Genome-wide identification, evolution and expression analysis of bone morphogenetic protein (BMP) gene family in chinese soft-shell turtle (Pelodiscus sinensis)

Abstract

Introduction: Bone morphogenetic proteins (BMPs) play a crucial role in bone formation and differentiation. Recent RNA-Seq results suggest that BMPs may be involved in the sex differentiation of P. sinensis, yet more relevant studies about BMPs in P. sinensis are lacking.Methods: Herein, we identified BMP gene family members, analyzed the phylogeny, collinear relationship, scaffold localization, gene structures, protein structures, transcription factors and dimorphic expression by using bioinformatic methods based on genomic and transcriptomic data of P. sinensis. Meanwhile, qRT-PCR was used to verify the RNA-Seq results and initially explore the function of the BMPs in the sex differentiation of P. sinensis.Results: A total of 11 BMP genes were identified, 10 of which were localized to their respective genomic scaffolds. Phylogenetic analysis revealed that BMP genes were divided into eight subfamilies and shared similar motifs (“WII”, “FPL”, “TNHA”, “CCVP”, and “CGC”) and domain (TGF-β superfamily). The results of the sexually dimorphic expression profile and qRT-PCR showed that Bmp2, Bmp3, Bmp15l, Bmp5, Bmp6 and Bmp8a were significantly upregulated in ovaries, while Bmp2lb, Bmp7, Bmp2bl and Bmp10 were remarkable upregulated in testes, suggesting that these genes may play a role in sex differentiation of P. sinensis.Discussion: Collectively, our comprehensive results enrich the basic date for studying the evolution and functions of BMP genes in P. sinensis.

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

“…Utilizing the whole-genome data of T. dalaica , we conducted a comparison to eliminate duplicate sequences, considering other species such as D. rerio , H. sapiens , C. carpio , and X. laevis . Furthermore, by integrating information from relevant literature [ 31 , 32 ], we successfully identified a total of 26 BMP gene sequences ( BMP1a - BMP16 ) in T. dalaica , which were subsequently categorized into five groups: BMP1/3/11/15 (Group I), BMP12/13/14 (Group II), BMP2/4/16 (Group III), BMP9/10 (Group IV), and BMP5/6/7 (Group V).…”

Identification of Sex-Specific Markers and Candidate Genes Using WGS Sequencing Reveals a ZW-Type Sex-Determination System in the Chinese Soft-Shell Turtle (Pelodiscus sinensis)

“…However, there is marked sexual dimorphism in body growth and calipash when comparing male and female P. sinensis, and males have higher economic and industrial value than females [3][4][5]. Therefore, there is an urgent need to breed monosexual populations of male P. sinensis to benefit the entire aquaculture industry [6,7]. Currently, sex-controlled breeding has been widely applied in aquaculture species [8,9].…”