Genome-wide identification, phylogeny and expression analysis of the bmp gene family associated with development and skeleton deformity in cobia (Rachycentron canadum)

Bone morphogenetic proteins (BMPs) are critical for controlling skeletal development of fish, which has significant influence on external morphology, functional exercise and even survival rate in aquaculture breeding. In this study, a total of 19 bmp genes were identified in cobia (Rachycentron canadum) and these genes were divided into six sub-families according to phylogenetic analysis, including bmp1, bmp3/11/15, bmp2/4/16, bmp9/10, bmp13/14 and bmp5/6/7/8 subfamily. The identified cobia BMPs, excepting for BMP1, all possessed a similar TGF_beta domain. Phylogenetic analysis revealed that the cobia bmp genes were most closely related to those of the golden pompano (Trachinotus ovatus). The tissue distribution of these bmps in adult cobia revealed that the highest expression of most bmp genes was found in the Meckel’s cartilage; the highest expression of bmp4 was identified in the vertebrae; five other bmps were highly expressed in non-skeleton tissues including liver, heart and gill. The expression of bmp genes were also identified during the larvae and juvenile stages (1–30 dph), and most bmps revealed no certain expression pattern excepting for bmp8a, which showed significantly lower mRNA level before 15 dph and then increased to a significantly higher level. Due to the high incidence of deformity during the larvae and juvenile stages of cobia, the difference of bmp mRNA levels between deformed and normal skeletons (the Meckel’s cartilage and vertebrae) were also investigated to understand the involvement of bmp genes in skeletal deformity. The results showed that most of the bmp genes were significantly inhibited in the deformed Meckel’s cartilage excepting for bmp1, bmp5 and bmp7b; while in the deformed vertebrae, expression of most bmps were significantly increased excepting for five genes (bmp1, bmp4, bmp5, bmp7b and bmp13b).