Analysis of Codon Use Characteristics of CSN3 Gene in River and Swamp Buffalo (Bubalus bubalis)

In this study, codon usage features of milk casein gene CSN3 for both river and swamp buffalo, and the differences in codon usage and evolutionary relationships between buffalo and other species were analyzed based on the data of CSN3 gene from 54 river buffalo and 70 swamp buffalo, and the data of Bos taurus, Bos mutus, Bos bison, Ovis aries, Mus musculus and Homo sapiens recruited from NCBI database. The results showed that codon usage features of CSN3 gene in two types of buffalo were similar. River and swamp buffalo had 26 and 27 biased codon, respectively. Among them, strongly biased codons for both types of buffalo were codon GUU, UCA, AGU, CCA, AGG, GGU and GGA (RSCU ≥ 2). Two types of buffalo only have one difference in the use of the Asp codon, that is, the river buffalo were not bias toward codon GAU and GAC, while swamp buffalo was bias toward codon GAC. Synonymous codon RSCUs of the encoding Asp and Cys of the river type buffalo were 1, while synonymous codon RSCU of swamp buffalo only codon Cys was 1. Furthermore, CSN3 gene of all species in this study were bias toward the synonymous codons with A and U at the third codon position. However,there were differences in the types and numbers of codon usage bias among different species. The differences in codon usage frequency between buffalo and other bovine species were less than those of between buffalo and mouse, and human. Cluster analysis showed two types buffalo gathered into one group, then in turn gathered with cattle, sheep, mouse and human.