The duck genome sequence and the evolution of avian genomes

The mallard is the principal natural reservoir for influenza A viruses. Influenza is a major threat to human health, responsible annually for 500,000 deaths. It is also a potential economic threat; where a pandemic of influenza could cost 800 billion USD. Influenza type A viruses are asymptomatic in ducks, even with most strains of highly pathogenic strains, which can kill other poultry within days. We analysed the genome sequences of ducks and other birds to identify genes that may explain this fundamental difference. We used a phylogenetic approach to compare the intensity of selection (dN/dS ratio) on genes between birds and mammals or ducks and other birds. These comparisons defined genes that evolve at a higher rate within specific clades or subject to positive selection within specific branches. Simple 1:1 orthologs were downloaded from Ensembl for birds and mammals or defined between chicken/duck by reciprocal best hits. Amino acid sequences were aligned using Clustalw and back translated to codon sequences using Pal2nal. Gblocks was used to eliminate regions of poor alignment. The maximum likelihood method Codeml was used to estimate dN/dS ratios. Likelihood ratio tests were performed to identify specific branches evolving at a higher rate than others (branch models) or to identify genes with amino acid sites subject to positive selection (branch-site models). From these and other tests we defined genes that correlate with life histories of birds, and innate immune system of the duck that may protect it from pathological effects of infections by influenza infections.