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

作者:Huang, G (Huang, Gai)[ 1,2 ] ; Wu, ZG (Wu, Zhiguo)[ 3 ] ; Percy, RG (Percy, Richard G.)[ 4 ] ; Bai, MZ (Bai, Mingzhou)[ 5 ] ; Li, Y (Li, Yang)[ 3 ] ; Frelichowski, JE (Frelichowski, James E.)[ 4 ] ; Hu, J (Hu, Jiang)[ 6 ] ; Wang, K (Wang, Kun)[ 3 ] ; Yu, JZ (Yu, John Z.)[ 4 ] ; Zhu, YX (Zhu, Yuxian)[ 1 ]

NATURE GENETICS

卷: 52 期: 5 页: 516-+

DOI: 10.1038/s41588-020-0607-4

出版年:MAY 2020

在线发表日期: APR 2020

文献类型:Article

摘要

Upon assembling the first Gossypium herbaceum (A(1)) genome and substantially improving the existing Gossypium arboreum (A(2)) and Gossypium hirsutum ((AD)(1)) genomes, we showed that all existing A-genomes may have originated from a common ancestor, referred to here as A(0), which was more phylogenetically related to A(1) than A(2). Further, allotetraploid formation was shown to have preceded the speciation of A(1) and A(2). Both A-genomes evolved independently, with no ancestor-progeny relationship. Gaussian probability density function analysis indicates that several long-terminal-repeat bursts that occurred from 5.7 million years ago to less than 0.61 million years ago contributed compellingly to A-genome size expansion, speciation and evolution. Abundant species-specific structural variations in genic regions changed the expression of many important genes, which may have led to fiber cell improvement in (AD)(1). Our findings resolve existing controversial concepts surrounding A-genome origins and provide valuable genomic resources for cotton genetic improvement.

Assembly of the first Gossypium herbaceum genome and improved Gossypium arboreum and Gossypium hirsutum genomes provide insights into the phylogenetic relationships and origin history of cotton A-genomes.

关键词

KeyWords Plus:PHYLOGENETIC ANALYSIS; DRAFT GENOME; FIBER; PREDICTION; TOOL; RECONSTRUCTION; SELECTION; ALIGNMENT; PROGRAM; FINDER

作者信息

通讯作者地址:

Wuhan University Wuhan Univ, Inst Adv Studies, Wuhan, Peoples R China.

United States Department of Agriculture (USDA) USDA ARS, Crop Germplasm Res Unit, Southern Plains Agr Res Ctr, College Stn, TX 77840 USA.

通讯作者地址: Zhu, YX (通讯作者)

Wuhan Univ, Inst Adv Studies, Wuhan, Peoples R China.

通讯作者地址: Yu, JZ (通讯作者)

USDA ARS, Crop Germplasm Res Unit, Southern Plains Agr Res Ctr, College Stn, TX 77840 USA.

地址:

[ 1 ]‎ Wuhan Univ, Inst Adv Studies, Wuhan, Peoples R China

[ 2 ]‎ Peking Univ, Sch Life Sci, State Key Lab Prot & Plant Gene Res, Beijing, Peoples R China

[ 3 ]‎ Wuhan Univ, Coll Life Sci, Wuhan, Peoples R China

[ 4 ]‎ USDA ARS, Crop Germplasm Res Unit, Southern Plains Agr Res Ctr, College Stn, TX 77840 USA

[ 5 ]‎ BGI Shenzhen, BGI Genom, Shenzhen, Peoples R China

[ 6 ]‎ Next Biosci Inst, Wuhan, Peoples R China

电子邮件地址:john.yu@usda.gov; zhuyx@whu.edu.cn