title: The cytonuclear dimension of allopolyploid evolution: an example from cotton using rubisco.
abstract: During allopolyploid speciation, two divergent nuclear genomes merge, yet only one (usually the maternal) of the two sets of progenitor organellar genomes is maintained. Rubisco (1,5-bisphosphate carboxylase/oxygenase) is composed of nuclear-encoded small subunits (SSUs) and plastome-encoded large subunits (LSUs), providing an ideal system to explore the evolutionary process of cytonuclear accommodation. Here, we take initial steps in this direction, using Gossypium allopolyploids as our model. SSU copies from divergent (5-10 My) progenitor diploids ("A" and "D" genomes) were combined at the time of polyploid formation 1-2 Ma, with the LSU encoded by the maternal A-genome parent. LSU genes from A- and D-genome diploids and AD-genome allopolyploids were sequenced, revealing several nonsynonymous substitutions and suggesting the possibility of differential selection on the nuclear-encoded rbcS partner following allopolyploid formation. Sequence data for the rbcS gene family revealed nonreciprocal homoeologous recombination between A- and D-rbcS homoeologs in all polyploid species but not in a synthetic intergenomic F1 hybrid, demonstrating "gene conversion" during allopolyploid evolution. All progenitor rbcS genes are retained and expressed in the five extant allopolyploid species, but analysis of the leaf transcriptome showed that A-homoeologs are preferentially expressed in both the allopolyploid and hybrid, consistent with the maternal origin of rbcL. Although rbcS genes from both progenitor genomes are expressed, some appear to have experienced mutations that may represent cytonuclear coevolution.
authors.affiliation: Department of Ecology, Evolution and Organismal Biology, Iowa State University, IA, USA.
authors.forename: Lei
authors.initials: L
authors.lastname: Gong
authors.forename: Armel
authors.initials: A
authors.lastname: Salmon
authors.forename: Mi-Jeong
authors.initials: MJ
authors.lastname: Yoo
authors.forename: Kara K
authors.initials: KK
authors.lastname: Grupp
authors.forename: Zining
authors.initials: Z
authors.lastname: Wang
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
authors.forename: Jonathan F
authors.initials: JF
authors.lastname: Wendel
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution / Q000235:genetics; D001483:Base Sequence; D002467:Cell Nucleus / Q000235:genetics*; D003433:Crosses, Genetic; D018076:DNA, Complementary / Q000235:genetics; D004171:Diploidy; D019143:Evolution, Molecular; D005785:Gene Conversion; D018506:Gene Expression Regulation, Plant; D020131:Genes, Duplicate / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D014644:Genetic Variation; D003368:Gossypium / Q000201:enzymology* / Q000235:genetics*; D059765:Homologous Recombination / Q000235:genetics; D006824:Hybridization, Genetic; D007438:Introns / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D010802:Phylogeny; D011123:Polyploidy; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012273:Ribulose-Bisphosphate Carboxylase / Q000737:chemistry / Q000235:genetics*; D016415:Sequence Alignment
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger; D012273:Ribulose-Bisphosphate Carboxylase