Beta-galactosidase gene family genome-wide identification and expression analysis of members related to fruit softening in melon (Cucumis melo L.)

BACKGROUND: Texture quality is impotent for melon (Cucumis melo L.) fruit. β-galactosidase (β-Gal, EC 3.2.1.23) is an important cell wall glycosyl hydrolase involved in fruit softening, However, the β-Gal gene (BGALs) family hasn’t been identified genome-wide in melon. Thus, it’s necessary to conduct an in-depth bioinformatic analysis on melon BGALs family and to seek out the key members who participated in melon fruit softening. RESULTS: A total of 21 BGALs members designated as CmBGAL1-CmBGAL21 were identified genome-wide in melon, clustered into A-G seven clades. Among them, three duplications CmBGAL1:CmBGAL3, CmBGAL19:CmBGAL21, and CmBGAL20:CmBGAL21 happened. For conserved domains, besides the Glyco_hydro_35 domain (PF01301), all the members also contained the GHD domain (PF17834) except for CmBGAL12, and the Gal_Lectin (PF02140) domain existed in most CmBGALs at the C-termini. Motifs, protein secondary and tertiary structure analysis showed that the CmBGAL12 is a unique member. Moreover, protein-protein association network analysis showed that the CmBGAL12 is the only node protein. Furthermore, spatiotemporal expression pattern analysis by quantitative real-time PCR (qRT-PCR) suggested that most of CmBGALs expressed in tissues with vigorous cell wall remodeling/disassembly. In addition, cis-acting regulatory elements analysis in promoters inferred that CmBGALs might participate in diverse responsiveness to phytohormone, biotic and abiotic signaling. CONCLUSIONS: A novel clade of CmBGAL members (Clade F) related to melon fruit softening was discovered, since their expression showed a specific surge in the mature fruit of ‘HPM’ with mealy texture (softening sharply), but not in ‘HDB’ with crisp texture (softening bluntly). The homologous CmBGAL7–11 in Clade F exhibited identical spatiotemporal expression patterns may multiple genes leading to melon fruit softening. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-09006-5.