Through multiple sequence alignment and phylogenetic analysis, the subgrouping of the crustacean hyperglycemic hormone (CHH) family was updated using the most complete, nonredundant sequence data set. All sequences from insects were clustered into a distinct subbranch with characters closer to CHH subfamily I. Several sequences that are controversial in their nomenclature and classification are discussed. The motif configuration of CHHs differs from that of molt-inhibiting hormone or gonad-inhibiting hormone in both N and C termini. These two motifs approach each other in tertiary structure models, and the motif preference reveals the critical roles of these regions in functional specificity. Two types of exon organizations of the CHH family genes were observed. Four-exon Chh genes were found in a wide range of pan-crustacean (crustacean and hexapod) taxa, except for the penaeid species, from which the 3-exon Chh genes were reported. Meanwhile, the 3-exon structure was found in the Mih gene and Moih genes from one brachyuran species. Combining gene scan skill and exon splicing rules found in this study, we define three more novel sequences from two insect genomes. The pattern of the exon-exon junction within the mature peptide segment is preserved in all CHH family members.
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