title: Extensive and biased intergenomic nonreciprocal DNA exchanges shaped a nascent polyploid genome, Gossypium (cotton).
abstract: Genome duplication is thought to be central to the evolution of morphological complexity, and some polyploids enjoy a variety of capabilities that transgress those of their diploid progenitors. Comparison of genomic sequences from several tetraploid (AtDt) Gossypium species and genotypes with putative diploid A- and D-genome progenitor species revealed that unidirectional DNA exchanges between homeologous chromosomes were the predominant mechanism responsible for allelic differences between the Gossypium tetraploids and their diploid progenitors. Homeologous gene conversion events (HeGCEs) gradually subsided, declining to rates similar to random mutation during radiation of the polyploid into multiple clades and species. Despite occurring in a common nucleus, preservation of HeGCE is asymmetric in the two tetraploid subgenomes. At-to-Dt conversion is far more abundant than the reciprocal, is enriched in heterochromatin, is highly correlated with GC content and transposon distribution, and may silence abundant A-genome-derived retrotransposons. Dt-to-At conversion is abundant in euchromatin and genes, frequently reversing losses of gene function. The long-standing observation that the nonspinnable-fibered D-genome contributes to the superior yield and quality of tetraploid cotton fibers may be explained by accelerated Dt to At conversion during cotton domestication and improvement, increasing dosage of alleles from the spinnable-fibered A-genome. HeGCE may provide an alternative to (rare) reciprocal DNA exchanges between chromosomes in heterochromatin, where genes have approximately five times greater abundance of Dt-to-At conversion than does adjacent intergenic DNA. Spanning exon-to-gene-sized regions, HeGCE is a natural noninvasive means of gene transfer with the precision of transformation, potentially important in genetic improvement of many crop plants.
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602 Department of Plant Biology, University of Georgia, Athens, Georgia 30602.
authors.forename: Hui
authors.initials: H
authors.lastname: Guo
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602 Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University, Tangshan, Hebei 063000, China.
authors.forename: Xiyin
authors.initials: X
authors.lastname: Wang
authors.affiliation: Munich Information Center for Protein Sequences Institute for Bioinformatics and System Biology, German Research Center for Environmental Health, 85764 Neuherberg, Germany.
authors.forename: Heidrun
authors.identifier: http://orcid.org/0000-0001-7830-8564
authors.initials: H
authors.lastname: Gundlach
authors.affiliation: Munich Information Center for Protein Sequences Institute for Bioinformatics and System Biology, German Research Center for Environmental Health, 85764 Neuherberg, Germany.
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.affiliation: Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi 39762.
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Peterson
authors.affiliation: Jamie Whitten Delta States Research Center, United States Department of Agriculture-Agricultural Research Service, Stoneville, Mississippi 38776.
authors.forename: Brian E
authors.initials: BE
authors.lastname: Scheffler
authors.affiliation: Department of Crop and Soil Science and Coastal Plain Experiment Station, Tifton, Georgia 31794.
authors.forename: Peng W
authors.initials: PW
authors.lastname: Chee
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602 Department of Plant Biology, University of Georgia, Athens, Georgia 30602 Department of Crop and Soil Science and Department of Genetics, University of Georgia, Athens, Georgia 30602 paterson@plantbio.uga.edu.
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D021901:DNA, Intergenic / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics*; D019143:Evolution, Molecular; D056426:Genetic Loci; D018745:Genome, Plant; D003368:Gossypium / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011123:Polyploidy; D018626:Retroelements / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D021901:DNA, Intergenic; D018744:DNA, Plant; D018626:Retroelements
keywords: cotton; heterochromatin; homeologous gene conversion; polyploidy