Analysis of cloacal-septum-related gene evolution in vertebrate development

A bioinformatics analysis was carried out to compare nucleotide and protein sequences of Hoxd13 (homeobox D13), a gene involved in cloacal septum development. Based on structure of cloacal septum, 10 vertebrate species were selected, among which 6 have cloacal septum development, whilst other 4 have persistent cloacal structure. Alignment of protein sequences has indicated that the DNA-binding domains of Hoxd13 are highly conserved. Six variants including G → S (sequence coordinate 177), A→S (sequence coordinate 190), S→N (sequence coordinate 203), A → T (sequence coordinate 227), G → S (sequence coordinate 256) and T→N (sequence coordinate 346) were identified within the non-DNA-binding domains. Topologies of phylogenetic trees constructed with both protein sequences and mRNA sequences were consistent with the direction of evolution. Taken together, variations in the Hoxd13 genes in such species may have influenced evolution of the cloacal septum.