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

Luo Lei; Junxian Zhu; Chen Chen; Yongchang Wang; Congcong Wu; Ming Qi; Yakun Wang; Xiaoli Liu; Xiaoyou Hong; Lingyun Yu; Haigang Chen; Chengqing Wei; Yihui Liu; Wei Li; Xinping Zhu

doi:10.3389/fgene.2023.1109478

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

Front Genet. 2023 Feb 1:14:1109478. doi: 10.3389/fgene.2023.1109478. eCollection 2023.

Authors

Luo Lei^{1

2}, Junxian Zhu^{1

3}, Chen Chen¹, Yongchang Wang¹, Congcong Wu¹, Ming Qi⁴, Yakun Wang¹, Xiaoli Liu¹, Xiaoyou Hong¹, Lingyun Yu¹, Haigang Chen¹, Chengqing Wei¹, Yihui Liu¹, Wei Li¹, Xinping Zhu^{1

2

3}

Affiliations

¹ Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China.
² Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu, China.
³ College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China.
⁴ Zhejiang Fisheries Technical Extension Center, Hangzhou, China.

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.

Keywords: Pelodiscus sinensis; bone morphogenetic protein; gene family; genome-wide; sex differentiation; transcriptome.

Grants and funding

This work was funded by the National Key R and D Program of China (2018YFD0900201), the National Natural Science Foundation of China (32102792), Funding by Science and Technology Projects in Guangzhou (202102021220), the Central Public-Interest Scientific Institution Basal Research Fund, CAFS (2020TD35), the National Freshwater Genetic Resource Center (NFGR-2022), the Guangdong Agricultural Research System (2019KJ150), the China-ASEAN Maritime Cooperation Fund (CAMC-2018F).