Genome-wide identification of the TGF-β superfamily and their expression in the Chinese mitten crab Eriocheir sinensis

Abstract

Transforming growth factor-β superfamily genes are multifunctional cytokines that play central roles in the regulation of cell proliferation, differentiation, apoptosis, adhesion, and migration. Identifying the TGF-β superfamily in crabs could provide a basis for elucidating the genetic regulatory mechanism of growth, development, sex differentiation and environmental adaptation. To understand the complexity and evolution of the TGF-β superfamily in the Chinese mitten crab Eriocheir sinensis, this study comprehensively and systematically analysed this superfamily in the genome of E. sinensis. A total of 9 TGF-β superfamily genes have been identified, including EsBMP2, EsBMP3, EsBMP7, EsBMP10, EsBMP15, EsGDF8, EsUnivin, EsINHB and EsINHBB. A wide variation in the number of motifs and CDSs was found among different subfamilies. The expression of EsBMP2 and EsBMP7 suggested that these genes may be the main genes controlling embryonic development in E. sinensis. EsBMP2, EsBMP7 and EsBMP10 are very highly expressed in the gills. The TGF-β superfamily genes presented different expression patterns during limb regeneration and molting. In addition, this gene family also responds to environmental stresses, including nanoplastic stress, cadmium stress, air exposure, and high-salinity stress, which provides a new perspective for understanding the strong tolerance and adaptability of crabs to environmental stress. To our knowledge, this study is the first genome-wide investigation of the TGF-β superfamily in crabs. This study identified the sequence structure, phylogenetic relationship, and gene expression profiles of the TGF-β superfamily genes in the Chinese mitten crab, and the above results lay a foundation for further investigation of the evolution and biological functions of this gene family.

Keywords: Chinese mitten crab; Gene expression; Genome-wide; Phylogeny; TGF-β superfamily.

Fig. 1

Phylogenetic tree of the TGF-β superfamily protein sequences. The tree consisted of 191 amino acid sequences of TGF-β superfamily genes from E. sinensis (marked in red) and other representative species.

Fig. 2

Conserved motifs and gene structure analysis of the TGF-β superfamily in E. sinensis. Boxes of different colours represent different motifs; UTR: untranslated region; CDS: coding sequence.

Fig. 3

Conserved domains of the TGF-β superfamily proteins in E. sinensis.

Fig. 4

Expression patterns of the TGF-β superfamily at different developmental stages (a) and in different tissues (b) of E. sinensis. M: megalopae; J: juvenile; A: adult; a: abdomen; c: cephalothorax; go: gonad; m: muscle; h: hepatopancreas; gi: gill; e: eyestalk; d: day.

Fig. 5

Expression profiles of EsBMP2 (a), EsBMP7 (b), EsBMP10 (c), and EsGDF8 (d) in different tissues of E. sinensis. The histogram represents the relative expression detected by RT-qPCR (mean ± SD). The line graph represents TPM in the transcriptome.

Fig. 6

Heatmap of the gene expression of the TGF-β superfamily in the muscle and eyestalk of E. sinensis at different regeneration stages (3 d, 15 d, and 30 d). C: control; d: day.

Fig. 7

Heatmap (a) and line graph (b) of the expression of the TGF-β superfamily genes in the gills of E. sinensis at different molting stages.

Fig. 8

Heatmap of TGF-β superfamily genes in the gills and hepatopancreas (a) and line graph of their expression in the gills (b) of E. sinensis under different abiotic stresses. C: control; Np: nanoplastic stress; Cd: cadmium exposure; NP-Cd: nanoplastic and cadmium exposure.

Fig. 9

Heatmap of TGF-β superfamily genes (a) and line graph of their expression (b) in the gills of E. sinensis under air exposure stress. C: control; d: day.

Fig. 10

Heatmap of TGF-β superfamily genes (a) and line graph of their expression (b) in haemocytes of E. sinensis under acute high-salinity stress. h: hour; 0, 16, 28, and 35 represent the salinity of 0 ppt, 16 ppt, 28 ppt, and 35 ppt, respectively.