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

Cotton (<italic>Gossypium</italic> 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 <italic>Gossypium</italic> 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 <italic>de novo</italic> assembly of 336 <italic>Gossypium</italic> 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 <italic>Gossypium tomentosum</italic> and <italic>Gossypium mustelinum</italic> formed an early diverging clade rooted by diploids, followed by splitting two sister clades of <italic>Gossypium darwinii</italic>–<italic>Gossypium barbadense</italic> and <italic>Gossypium hirsutum</italic>–<italic>Gossypium ekmanianum</italic>–<italic>Gossypium stephensii</italic>. Within the <italic>G. hirsutum</italic> clade the resolution of cultivated accessions was less polyphyletic with landrace and wild accessions than in <italic>G. barbadense</italic> suggesting some selection on plastome in the domestication of this adaptable species of cotton. The nucleotide diversity of <italic>G. hirsutum</italic> was higher than that of <italic>G. barbadense</italic>. We specifically compared the plastomes of <italic>G. hirsutum</italic> and <italic>G. barbadense</italic> 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. [ABSTRACT FROM AUTHOR]