Pangenome Identification and Analysis of Terpene Synthase Gene Family Members in Gossypium

Terpene synthases (TPSs), key gatekeepers in the biosynthesis of herbivore-induced terpenes, are pivotal in the diversity of terpene chemotypes across and within plant species. Here, we constructed a gene-based pangenome of the <i>Gossypium</i> genus by integrating the genomes of 17 diploid and 10 tetraploid species. Within this pangenome, 208 <i>TPS</i> syntelog groups (SGs) were identified, comprising 2 core SGs (TPS5 and TPS42) present in all 27 analyzed genomes, 6 softcore SGs (TPS11, TPS12, TPS13, TPS35, TPS37, and TPS47) found in 25 to 26 genomes, 131 dispensable SGs identified in 2 to 24 genomes, and 69 private SGs exclusive to a single genome. The mutational load analysis of these identified <i>TPS</i> genes across 216 cotton accessions revealed a great number of splicing variants and complex splicing patterns. The nonsynonymous/synonymous Ka/Ks value for all 52 analyzed <i>TPS</i> SGs was less than one, indicating that these genes were subject to purifying selection. Of 208 <i>TPS</i> SGs encompassing 1795 genes, 362 genes derived from 102 SGs were identified as atypical and truncated. The structural analysis of <i>TPS</i> genes revealed that gene truncation is a major mechanism contributing to the formation of atypical genes. An integrated analysis of three RNA-seq datasets from cotton plants subjected to herbivore infestation highlighted nine upregulated <i>TPSs</i>, which included six previously characterized <i>TPSs</i> in <i>G. hirsutum</i> (<i>AD1_TPS10</i>, <i>AD1_TPS12</i>, <i>AD1_TPS40</i>, <i>AD1_TPS42</i>, <i>AD1_TPS89</i>, and <i>AD1_TPS104</i>), two private <i>TPSs</i> (<i>AD1_TPS100</i> and <i>AD2_TPS125</i>), and one atypical <i>TPS</i> (<i>AD2_TPS41</i>). Also, a TPS-associated coexpression module of eight genes involved in the terpenoid biosynthesis pathway was identified in the transcriptomic data of herbivore-infested <i>G. hirsutum</i>. These findings will help us understand the contributions of <i>TPS</i> family members to interspecific terpene chemotypes within <i>Gossypium</i> and offer valuable resources for breeding insect-resistant cotton cultivars.