title: Comparative genomic de-convolution of the cotton genome revealed a decaploid ancestor and widespread chromosomal fractionation.
abstract: The 'apparently' simple genomes of many angiosperms mask complex evolutionary histories. The reference genome sequence for cotton (Gossypium spp.) revealed a ploidy change of a complexity unprecedented to date, indeed that could not be distinguished as to its exact dosage. Herein, by developing several comparative, computational and statistical approaches, we revealed a 5× multiplication in the cotton lineage of an ancestral genome common to cotton and cacao, and proposed evolutionary models to show how such a decaploid ancestor formed. The c. 70% gene loss necessary to bring the ancestral decaploid to its current gene count appears to fit an approximate geometrical model; that is, although many genes may be lost by single-gene deletion events, some may be lost in groups of consecutive genes. Gene loss following cotton decaploidy has largely just reduced gene copy numbers of some homologous groups. We designed a novel approach to deconvolute layers of chromosome homology, providing definitive information on gene orthology and paralogy across broad evolutionary distances, both of fundamental value and serving as an important platform to support further studies in and beyond cotton and genomics communities.
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA.|Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei, 063000, China.|School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, 063000, China.
authors.forename: Xiyin
authors.initials: X
authors.lastname: Wang
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA.|Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
authors.forename: Hui
authors.initials: H
authors.lastname: Guo
authors.affiliation: Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei, 063000, China.|School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, 063000, China.
authors.forename: Jinpeng
authors.initials: J
authors.lastname: Wang
authors.affiliation: Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei, 063000, China.|School of Sciences, North China University of Science and Technology, Tangshan, Hebei, 063000, China.
authors.forename: Tianyu
authors.initials: T
authors.lastname: Lei
authors.affiliation: Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei, 063000, China.|School of Sciences, North China University of Science and Technology, Tangshan, Hebei, 063000, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.affiliation: Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei, 063000, China.|School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, 063000, China.
authors.forename: Zhenyi
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei, 063000, China.|School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, 063000, China.
authors.forename: Yuxian
authors.initials: Y
authors.lastname: Li
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA.
authors.forename: Tae-Ho
authors.initials: TH
authors.lastname: Lee
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA.
authors.forename: Jingping
authors.initials: J
authors.lastname: Li
authors.affiliation: Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.|School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, 85721, USA.|Data2Bio LLC, 2079 Roy J. Carver Co-Lab, Ames, IA, 50011, USA.
authors.forename: Haibao
authors.initials: H
authors.lastname: Tang
authors.affiliation: Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei, 063000, China.|School of Sciences, North China University of Science and Technology, Tangshan, Hebei, 063000, China.
authors.forename: Dianchuan
authors.initials: D
authors.lastname: Jin
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA.|Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
mesh_terms: D002099:Cacao / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics*; D020440:Gene Duplication; D017343:Genes, Plant; D018745:Genome, Plant; D003368:Gossypium / Q000235:genetics*; D008954:Models, Biological; D010802:Phylogeny; D011123:Polyploidy; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D027843:Vitis / Q000235:genetics
keywords: cotton (Gossypium spp.); gene colinearity; gene loss; genomics; polyploidy