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Background  Melatonin 2-hydroxylase (M2H) is the first enzyme in the catabolism pathway of melatonin, which catalyzes the production of 2-hydroxymelatonin (2-OHM) from melatonin. The content of 2-hydroxymelatonin in plants is much higher than that of melatonin. So M2H may be a key enzyme in the metabolic pathway of melatonin.    Method  We conducted a systematic analysis of the  M2H  gene family in  Gossypium hirsutum  based on the whole genome sequence by integrating the structural characteristics, phylogenetic relationships, expression profile, and biological stress of the members of the  Gossypium hirsutum M2H  gene family.    Result  We identified 265  M2H  genes in the whole genome of  Gossypium hirsutum , which were divided into 7 clades (clades I-VII) according to phylogenetic analysis. Most  M2H  members in each group had similar motif composition and gene structure characteristics. More than half of  GhM2H  members contain ABA-responsive elements and MeJA-responsive elements. Under different stress conditions, the expression levels of the gene changed, indicating that  GhM2H  members were involved in the regulation of abiotic stress. Some genes in the  GhM2H  family were involved in regulating melatonin levels in cotton under salt stress, and some genes were regulated by exogenous melatonin.    Conclusion  This study is helpful to explore the function of GhM2H, the downstream metabolism gene of melatonin in cotton, and lay the foundation for better exploring the molecular mechanism of melatonin improving cotton's response to abiotic stress.    Supplementary Information  The online version contains supplementary material available at 10.1186/s40659-021-00358-y.

Genome-wide identification and characteristic analysis of the downstream melatonin metabolism gene GhM2H in Gossypium hirsutum L.