Genome-wide identification, characterization and expression analysis of the BMP family associated with beak-like teeth in Oplegnathus

Abstract

Bone morphogenetic proteins (BMPs), which belong to the transforming growth factor beta (TGF-β) family, are critical for the control of developmental processes such as dorsal-ventral axis formation, somite and tooth formation, skeletal development, and limb formation. Despite Oplegnathus having typical healing beak-like teeth and tooth development showing a trend from discrete to healing, the potential role of BMPs in the development of the beak-like teeth is incompletely understood. In the present study, 19 and 16 BMP genes were found in O. fasciatus and O. punctatus, respectively, and divided into the BMP2/4/16, BMP5/6/7/8, BMP9/10, BMP12/13/14, BMP3/15 and BMP11 subfamilies. Similar TGFb and TGF_β gene domains and conserved protein motifs were found in the same subfamily; furthermore, two common tandem repeat genes (BMP9 and BMP3a-1) were identified in both Oplegnathus fasciatus and Oplegnathus punctatus. Selection pressure analysis revealed 13 amino acid sites in the transmembrane region of BMP3, BMP7, and BMP9 proteins of O. fasciatus and O. punctatus, which may be related to the diversity and functional differentiation of genes within the BMP family. The qPCR-based developmental/temporal expression patterns of BMPs showed a trend of high expression at 30 days past hatching (dph), which exactly corresponds to the ossification period of the bones and beak-like teeth in Oplegnathus. Tissue-specific expression was found for the BMP4 gene, which was upregulated in the epithelial and mesenchymal tissues of the beak-like teeth, suggesting that it also plays a regulatory role in the development of the beak-like teeth in O. punctatus. Our investigation not only provides a scientific basis for comprehensively understanding the BMP gene family but also helps screen the key genes responsible for beak-like tooth healing in O. punctatus and sheds light on the developmental regulatory mechanism.

Keywords: BMP; Oplegnathus fasciatus; Oplegnathus punctatus; adaptive evolution; gene expression; gene family; tooth development.

FIGURE 1

Beak-like tooth morphology of Oplegnathus. (A) Photographs of the overall morphology of the beak-like teeth of Oplegnathus. (B) Enlarged image of locoregional details of the inner teeth of Oplegnathus. (C) Enlarged image of locoregional details of the outer teeth of Oplegnathus. (D–F) Reconstructed micro-CT scans showing the nested dentition of adult Oplegnathus. (E) Three-dimensional arrangement of the inner and outer teeth of Oplegnathus. (G–I) Micro-CT scans showing the developmental changes of the nested dentition of Oplegnathus at 30, 50 and 70 dph. (J–L) Alizarin red staining results of beak-like teeth in different developmental stages of Oplegnathus. (J) indicates that the 45-dph beak-like teeth are in a cartilaginous state and separately arranged, (K) indicates that the 50-dph beak-like teeth are ossified and have a tendency to heal, and (L) indicates that complete healing of the beak-like teeth has occurred by 90 dph (scale bars: 5 mm in (A); 1 mm in (B,C,I); 2 mm in (D,F); 500 μm in (G,H); 100 μm in F and H; and 100 μm in (J–L).

FIGURE 2

The conserved BMP domains and motifs in Oplegnathus and T. rubripes.

FIGURE 3

Multiple sequence alignment of the conserved domains of proteins in the Oplegnathus BMP gene family.

FIGURE 4

Chromosome localization of BMP genes in O. fasciatus and O. punctatus. (A) Represents O. fasciatus; (B) represents O. punctatus. The prefix “F" in the chromosome names in Panel (B) indicates that the reference genomic data are from female O. punctatus.

FIGURE 5

Chromosome localization and collinearity analysis of BMP genes in O. fasciatus and O. punctatus. (A) Represents O. fasciatus; (B) represents O. punctatus.

FIGURE 6

Phylogenetic tree of BMP gene family members in 11 species.

FIGURE 7

Heatmap of gene copy number comparisons of BMP genes in 11 species. (A) Shows a summary of the gene copy number comparison. (B) Shows the detailed gene copy number comparison. The different colors in the Figure refer to different BMP subfamilies, the numbers on the heatmap indicate the number of gene copies, and the gray color indicates the deletion of the BMP genes.

FIGURE 8

Relative expression levels of BMP genes in selected tissues of O. punctatus. (A) Shows the tissue-specific expression patterns of BMP2, BMP3b-1, BMP3b-2 and BMP4; (B) shows the tissue-specific expression patterns of BMP6, BMP7a, BMP7b and BMP8; (C) shows the tissue-specific expression patterns of BMP9, BMP10, BMP11-1, BMP11-2, BMP11-3 and BMP16. G represents the gills; L represents the liver; S represents the spleen; B represents the brain; J represents the surrounding tissue of the beak-like teeth; I represents the intestine; M represents the muscle; H represents the heart. Different lowercase letters above the standard error bars indicate significant differences in expression.

FIGURE 9

Relative expression levels of BMP genes in selected developmental stages of O. punctatus. (A1,A2) Represent temporal expression pattern one; (A1) shows the temporal expression pattern of BMP2, BMP3b-1 and BMP4; (A2) shows the temporal expression pattern of BMP11-1, BMP11-2, BMP11-3, and BMP16. (B1,B2) Represent temporal expression pattern two; (B1) shows the temporal expression pattern of BMP3b-2, BMP7a and BMP7b; (B2) shows the temporal expression pattern of BMP6, BMP8 and BMP10. (C) Represents temporal expression pattern three, the temporal expression pattern of BMP9 .

FIGURE 10

Expression of beak-like teeth-specific BMP genes at critical nodes in beak-like teeth development of O. punctatus. The upper panel indicates the results of alizarin red bone staining at critical time of beak-like teeth development, and the lower panel of heatmap indicates the chronological expression of BMP genes that are highly expressed in the surrounding tissue of the beak-like teeth.