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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Publications at this Location » Publication #362376

Research Project: Advanced Genomic and Bioinformatic Tools for Accelerated Cotton Genetic Improvement

Location: Crop Germplasm Research

Title: Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution

item HUANG, GAI - Peking University
item WU, ZHIGUO - Wuhan University
item Percy, Richard
item BAI, MINGZHOU - Bgi Shenzhen
item LI, YANG - Wuhan University
item Frelichowski, James - Jim
item HU, JIANG - Nextomics Biosciences Co, Ltd
item WANG, KUN - Wuhan University
item Yu, John
item ZHU, YUXIAN - Wuhan University

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/4/2020
Publication Date: 4/13/2020
Citation: Huang, G., Wu, Z., Percy, R.G., Bai, M., Li, Y., Frelichowski, J.E., Hu, J., Wang, K., Yu, J., Zhu, Y. 2020. Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution. Nature Genetics.

Interpretive Summary: Decoding cultivated cotton genomes opens the door to solve the mystery of their evolutionary history and phylogenetic relationship for more effective exploitation. In this study, we sequenced, assembled, and analyzed three cultivated cotton species: a tree cotton, a Levant cotton, and an Upland cotton. Compelling evidences were obtained from the study to suggest that all current existent A-genomes in these three species may originate from a common ancestor. Neither tree cotton nor Levant cotton was the true donor of A-genome to Upland cotton during its preceded hybridization. The divergent times for the respective A-genomes were established, and their genomic architecture and gene annotation were provided. The large body of detailed data and new knowledge we report here will advance many basic and applied studies into how multi-genome plants develop, how they respond to their environments, and how their genetics can be manipulated for improvement of crop plants.

Technical Abstract: Uncertainty for the actual A-genome donor of widely cultivated allotetraploid Gossypium hirsutum has persisted and stimulated multiple speculations. Here, we sequenced and assembled A1-genome G. herbaceum for the first time, updated G. arboreum and G. hirsutum genomes using high-coverage PacBio sequencing and Hi-C data, which reduced at least 65.7% of gaps in current genomes comparing to released respective assemblies. Compared with genomes-sequenced plants in Malvales, both A1- and A2-genome harbor the most abundant transposable elements (TEs) reaching up to approximately 80%. TEs as the major drive force shaped genomic structure and size in Malvales plants. Based on in-depth comparative genomics, phylogenetics, population genetic analyses and Gaussian probability density function assay, we obtained compelling evidences to suggest that all current existing A-genomes, including A1, A2 and the At-subgenome in Gossypium hirsutum, may originate from a common ancestor named A0 and allotetraploid formation preceded the speciation of A1 and A2. Our work solves the biological puzzle regarding previous conflict phylogenetic data and it provides valuable genomic resources to facilitate cotton genetic improvement.