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Pif is an acid matrix protein that is known to be a key macromolecule in the shell nacre formation of molluscs. However, the investigation into the Pif gene at the whole genome level has seldom been carried out, limiting the systematic understanding of its evolution and function. The Yesso scallop (Patinopecten yessoensis), an ancient bivalve with important economic value and evolutionary status, has suffered severe shell infestation by Polydora that badly damaged shell structures. In this study, a total of eight Pif homologous genes (PyPif1–7 and PyBMSP) were identified in the whole genome of the Yesso scallop with diverse gene structures. Two conserved functional domains, VWA and chitin-binding domains, were detected in all PyPif proteins, although with variation in number of copies. Phylogenetic analysis of the Pifs among different molluscan species suggested the molecular evolution of Pif genes was consistent with taxonomic relationships. High sequence divergence of Pif proteins existed among the different species, but a high level of similarity was found in BMSPs, which own four VWA domains. High expression levels of PyBMSP in the central mantles of the healthy and Polydora shell infested Yesso scallops indicated its important role in shell formation. The other PyPifs (PyPif2, PyPif3, PyPif4, PyPif5, PyPif6) may function when the shell is injured, as significantly increased expression levels of these genes were found in the edge mantles of the infested scallops. In addition, haemocytes may also participate in shell repair by up-regulating the expression of PyPifs. This study provides new insights into the evolution and expression patterns of Pif genes in molluscs, which are valuable for elucidating the mechanism of shell repair and formation.

Porphyrins, one of the most common shell pigments, are by-products of the haem pathway. 5-Aminolaevulinate synthase (ALAS) is the first and rate-limiting enzyme in this pathway and has been well studied in vertebrate species. However, the function of ALAS in shell colouration has been poorly studied in molluscs, which are renowned for their colourful shells. In the present study, an ALAS gene, named PyALAS, was identified through whole-genome scanning in the Yesso scallop (Patinopecten yessoensis), an economically and evolutionarily important bivalve species in which the shell colour represents polymorphism. Two conserved domains were detected in the PyALAS protein sequence, including a Preseq-ALAS domain and a 5-ALAS domain, confirming the identification of PyALAS. Phylogenetic analysis of the ALAS proteins among various invertebrate and vertebrate species revealed a high consistency between the molecular evolution of ALAS and the species taxonomy. PyALAS was ubiquitously expressed in most adult tissues of the Yesso scallop. The left mantle expressed a significantly higher level of PyALAS than the right side in brown scallops, whereas there was no significant difference in white scallops. Significantly different expression levels of PyALAS was also detected between the two different shell colour strains. These data indicate that PyALAS plays an important role in shell colouration in Yesso scallops and the present study provides new insights into the molecular mechanism of shell colouration in molluscs.