title: Evolutionary Conservation and Divergence of Gene Coexpression Networks in Gossypium (Cotton) Seeds.
abstract: The cotton genus (Gossypium) provides a superior system for the study of diversification, genome evolution, polyploidization, and human-mediated selection. To gain insight into phenotypic diversification in cotton seeds, we conducted coexpression network analysis of developing seeds from diploid and allopolyploid cotton species and explored network properties. Key network modules and functional associations were identified related to seed oil content and seed weight. We compared species-specific networks to reveal topological changes, including rewired edges and differentially coexpressed genes, associated with speciation, polyploidy, and cotton domestication. Network comparisons among species indicate that topologies are altered in addition to gene expression profiles, indicating that changes in transcriptomic coexpression relationships play a role in the developmental architecture of cotton seed development. The global network topology of allopolyploids, especially for domesticated G. hirsutum, resembles the network of the A-genome diploid more than that of the D-genome parent, despite its D-like phenotype in oil content. Expression modifications associated with allopolyploidy include coexpression level dominance and transgressive expression, suggesting that the transcriptomic architecture in polyploids is to some extent a modular combination of that of its progenitor genomes. Among allopolyploids, intermodular relationships are more preserved between two different wild allopolyploid species than they are between wild and domesticated forms of a cultivated cotton, and regulatory connections of oil synthesis-related pathways are denser and more closely clustered in domesticated vs. wild G. hirsutum. These results demonstrate substantial modification of genic coexpression under domestication. Our work demonstrates how network inference informs our understanding of the transcriptomic architecture of phenotypic variation associated with temporal scales ranging from thousands (domestication) to millions (speciation) of years, and by polyploidy.
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, USA.
authors.forename: Guanjing
authors.initials: G
authors.lastname: Hu
authors.affiliation: Agricultural Research Organization (Volcani Center), Bet Dagan, Israel.
authors.forename: Ran
authors.initials: R
authors.lastname: Hovav
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, USA.
authors.forename: Corrinne E
authors.initials: CE
authors.lastname: Grover
authors.affiliation: Agricultural Research Organization (Volcani Center), Bet Dagan, Israel.
authors.forename: Adi
authors.initials: A
authors.lastname: Faigenboim-Doron
authors.affiliation: Agricultural Research Organization (Volcani Center), Bet Dagan, Israel.
authors.forename: Noa
authors.initials: N
authors.lastname: Kadmon
authors.affiliation: Biology Department, Brigham Young University, Provo, USA.
authors.forename: Justin T
authors.initials: JT
authors.lastname: Page
authors.affiliation: Biology Department, Brigham Young University, Provo, USA.
authors.forename: Joshua A
authors.initials: JA
authors.lastname: Udall
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, USA.
authors.forename: Jonathan F
authors.initials: JF
authors.lastname: Wendel
mesh_terms: D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant; D003368:Gossypium / Q000235:genetics*; D006801:Humans; D011123:Polyploidy; D012639:Seeds / Q000235:genetics*; D012641:Selection, Genetic
keywords: Gossypium; domestication; gene coexpression network; oil seed; polyploid evolution