J Syst Evol

• Research Article •    

Genetic diversity and evolution of the plastome in allotetraploid cotton (Gossypium spp.)

Xin-Lin Yan1,2†, Sheng-Long Kan2,3†, Mei-Xia Wang4†, Yong-Yao Li2, Luke R. Tembrock5, Wen-Chuang He2, Li-Yun Nie2, Guan-Jing Hu2,6, Dao-Jun Yuan1,7,8*, Xiong-Feng Ma6*, and Zhi-Qiang Wu1,2*   

  1. 1 College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
    2 Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China;
    3 Marine College, Shandong University, Weihai 264209, China;
    4 Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang 330045, China;
    5 Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA;
    6 National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
    7 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
    8 College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
    These authors contributed equally to this work.
    *Author for correspondence. Dao-Jun Yuan. E-mail:robert@mail.hzau.edu.cn;Xiong-Feng Ma. E-mail:maxf_caas@163.com;Zhi-Qiang Wu. E-mail:wuzhiqiang@caas.cn
  • Received:2023-11-30 Accepted:2024-03-17 Online:2024-04-16

Abstract: Cotton (Gossypium spp.) is a vital global source of renewable fiber and ranks among the world's most important cash crops. While extensive nuclear genomic data of Gossypium has been explored, the organellar genomic resources of allotetraploid cotton, remain largely untapped at the population level. The plastid genome (plastome) is well suited for studying plant species relationships and diversity due to its nonrecombinant uniparental inheritance. Here, we conducted de novo assembly of 336 Gossypium plastomes, mainly from domesticated cultivars, and generated a pan-plastome level resource for population structure and genetic diversity analyses. The assembled plastomes exhibited a typical quadripartite structure and varied in length from 160 103 to 160 597 bp. At the species level, seven allotetraploid species were resolved into three clades, where Gossypium tomentosum and Gossypium mustelinum formed an early diverging clade rooted by diploids, followed by splitting two sister clades of Gossypium darwiniiGossypium barbadense and Gossypium hirsutumGossypium ekmanianumGossypium stephensii. Within the G. hirsutum clade the resolution of cultivated accessions was less polyphyletic with landrace and wild accessions than in G. barbadense suggesting some selection on plastome in the domestication of this adaptable species of cotton. The nucleotide diversity of G. hirsutum was higher than that of G. barbadense. We specifically compared the plastomes of G. hirsutum and G. barbadense to find mutational hotspots within each species as potential molecular markers. These findings contribute a valuable resource for exploring cotton evolution as well as in the breeding of new cotton cultivars and the preservation of wild and cultivated germplasm.

Key words: crop wild relatives, G. barbadense, G. hirsutum, pan-plastome, polyploidy