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To gain access to the molecular mechanisms of spermatogenesis, the genes from a subtractive screen of the carp testis cDNA library were investigated. In this study, a male-specific homolog of the meichroacidin gene, called MSAP (MORN motif-containing sperm-specific axonemal protein), was isolated and further characterized. Database search and zoo-Western blot analyses revealed that MSAP homologs might be widespread in a variety of phyla but divergent in their C-terminal length and sequences. Carp MSAP is exclusively transcribed in testis, while mouse meichroacidin message is present in gonads of both sexes, although especially enriched in testis. In mouse, meichroacidin is expressed in male germ cells of meiotic stages, while carp MSAP is expressed during late spermiogenesis and accumulated in mature spermatozoa, in which MSAP is localized to the basal body and flagellum. Contrary to mouse meichroacidin revealed previously, existence of multiple pI variants of MSAP in two-dimensional electrophoresis suggested regulatory differences of the homologous molecules between mammal and teleost. These results indicate that MSAP homologs may play different roles in male germline development between vertebrates. Proteomic analysis and immunolocalization disclosed that MSAP is associated with septin7, a conserved GTPase that may participate in cellular morphogenesis, in the basal body of carp sperm. These findings suggest the involvement of carp MSAP in flagellar differentiation during spermiogenesis.