Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, USA.
Agricultural Research Organization (Volcani Center), Bet Dagan, Israel.
Genome Biol Evol. 2016 Dec 1;8(12):3765-3783. doi: 10.1093/gbe/evw280.
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.
棉花属（Gossypium）为研究多样化、基因组进化、多倍体化和人为选择提供了一个优越的系统。为了深入了解棉花种子的表型多样化，我们对二倍体和异源多倍体棉花物种的发育种子进行了共表达网络分析，并探讨了网络特性。确定了与种子含油量和种子重量相关的关键网络模块和功能关联。我们比较了物种特异性网络，以揭示与物种形成、多倍体化和棉花驯化相关的拓扑变化，包括重连边缘和差异共表达基因。物种间的网络比较表明，拓扑结构发生了变化，除了基因表达谱外，这表明转录组共表达关系的变化在棉花种子发育的发育架构中发挥了作用。异源多倍体的全局网络拓扑结构，特别是驯化的 G. hirsutum，与其 A 基因组二倍体的网络更为相似，而与其 D 基因组亲本的网络更为相似，尽管其在含油量方面表现出 D 样表型。与异源多倍体相关的表达修饰包括共表达水平优势和超越表达，这表明多倍体的转录组结构在某种程度上是其前体基因组的模块化组合。在异源多倍体中，两个不同的野生异源多倍体物种之间的模块间关系比野生和栽培棉之间的关系更为保留，并且与油合成相关途径的调控连接在栽培棉中比在野生棉中更为密集和更紧密地聚集。这些结果表明，在驯化过程中，基因共表达发生了实质性的修饰。我们的工作展示了网络推断如何告知我们对与时间尺度从数千（驯化）到数百万（物种形成）相关的表型变异的转录组结构的理解，以及多倍体化的影响。
