title: Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set.
abstract: Oryza (23 species; 10 genome types) contains the world's most important food crop - rice. Although the rice genome serves as an essential tool for biological research, little is known about the evolution of the other Oryza genome types. They contain a historical record of genomic changes that led to diversification of this genus around the world as well as an untapped reservoir of agriculturally important traits. To investigate the evolution of the collective Oryza genome, we sequenced and compared nine orthologous genomic regions encompassing the Adh1-Adh2 genes (from six diploid genome types) with the rice reference sequence. Our analysis revealed the architectural complexities and dynamic evolution of this region that have occurred over the past approximately 15 million years. Of the 46 intact genes and four pseudogenes in the japonica genome, 38 (76%) fell into eight multigene families. Analysis of the evolutionary history of each family revealed independent and lineage-specific gain and loss of gene family members as frequent causes of synteny disruption. Transposable elements were shown to mediate massive replacement of intergenic space (>95%), gene disruption, and gene/gene fragment movement. Three cases of long-range structural variation (inversions/deletions) spanning several hundred kilobases were identified that contributed significantly to genome diversification.
authors.affiliation: Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA.
authors.forename: Jetty S S
authors.initials: JS
authors.lastname: Ammiraju
authors.forename: Fei
authors.initials: F
authors.lastname: Lu
authors.forename: Abhijit
authors.initials: A
authors.lastname: Sanyal
authors.forename: Yeisoo
authors.initials: Y
authors.lastname: Yu
authors.forename: Xiang
authors.initials: X
authors.lastname: Song
authors.forename: Ning
authors.initials: N
authors.lastname: Jiang
authors.forename: Ana Clara
authors.initials: AC
authors.lastname: Pontaroli
authors.forename: Teri
authors.initials: T
authors.lastname: Rambo
authors.forename: Jennifer
authors.initials: J
authors.lastname: Currie
authors.forename: Kristi
authors.initials: K
authors.lastname: Collura
authors.forename: Jayson
authors.initials: J
authors.lastname: Talag
authors.forename: Chuanzhu
authors.initials: C
authors.lastname: Fan
authors.forename: Jose Luis
authors.initials: JL
authors.lastname: Goicoechea
authors.forename: Andrea
authors.initials: A
authors.lastname: Zuccolo
authors.forename: Jinfeng
authors.initials: J
authors.lastname: Chen
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Bennetzen
authors.forename: Mingsheng
authors.initials: M
authors.lastname: Chen
authors.forename: Scott
authors.initials: S
authors.lastname: Jackson
authors.forename: Rod A
authors.initials: RA
authors.lastname: Wing
mesh_terms: D019143:Evolution, Molecular; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D008969:Molecular Sequence Data; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000502:physiology
chemical_list: D010940:Plant Proteins