title: Analysis of collinear regions of Oryza AA and CC genomes.
abstract: Comparative analyses of genome structure and sequence of closely related species have yielded insights into the evolution and function of plant genomes. A total of 103,844 BAC end sequences delegated approximately 73.8 Mb of O. officinalis that belongs to the CC genome type of the rice genus Oryza were obtained and compared with the genome sequences of rice cultivar, O. sativa ssp. japonica cv. Nipponbare. We found that more than 45% of O. officinalis genome consists of repeat sequences, which is higher than that of Nipponbare cultivar. To further investigate the evolutionary divergence of AA and CC genomes, two BAC-contigs of O. officinalis were compared with the collinear genomic regions of Nipponbare. Of 57 genes predicted in the AA genome orthologous regions, 39 had orthologs in the regions of the CC genome. Alignment of the orthologous regions indicated that the CC genome has undergone expansion in both genic and intergenic regions through primarily retroelement insertion. Particularly, the density of RNA transposable elements was 17.95% and 1.78% in O. officinalis and O. sativa, respectively. This explains why the orthologous region is about 100 kb longer in the CC genome in comparison to the AA genome.
authors.affiliation: College of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Feng
authors.forename: Tao
authors.initials: T
authors.lastname: Huang
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhao
authors.forename: Jingjie
authors.initials: J
authors.lastname: Zhu
authors.forename: Zhixin
authors.initials: Z
authors.lastname: Lin
authors.forename: Bin
authors.initials: B
authors.lastname: Han
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics; D004251:DNA Transposable Elements; D018745:Genome, Plant; D023281:Genomics; D005838:Genotype; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D010940:Plant Proteins