Codon Usage Bias Analysis of FSHβ Gene among Bovine Species

Purpose In order to know codon usage bias of FSHβ gene and its differences among bovine species.

Method Polymorphisms in the coding region of FSHβ gene in 36 Binglangjiang buffalo, 32 Diandongnan buffalo, 26 gayal and 29 Zhongdian yak were detected by using the method of PCR direct sequencing. Combined with published homologous sequences of cattle, bison, goat and sheep together, the data obtained in this study was analyzed to make clear the synonymous codon usage bias of FSHβ gene and its differences among bovine species.

Result There were 20 shared preferred codons among bovine species, viz. codon UUC, CUG, AUC, GUG, UCC, AGC, CCC, CCA, ACC, ACG, GCA, UAC, CAG, ACC, GAC, GAG, UGC, AGA, AGG and codon GGC. Except for codon CCA, GCA and AGA, other codons ended with G/C. Codon CAU and CAC which encode His were different in two types of buffalo: codon CAU was preferred in river buffalo, whereas they had no usage bias in swamp buffalo. Codon AAA and AAG which encode Lys had no usage bias in river and swamp buffalo, but codon AAG was preferred in bison and goat, while codon AAA was preferred in cattle, gayal, yak and sheep. Clustering analysis based on RSCU values revealed that river and swamp buffalo clustered together, and cattle, gayal, yak and sheep clustered together, and bison and goat clustered together.

Conclusion There are some synonymous codon usage bias among the FSHβ gene of different bovine species, but the difference was small. Furthermore, river and swamp buffalo was most similar. All bovine species prefer codons ended with G/C.