Abstract: Hox gene family is a set of key genes of embryo development and one of the important models to study gene duplication and chromosome doubling during biological evolution. In this paper, by using comparative genomics and bioinformatics approach, we extracted HoxA2b gene sequence from the carp genome database and accomplished sequence analysis and comparison, and drew four kinds of homologous evolutionary tree. As a result, it is found that HoxA2b gene is very conservative and the homology of most of Cyprinidae HoxA2b genes is between 99%-100%. We found a conserved sequence whose length is 188 bp, encoding 62 amino acids. The homology in the conserved region of carp HoxA2b gene with other 20 organisms is about 85%-100% and the relative genetic distance is between 1.14-1.55. By analysis the rate of base substitution, we found that the nonsynonymous nucleotide substitution rate is much higher than synonymous nucleotide substitution rate. The carp HoxA2b gene has greater genetic variation and has far genetic distance with other organisms which may be related to carp genome replication and chromosome doubling.

Key words: common carp, homeobox gene, sequence homology, phylogenetic tree