Abstract
BackgroundRice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses. Therefore, decoding its entire genome will be a prerequisite for applied and basic research on this species and all other cereals.ResultsWe have determined and analyzed the complete sequences of two of its chromosomes, 11 and 12, which total 55.9 Mb (14.3% of the entire genome length), based on a set of overlapping clones. A total of 5,993 non-transposable element related genes are present on these chromosomes. Among them are 289 disease resistance-like and 28 defense-response genes, a higher proportion of these categories than on any other rice chromosome. A three-Mb segment on both chromosomes resulted from a duplication 7.7 million years ago (mya), the most recent large-scale duplication in the rice genome. Paralogous gene copies within this segmental duplication can be aligned with genomic assemblies from sorghum and maize. Although these gene copies are preserved on both chromosomes, their expression patterns have diverged. When the gene order of rice chromosomes 11 and 12 was compared to wheat gene loci, significant synteny between these orthologous regions was detected, illustrating the presence of conserved genes alternating with recently evolved genes.ConclusionBecause the resistance and defense response genes, enriched on these chromosomes relative to the whole genome, also occur in clusters, they provide a preferred target for breeding durable disease resistance in rice and the isolation of their allelic variants. The recent duplication of a large chromosomal segment coupled with the high density of disease resistance gene clusters makes this the most recently evolved part of the rice genome. Based on syntenic alignments of these chromosomes, rice chromosome 11 and 12 do not appear to have resulted from a single whole-genome duplication event as previously suggested.
Highlights
Rice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses
General features of chromosomes 11 and 12 A total of 255 and 269 bacterial artificial chromosome (BAC)/P1-derived artificial chromosome (PAC) clones were sequenced from chromosomes 11 and 12, respectively
A few physical gaps remain on the two pseudomolecules; six and one on chromosomes 11 and 12, respectively (Accession Numbers: chromosome 11: DP000010, chromosome 12: DP000011)
Summary
Rice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses. Access to the rice genome sequence will enable identification of genes responsible for traits and alleles that will be essential to meet the growing demands of food production in the coming years. Towards this end, wholegenome shotgun-based draft sequences of the indica and japonica subspecies of rice were reported previously [3,4,5] while the International Rice Genome Sequencing Project (IRGSP), using a clone-by-clone approach, focused on generating a high quality, finished sequence of the rice genome [6]. Access to the rice genome has served as a catalyst for investigations on comparative genomics, functional genomics, map-based gene cloning and molecular breeding in rice [7,8]
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