In silico molecular characterization of TGF-β gene family in Bufo bufo: genome-wide analysis

Abstract

Bufo bufo is a living example of evolutionary processes due to its numerous physiological and ecological adaptations. This is the first study to genetically characterize the TGF-β gene family in B. bufo at the genome-wide level, and a total of 28 TGF-β gene family homologs are identified. Physicochemical characteristics of TGF-β homologs exhibit a basic nature except for BMP1, BMP4, BMP10, BMP15, AMH, INHA, NODAL Modulator and TGFB1. Phylogenetic analysis divided the TGF-β gene family homologs into 2 major clades along with other vertebrate species. In domain and motif composition analysis, the gene structure for all TGF-β homologs exhibited homogeneity except BMP1. We have identified the TGF-β propeptide domain together with the TGF-β in all family homologs of TGF-β superfamily. Gene structure comparisons indicated that the TGF-β gene family have arisen by gene duplications. We also identified 10 duplicated gene pairs, all of which were detected to be segmental duplications. The Ka/Ks test ratio findings for every pair of genes revealed that none of the ratios surpassed 1 except for one gene pair (INHA/BMP1), indicating that these proteins are under positive selection. Circos analysis showed that TGF-β gene family homologs are arranged in 11 dispersed clusters and all were segmentally arrayed in the genome. This study provides a molecular basis for TGF-β ligand protein functional analysis and may serve as a reference for in-depth phylogenomics and may promote the development of novel strategies.

Communicated by Ramaswamy H. Sarma

Keywords:

• Bufo bufo
• TGF-β gene family
• genetic characterization
• phylogenetic

Novelty statement

First study to molecular characterize the TGF- β Gene family in Bufo bufo.

Disclosure statement

Authors have declare no conflict of interest.

Data availability statement

All data is included in the manuscript or as a supplementary material.

Authors’ Contribution

Mehwish Sultana: Conceptualization, Investigation, Data analysis, original draft writing; Muhammad Tayyab: Original draft writing; Investigation, Data analysis; Sunil: Data analysis, Review and editing; Shakeela Parveen: Supervision, Data analysis, Review and editing; Saba Saeed: Investigation, Review and editing; Muhammad Hussain: original draft writing, Review and editing; Saman Shabbir: Original draft writing; Zainab Riaz: Original draft writing. All authors read and approved the final manuscript.