title: A BAC physical map of aus rice cultivar 'Kasalath', and the map-based genomic sequence of 'Kasalath' chromosome 1.
abstract: Comparative analysis using available genomic resources within closely related species is an effective way to investigate genomic sequence and structural diversity. Rice (Oryza sativa L.) has undergone significant physiological and morphological changes during its domestication and local adaptation. We present a complete bacterial artificial chromosome (BAC) physical map for the aus rice cultivar 'Kasalath', which covers 90% of the sequence of temperate japonica rice cultivar 'Nipponbare'. Examination of physical distances between computational and experimental measurements of 'Kasalath' BAC insert size revealed the presence of more than 500 genomic regions that appear to have significant chromosome structural changes between the two cultivars. In particular, a genomic region on the long arm of 'Kasalath' chromosome 11 carrying a disease-resistance gene cluster was greatly expanded relative to the 'Nipponbare' genome. We also decoded 41.37 Mb of high-quality genomic sequence from 'Kasalath' chromosome 1. Extensive comparisons of chromosome 1 between 'Kasalath' and 'Nipponbare' led to the discovery of 317,843 single-nucleotide polymorphisms (SNPs) and 66,331 insertion/deletion (indel) sites. Nearly two-thirds of the expressed genes on rice chromosome 1 carried natural variations involving SNPs and/or indels that resulted in substitutions, insertions or deletions of amino acids in one cultivar relative to the other. We also observed gain and loss of genes caused by large indels. This study provides an important framework and an invaluable dataset for further understanding of the molecular mechanisms underlying the evolution and functions of the rice genome.
authors: Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki , 305-8602, Japan.
authors: Hiroyuki
authors: H
authors: Kanamori
authors: Masaki
authors: M
authors: Fujisawa
authors: Satoshi
authors: S
authors: Katagiri
authors: Youko
authors: Y
authors: Oono
authors: Hiroko
authors: H
authors: Fujisawa
authors: Wataru
authors: W
authors: Karasawa
authors: Kanako
authors: K
authors: Kurita
authors: Harumi
authors: H
authors: Sasaki
authors: Satomi
authors: S
authors: Mori
authors: Masao
authors: M
authors: Hamada
authors: Yoshiyuki
authors: Y
authors: Mukai
authors: Takayuki
authors: T
authors: Yazawa
authors: Hiroshi
authors: H
authors: Mizuno
authors: Nobukazu
authors: N
authors: Namiki
authors: Takuji
authors: T
authors: Sasaki
authors: Yuichi
authors: Y
authors: Katayose
authors: Takashi
authors: T
authors: Matsumoto
authors: Jianzhong
authors: J
authors: Wu
mesh_terms: D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D032461:Chromosomes, Plant / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D014644:Genetic Variation; D018745:Genome, Plant; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics*; D020161:Physical Chromosome Mapping
keywords: BAC physical map; Oryza sativa L.; comparative genomics; expressed gene; rice resource; structural variation