Genome-Wide Analysis of Caffeoyl-CoA-O-methyltransferase (CCoAOMT) Family Genes and the Roles of GhCCoAOMT7 in Lignin Synthesis in Cotton

Caffeoyl coenzyme A-O-methyltransferase (CCoAOMT) has a critical function in the lignin biosynthesis pathway. However, its functions in cotton are not clear. In this research, we observed 50 CCoAOMT genes from four cotton species, including two diploids (Gossypium arboretum, 9, and Gossypium raimondii, 8) and two tetraploids (Gossypium hirsutum, 16, and Gossypium barbadense, 17), performed bioinformatic analysis, and focused on the involvement and functions of GhCCoAOMT7 in lignin synthesis of Gossypium hirsutum. CCoAOMT proteins were divided into four subgroups based on the phylogenetic tree analysis. Motif analysis revealed that all CCoAOMT proteins possess conserved Methyltransf_3 domains, and conserved structural features were identified based on the genes' exon-intron organization. A synteny analysis suggested that segmental duplications were the primary cause in the expansion of the CCoAOMT genes family. Transcriptomic data analysis of GhCCoAOMTs revealed that GhCCoAOMT2, GhCCoAOMT7, and GhCCoAOMT14 were highly expressed in stems. Subcellular localization experiments of GhCCoAOMT2, GhCCoAOMT7, and GhCCoAOMT14 showed that GhCCoAOMT2, GhCCoAOMT7, and GhCCoAOMT14 were localized in the nucleus and plasma membrane. However, there are no cis-regulatory elements related to lignin synthesis in the GhCCoAOMT7 gene promoter. GhCCoAOMT7 expression was inhibited by virus-induced gene silencing technology to obtain gene silencing lines, the suppression of GhCCoAOMT7 expression resulted in a 56% reduction in the lignin content in cotton stems, and the phloroglucinol staining area corresponding to the xylem was significantly decreased, indicating that GhCCoAOMT7 positively regulates lignin synthesis. Our results provided fundamental information regarding CCoAOMTs and highlighted their potential functions in cotton lignin biosynthesis and lignification.