Genome organization and evolution of rice (Oryza sativa L.)

The organization and evolution of chromosome 8 and the nucleotide-binding site-leucine-rich repeat (NBS-LRR)-encoding gene family in the genome of rice, Oryza sativa L., were determined in this study. Toward these goals, three large-insert genomic DNA libraries of maize inbred line B73 were generated in pBeloBAC11, pECBAC1, and pCLD04541 vectors using BamHI, EcoRI and HindIII, respectively. The three libraries collectively contain 251,137 clones, and have average insert sizes of 110, 140 and 115 kilobase pairs, respectively, insert-empty clones of <5% and chloroplast DNA clones of <2%, thus providing 12.3 haploid genome equivalents. Cloned maize DNAs were stable in the vectors, and the clones are highly amenable to genome research of maize and related species.; The genome organization and evolution of chromosome 8 and the NBS-LRR family in rice were determined using the two rice subspecies, indica and japonica, as well as maize as references. The result showed that different regions of chromosome 8 evolve at different rates; some regions evolve rapidly, whereas others are highly conserved. These differential evolutionary rates were associated with recombination rate, sequence organization and functions of containing genes and generated segmental structures within the chromosome.; The NBS-LRR family in the two subspecies of rice, indica and japonica, is organized in clusters of single subfamilies and superclusters of two or more subfamilies of monophyletic or polyphyletic origin. Japonica is estimated to have about 62 loci for 12 of its 14 NBS-LRR subfamilies, and indica has about 142 loci for ten of its 14 NBS-LRR subfamilies. Indica seems to have twice as many as NBS-LRR loci than japonica. Combined data analysis of both genotypes revealed that at least 73 loci of the NBS-LRR family were originated before the split between indica and japonica 2–3 million years ago, and since, 51 of the 73 loci significantly evolved. Moreover, at least 51 and 10 new clusters and superclusters were originated in the indica or japonica genome during the past 2–3 million years, respectively. The rapid evolution and organization of the NBS-LRR family in rice may result from a process of the “birth-and-death”, supercluster formation and adaptive selection.