ( Oryza sativa L. ssp. japonica )

Abstract

The genome of the japonica subspecies of rice, an important cereal and model monocot, was sequenced and assembled by whole-genome shotgun sequencing. The assembled sequence covers 93% of the 420-megabase genome. Gene predictions on the assembled sequence suggest that the genome contains 32,000 to 50,000 genes. Homologs of 98% of the known maize, wheat, and barley proteins are found in rice. Synteny and gene homology between rice and the other cereal genomes are extensive, whereas synteny with Arabidopsis is limited. Assignment of candidate rice orthologs to Arabidopsis genes is possible in many cases. The rice genome sequence provides a foundation for the improvement of cereals, our most important crops.

Expanding the organismal scope of proteomics: Cross‐species protein identification by mass spectrometry and its implications

“…These sequenced genomes can represent many phylogenetically related organisms depending on the nucleotide substitution rate in those lineages and the ability to annotate future genomic sequences [56,57]. For example, research in maize and other economically important grasses, such as wheat and barley, will benefit from the complete sequence of the rice genome, as 98% of the known proteins from these grasses have homologs in rice [58].…”

PeroxiBase: A class III plant peroxidase database

“…Newly duplicated genes were likely conserved because they acquired new modes of expression, regulation (subfunctionalization) or novel functions (neofunctionalization). The automated annotation of the whole genomes of Arabidopsis (Arabidopsis Genome Initiative, 2000) and Oryza sativa (Goff et al, 2002;Yu et al, 2002), the automated clustering and assembling of EST sequences, and numerous EST projects led to the identification of a large number of sequences coding for class III plant peroxidases. We decided to construct a database devoted to this large, multigenic family because in our experience automated processing sometimes yields sequences of poor quality.…”

The tomato genome: implications for plant breeding, genomics and evolution

“…It was a milestone in plant biology and made Arabidopsis one of the most popular species for basic plant research. Rice, a staple food in most of the world, was the second available plant genome in 2002 [4,5]. Rapid progress in the development of new sequencing technology and bioinformatic tools in recent years has allowed faster and more efficient sequencing, and assembly of genomes at lower cost.…”

“…As many as 20 plant genomes have been sequenced and assembled in the last two years [6-25]. Genome sequences of plants belonging to different groups, such as two plants from the early land plant clades (a moss Physcomitrella patens and a spikemoss Selaginella moellendorffii ) and numerous economically important monocots (Box 1), such as rice, maize, sorghum, and so on, have now been decoded [4,5,25-28] (Figure 1). Eudicots (Box 1), the largest group in flowering plants, are composed of two major clades, the Eurosids and Euasterids.…”