Genome-wide investigation of the TGF-β superfamily in scallops

Abstract

Background: Transforming growth factor β (TGF-β) superfamily genes can regulate various processes, especially in embryogenesis, adult development, and homeostasis. To understand the evolution and divergence patterns of the TGF-β superfamily in scallops, genome-wide data from the Bay scallop (Argopecten irradians), the Zhikong scallop (Chlamys farreri) and the Yesso scallop (Mizuhopecten yessoensis) were systematically analysed using bioinformatics methods.

Results: Twelve members of the TGF-β superfamily were identified for each scallop. The phylogenetic tree showed that these genes were grouped into 11 clusters, including BMPs, ADMP, NODAL, GDF, activin/inhibin and AMH. The number of exons and the conserved motif showed some differences between different clusters, while genes in the same cluster exhibited high similarity. Selective pressure analysis revealed that the TGF-β superfamily in scallops was evolutionarily conserved. The spatiotemporal expression profiles suggested that different TGF-β members have distinct functions. Several BMP-like and NODAL-like genes were highly expressed in early developmental stages, patterning the embryonic body plan. GDF8/11-like genes showed high expression in striated muscle and smooth muscle, suggesting that these genes may play a critical role in regulating muscle growth. Further analysis revealed a possible duplication of AMH, which played a key role in gonadal growth/maturation in scallops. In addition, this study found that several genes were involved in heat and hypoxia stress in scallops, providing new insights into the function of the TGF-β superfamily.

Conclusion: Characteristics of the TGF-β superfamily in scallops were identified, including sequence structure, phylogenetic relationships, and selection pressure. The expression profiles of these genes in different tissues, at different developmental stages and under different stresses were investigated. Generally, the current study lays a foundation for further study of their pleiotropic biological functions in scallops.

Keywords: Gene expression; Genome-wide; Phylogeny; Scallop; TGF-β superfamily.

Fig. 1

Phylogenetic tree of TGF-β superfamily protein sequences. This tree consists of 164 amino acid sequences of TGF-β superfamily genes from scallops (marked in red) and other representative species. The full names of the species and the corresponding accession numbers of the TGF-β proteins are listed in Supplementary Table S3

Fig. 2

Conserved motif composition and exon-intron structure of TGF-β superfamily members in scallops. The conserved motifs, numbered from 1 to 20, are indicated by different colored boxes

Fig. 3

Conserved domains of the TGF-β superfamily proteins in scallops

Fig. 4

Temporal expression profiles of the TGF-β superfamily genes in the early developmental stages of C. farreri (A) and M. yessoensis (B)

Fig. 5

Spatial expression profiles of the TGF-β superfamily genes in the adult tissues of C. farreri (A) and M. yessoensis (B)

Fig. 6

Validation of spatial expression profiles of CfTGFβ-01 (A), CfTGFβ-02 (B), CfTGFβ-03 (C), CfTGFβ-05 (D), CfTGFβ-08 (E), and CfTGFβ-09 (F) in C. farreri. These data by RT-qPCR are expressed as the mean ± SD relative to the reference gene. The histogram represents the relative expression detected by RT-qPCR. The line graph represents TPM in the transcriptome

Fig. 7

The expression profiles of TGF-β superfamily genes under heat stress, hypoxia stress or heat plus hypoxia stress in A. irradians (A), C. farreri (B) and M. yessoensis (C)