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.