title: Polyploid evolution in Oryza officinalis complex of the genus Oryza.
abstract: BACKGROUND
  Polyploidization is a prominent process in plant evolution, whereas the mechanism and tempo-spatial process remained poorly understood. Oryza officinalis complex, a polyploid complex in the genus Oryza, could exemplify the issues not only for it covering a variety of ploidy levels, but also for the pantropical geographic pattern of its polyploids in Asia, Africa, Australia and Americas, in which a pivotal genome, the C-genome, witnessed all the polyploidization process.
  
  
  RESULTS
  Tracing the C-genome evolutionary history in Oryza officinalis complex, this study revealed the genomic relationships, polyploid forming and diverging times, and diploidization process, based on phylogeny, molecular-clock analyses and fluorescent in situ hybridization using genome-specific probes. Results showed that C-genome split with B-genome at ca. 4.8 Mya, followed by a series of speciation of C-genome diploids (ca. 1.8-0.9 Mya), which then partook in successive polyploidization events, forming CCDD tetraploids in ca. 0.9 Mya, and stepwise forming BBCC tetraploids between ca. 0.3-0.6 Mya. Inter-genomic translocations between B- and C-genomes were identified in BBCC tetraploid, O. punctata. Distinct FISH (fluorescent in situ hybridization) patterns among three CCDD species were visualized by C-genome-specific probes. B-genome was modified before forming the BBCC tetraploid, O. malampuzhaensis.
  
  
  CONCLUSIONS
  C-genome, shared by all polyploid species in the complex, had experienced different evolutionary history particularly after polyploidization, e.g., inter-genomic exchange in BBCC and genomic invasion in CCDD tetraploids. It diverged from B-genome at 4.8 Mya, then participated in the tetraploid formation spanning from 0.9 to 0.3 Mya, and spread into tropics of the disjunct continents by transcontinentally long-distance dispersal, instead of vicariance, as proposed by this study, given that the continental splitting was much earlier than the C-genome species radiation. We also find reliable evidence indicated that an extinct BB diploid species in Asia was presumptively the direct genomic donor of their sympatric tetraploids.
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, PR China. wangbsh@ibcas.ac.cn
authors.forename: Baosheng
authors.initials: B
authors.lastname: Wang
authors.forename: Zhuoya
authors.initials: Z
authors.lastname: Ding
authors.forename: Wei
authors.initials: W
authors.lastname: Liu
authors.forename: Jin
authors.initials: J
authors.lastname: Pan
authors.forename: Changbao
authors.initials: C
authors.lastname: Li
authors.forename: Song
authors.initials: S
authors.lastname: Ge
authors.forename: Daming
authors.initials: D
authors.lastname: Zhang
mesh_terms: D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D017343:Genes, Plant; D018745:Genome, Plant; D017404:In Situ Hybridization, Fluorescence; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D011123:Polyploidy; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant