3.8 MITF gene family analysis
In shellfish, it has been reported that microphthalmia-associated transcription factor (MITF) plays an important role in immune defense and shell color formation (Zhang, et al., 2017; Zhang, et al., 2018). The MITF gene family consists of three subfamilies, namely TFEB, TFEC, and TFE3, in the Pfam database (Zhao, Zhao, Zhou, & Mattei, 1993). In this study, we detected two genes from the Asian Clam genome, namely EVM0008002 and EVM0031201, which were identified as MITF genes. Most species in the phylogenetic analysis possessed one or two MITF genes, while L. gigantea was apparently missing MITF genes (Supporting Information Table S14). This finding implies that L. gigantea may have lost some functions of immune defense or shell color due to the deletion of MITF genes. Additionally, there were five and seven MITF genes in C. virginica and L. anatina , respectively (Supporting Information Table S14). Combined with the gene family expansion and contraction analysis, we found the MITF gene family expanded in C. virginica and L. anatina and contracted inL. gigantea . Proteins from all species were aligned to a super-alignment matrix with the guidance of protein alignment, and the genic tree comprising MITF family genes from all involved species was successfully constructed using MUSCLE (Figure 5). Firstly, MITF family genes originated from the same species showed the most recent genetic relationships. Secondly, like family Mytilidae represented by B. platifrons and M. coruscus , family Ostreidae represented byC. gigas and C. virginica , those from the same families were clustered together. Additionally, the clustering relationships of MITF family genes were also similar to those shown by the phylogenetic tree of single-copy orthologs. This finding indirectly corroborates the reliability of the phylogenetic relationship analysis. Meanwhile, we observed that C. fluminea had a greater genetic distance from other marine bivalves via the MITF and phylogenetic tree analyses. It is probably because the divergence of Corbiucula from marine bivalves, and the migration from marine to freshwater is an ancient event.