Genome-wide identification and structural analysis of the BMP gene family in Triplophysa dalaica

Abstract

Background: Bone morphogenetic proteins (BMPs) are part of the transforming growth factor beta (TGF-β) superfamily and play crucial roles in bone development, as well as in the formation and maintenance of various organs. Triplophysa dalaica, a small loach fish that primarily inhabits relatively high elevations and cooler water bodies, was the focus of this study. Understanding the function of BMP genes during the morphogenesis of T. dalaica helps to clarify the mechanisms of its evolution and serves as a reference for the study of BMP genes in other bony fishes. The data for the T. dalaica transcriptome and genome used in this investigation were derived from the outcomes of our laboratory sequencing.

Results: This study identified a total of 26 BMP genes, all of which, except for BMP1, possess similar TGF-β structural domains. We conducted an analysis of these 26 BMP genes, examining their physicochemical properties, subcellular localization, phylogenetic relationships, covariance within and among species, chromosomal localization, gene structure, conserved motifs, conserved structural domains, and expression patterns. Our findings indicated that three BMP genes were associated with unstable proteins, while 11 BMP genes were located within the extracellular matrix. Furthermore, some BMP genes were duplicated, with the majority being enriched in the GO:0008083 pathway, which is related to growth factor activity. It was hypothesized that genes within the BMP1/3/11/15 subgroup (Group I) play a significant role in the growth and development of T. dalaica. By analyzing the expression patterns of proteins in nine tissues (gonad, kidney, gill, spleen, brain, liver, fin, heart, and muscle), we found that BMP genes play diverse regulatory roles during different stages of growth and development and exhibit characteristics of division of labor.

Conclusions: This study contributes to a deeper understanding of BMP gene family member expression patterns in high-altitude, high-salinity environments and provides valuable insights for future research on the BMP gene family in bony fishes.

Keywords: Bone morphogenetic protein; Gene expression; Gene family; Triplophysa dalaica.

Fig. 1

Expression of different genes in each tissue. a,b,c Three letters and the same letter indicate no significant difference, and different letters indicate significant differences

Fig. 2

Phylogenetic analysis of the BMP genes of T. dalaica and selected species. The different colors on the outer ring in the figure represent the different groups, the different species are represented by different colors, and the BMP gene of T. dalaica is marked by a red star

Fig. 3

Analysis of BMP gene covariance in T. dalaica. The gray line indicates the genome covariance of T. dalaica, and the colored line connecting the BMP genes indicates the duplication of BMP genes in T. dalaica. The position of the BMP genes on the chromosomes is indicated by the short black line, and the density of the genes on each chromosome is shown at the same time

Fig. 4

Analysis of the BMP gene expression pattern in T. dalaica. The square color scale of the heatmap indicates the TPM values after row normalization; the specific values are marked in the color block, and the maximum value is indicated in red

Fig. 5

Interspecies covariance analysis of T. dalaica with D. rerio and C. carpio. a represents the covariance results of T. dalaica with D. rerio, b represents the covariance results of T. dalaica with C. carpio, gray lines represent the covariance blocks of T. dalaica with D. rerio and C. carpio, and red lines represent the highlighted BMP gene blocks. The abbreviations "Td", "Dr" and "Cc" denote T. dalaica, D. rerio and C. carpio, respectively

Fig. 6

Chromosomal locations of BMP genes in the T. dalaica genome

Fig. 7

Gene structure of the BMP gene of T. dalaica. The phylogenetic tree on the left was constructed in MEGA11 based on the neighbor‒joining method, with a bootstrap value of 1000, and different colors represent different groups

Fig. 8

Conserved motifs of the BMP gene of T. dalaica. a The phylogenetic tree on the left was constructed in MEGA11 based on the neighbor‒joining method, with a bootstrap value of 1000, and different colors represent different groups. b All motifs were identified by the MEME database, and different colored blocks represent different motifs

Fig. 9

Structural domains of the BMP gene of T. dalaica. The phylogenetic tree on the left was constructed in MEGA11 based on the neighbor‒joining method, with a bootstrap value of 1000, and different colors represent different groups