title: Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza.
abstract: Long terminal repeat (LTR) retrotransposons constitute a significant portion of most eukaryote genomes and can dramatically change genome size and organization. Although LTR retrotransposon content variation is well documented, the dynamics of genomic flux caused by their activity are poorly understood on an evolutionary time scale. This is primarily because of the lack of an experimental system composed of closely related species whose divergence times are within the limits of the ability to detect ancestrally related retrotransposons. The genus Oryza, with 24 species, ten genome types, different ploidy levels and over threefold genome size variation, constitutes an ideal experimental system to explore genus-level transposon dynamics. Here we present data on the discovery and characterization of an LTR retrotransposon family named RWG in the genus Oryza. Comparative analysis of transposon content (approximately 20 to 27,000 copies) and transpositional history of this family across the genus revealed a broad spectrum of independent and lineage-specific changes that have implications for the evolution of genome size and organization. In particular, we provide evidence that the basal GG genome of Oryza (O. granulata) has expanded by nearly 25% by a burst of the RWG lineage Gran3 subsequent to speciation. Finally we describe the recent evolutionary origin of Dasheng, a large retrotransposon derivative of the RWG family, specifically found in the A, B and C genome lineages of Oryza.
authors.affiliation: Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Jetty S S
authors.initials: JS
authors.lastname: Ammiraju
authors.forename: Andrea
authors.initials: A
authors.lastname: Zuccolo
authors.forename: Yeisoo
authors.initials: Y
authors.lastname: Yu
authors.forename: Xiang
authors.initials: X
authors.lastname: Song
authors.forename: Benoit
authors.initials: B
authors.lastname: Piegu
authors.forename: Frederic
authors.initials: F
authors.lastname: Chevalier
authors.forename: Jason G
authors.initials: JG
authors.lastname: Walling
authors.forename: Jianxin
authors.initials: J
authors.lastname: Ma
authors.forename: Jayson
authors.initials: J
authors.lastname: Talag
authors.forename: Darshan S
authors.initials: DS
authors.lastname: Brar
authors.forename: Phillip J
authors.initials: PJ
authors.lastname: SanMiguel
authors.forename: Ning
authors.initials: N
authors.lastname: Jiang
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
authors.forename: Olivier
authors.initials: O
authors.lastname: Panaud
authors.forename: Rod A
authors.initials: RA
authors.lastname: Wing
mesh_terms: D019143:Evolution, Molecular; D017343:Genes, Plant; D018745:Genome, Plant; D005810:Multigene Family / Q000235:genetics*; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins; D018626:Retroelements / Q000235:genetics*; D020079:Terminal Repeat Sequences
chemical_list: D010940:Plant Proteins; D018626:Retroelements