Campus Units

Ecology, Evolution and Organismal Biology

Document Type

Article

Publication Version

Published Version

Publication Date

8-2020

Journal or Book Title

G3: Genes, Genomes, Genetics

Volume

10

Issue

8

First Page

2879

Last Page

2892

DOI

10.1534/g3.120.401362

Abstract

Gossypium hirsutum L. (Upland cotton) has an evolutionary history involving inter-genomic hybridization, polyploidization, and subsequent domestication. We analyzed the developmental dynamics of the cotton fiber transcriptome accompanying domestication using gene coexpression networks for both joint and homoeologous networks. Remarkably, most genes exhibited expression for at least one homoeolog, confirming previous reports of widespread gene usage in cotton fibers. Most coexpression modules comprising the joint network are preserved in each subgenomic network and are enriched for similar biological processes, showing a general preservation of network modular structure for the two co-resident genomes in the polyploid. Interestingly, only one fifth of homoeologs co-occur in the same module when separated, despite similar modular structures between the joint and homoeologous networks. These results suggest that the genome-wide divergence between homoeologous genes is sufficient to separate their co-expression profiles at the intermodular level, despite conservation of intramodular relationships within each subgenome. Most modules exhibit D-homoeolog expression bias, although specific modules do exhibit A-homoeolog bias. Comparisons between wild and domesticated coexpression networks revealed a much tighter and denser network structure in domesticated fiber, as evidenced by its fewer modules, 13-fold increase in the number of development-related module member genes, and the poor preservation of the wild network topology. These results demonstrate the amazing complexity that underlies the domestication of cotton fiber.

Comments

This article is published as Gallagher, Joseph P., Corrinne E. Grover, Guanjing Hu, Josef J. Jareczek, and Jonathan F. Wendel. "Conservation and Divergence in Duplicated Fiber Coexpression Networks Accompanying Domestication of the Polyploid Gossypium hirsutum L." G3: Genes, Genomes, Genetics 10, no. 8 (2020): 2879-2892. doi: 10.1534/g3.120.401362.

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.

Copyright Owner

Gallagher et al.

Language

en

File Format

application/pdf

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