title: Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza.
abstract: Despite knowledge that polyploidy is widespread and a major evolutionary force in flowering plant diversification, detailed comparative molecular studies on polyploidy have been confined to only a few species and families. The genus Oryza is composed of 23 species that are classified into ten distinct 'genome types' (six diploid and four polyploid), and is emerging as a powerful new model system to study polyploidy. Here we report the identification, sequence and comprehensive comparative annotation of eight homoeologous genomes from a single orthologous region (Adh1-Adh2) from four allopolyploid species representing each of the known Oryza genome types (BC, CD, HJ and KL). Detailed comparative phylogenomic analyses of these regions within and across species and ploidy levels provided several insights into the spatio-temporal dynamics of genome organization and evolution of this region in 'natural' polyploids of Oryza. The major findings of this study are that: (i) homoeologous genomic regions within the same nucleus experience both independent and parallel evolution, (ii) differential lineage-specific selection pressures do not occur between polyploids and their diploid progenitors, (iii) there have been no dramatic structural changes relative to the diploid ancestors, (iv) a variation in the molecular evolutionary rate exists between the two genomes in the BC complex species even though the BC and CD polyploid species appear to have arisen <2 million years ago, and (v) there are no clear distinctions in the patterns of genome evolution in the diploid versus polyploid species.
authors.affiliation: Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USABiodiversity Synthesis Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USADepartment of Genetics, University of Georgia, Athens, GA 30602-7223, USAState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, ChinaDepartment of Agronomy, Purdue University, West Lafayette, IN 47907-2054, USADepartment of Horticulture, Michigan State University, East Lansing, MI 48823, USA.
authors.forename: Jetty S S
authors.initials: JS
authors.lastname: Ammiraju
authors.forename: Chuanzhu
authors.initials: C
authors.lastname: Fan
authors.forename: Yeisoo
authors.initials: Y
authors.lastname: Yu
authors.forename: Xiang
authors.initials: X
authors.lastname: Song
authors.forename: Karen A
authors.initials: KA
authors.lastname: Cranston
authors.forename: Ana Clara
authors.initials: AC
authors.lastname: Pontaroli
authors.forename: Fei
authors.initials: F
authors.lastname: Lu
authors.forename: Abhijit
authors.initials: A
authors.lastname: Sanyal
authors.forename: Ning
authors.initials: N
authors.lastname: Jiang
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: 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: D022202:Chromosomes, Artificial, Bacterial; D019143:Evolution, Molecular; D017343:Genes, Plant; D018745:Genome, Plant; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D018626:Retroelements; D057891:Tetraploidy
chemical_list: D018626:Retroelements