title: Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes.
abstract: Comparative genomics is a powerful tool to decipher gene and genome evolution. Placing multiple genome comparisons in a phylogenetic context improves the sensitivity of evolutionary inferences. In the genus Oryza, this comparative approach can be used to investigate gene function, genome evolution, domestication, polyploidy, and ecological adaptation. A large genomic region surrounding the MONOCULM1 (MOC1) locus was chosen for study in 14 Oryza species, including 10 diploids and 4 allotetraploids. Sequencing and annotation of 18 bacterial artificial chromosome clones for these species revealed highly conserved gene colinearity and structure in the MOC1 region. Since the Oryza radiation about 14 Mya, differences in transposon amplification appear to be responsible for the different current sizes of the Oryza genomes. In the MOC1 region, transposons were only conserved between genomes of the same type (e.g., AA or BB). In addition to the conserved gene content, several apparent genes have been generated de novo or uniquely retained in the AA lineage. Two different 3-gene segments have been inserted into the MOC1 region of O. coarctata (KK) or O. sativa by unknown mechanism(s). Large and apparently noncoding sequences flanking the MOC1 gene were observed to be under strong purifying selection. The allotetraploids Oryza alta and Oryza minuta were found to be products of recent polyploidization, less than 1.6 and 0.4 Mya, respectively. In allotetraploids, pseudogenization of duplicated genes was common, caused by large deletions, small frame-shifting insertions/deletions, or nonsense mutations.
authors.affiliation: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Lu
authors.forename: Jetty S S
authors.initials: JS
authors.lastname: Ammiraju
authors.forename: Abhijit
authors.initials: A
authors.lastname: Sanyal
authors.forename: Shengli
authors.initials: S
authors.lastname: Zhang
authors.forename: Rentao
authors.initials: R
authors.lastname: Song
authors.forename: Jinfeng
authors.initials: J
authors.lastname: Chen
authors.forename: Guisheng
authors.initials: G
authors.lastname: Li
authors.forename: Yi
authors.initials: Y
authors.lastname: Sui
authors.forename: Xiang
authors.initials: X
authors.lastname: Song
authors.forename: Zhukuan
authors.initials: Z
authors.lastname: Cheng
authors.forename: Antonio Costa
authors.initials: AC
authors.lastname: de Oliveira
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Bennetzen
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
authors.forename: Rod A
authors.initials: RA
authors.lastname: Wing
authors.forename: Mingsheng
authors.initials: M
authors.lastname: Chen
mesh_terms: D001483:Base Sequence; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D008969:Molecular Sequence Data; D009154:Mutation; D009687:Nuclear Proteins / Q000235:genetics*; D012275:Oryza / Q000235:genetics*; D011003:Ploidies; D017422:Sequence Analysis, DNA
chemical_list: D009687:Nuclear Proteins