title: Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice.
abstract: Insertions and precise eliminations of transposable elements generated numerous transposon insertion polymorphisms (TIPs) in rice (Oryza sativa). We observed that TIPs represent more than 50% of large insertions and deletions (>100 bp) in the rice genome. Using a comparative genomic approach, we identified 2,041 TIPs between the genomes of two cultivars, japonica Nipponbare and indica 93-11. We also identified 691 TIPs between Nipponbare and indica Guangluai 4 in the 23-Mb collinear regions of chromosome 4. Among them, retrotransposon-based insertion polymorphisms were used to reveal the evolutionary relationships of these three cultivars. Our conservative estimates suggest that the TIPs generated approximately 14% of the genomic DNA sequence differences between subspecies indica and japonica. It was also found that more than 10% of TIPs were located in expressed gene regions, representing an important source of genetic variation. Transcript evidence implies that these TIPs induced a series of genetic differences between two subspecies, including interrupting host genes, creating different expression forms, drastically changing intron length, and affecting expression levels of adjacent genes. These analyses provide genome-wide insights into evolutionary history and genetic variation of rice.
authors.affiliation: National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China.
authors.forename: Xuehui
authors.initials: X
authors.lastname: Huang
authors.forename: Guojun
authors.initials: G
authors.lastname: Lu
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhao
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Liu
authors.forename: Bin
authors.initials: B
authors.lastname: Han
mesh_terms: D001483:Base Sequence; D004251:DNA Transposable Elements; D018076:DNA, Complementary; D019143:Evolution, Molecular; D015870:Gene Expression; D018745:Genome, Plant; D007438:Introns; D012275:Oryza / Q000235:genetics*; D011110:Polymorphism, Genetic; D011401:Promoter Regions, Genetic; D018626:Retroelements
chemical_list: D004251:DNA Transposable Elements; D018076:DNA, Complementary; D018626:Retroelements