In silico molecular characterization of TGF-ß 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-ß gene family in B. bufo at the genome-wide level, and a total of 28 TGF-ß gene family homologs are identified. Physicochemical characteristics of TGF-ß homologs exhibit a basic nature except for BMP1, BMP4, BMP10, BMP15, AMH, INHA, NODAL Modulator and TGFB1. Phylogenetic analysis divided the TGF-ß gene family homologs into 2 major clades along with other vertebrate species. In domain and motif composition analysis, the gene structure for all TGF-ß homologs exhibited homogeneity except BMP1. We have identified the TGF-ß propeptide domain together with the TGF-ß in all family homologs of TGF-ß superfamily. Gene structure comparisons indicated that the TGF-ß 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-ß 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-ß 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.