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Duck Genome, Transcriptome Studies Point to Genes Related to Flu Response

NEW YORK (GenomeWeb News) – An analysis of the duck genome in combination with its transcriptome, published online yesterday in Nature Genetics, uncovered genes whose expression patterns are altered in response to infection with avian influenza viruses.

The researchers, led by Ning Li, a professor at China Agricultural University in Beijing, sequenced the genome of a 10-week-old female Bejing duck, Anas platyrhynchos. They further examined the lung transcriptomes of ducks infected with a highly pathogenic or weakly pathogenic flu strain and control ducks.

Ducks are a natural reservoir of the influenza A virus and have been found to harbor nearly all of the known hemagglutinin and neuraminidase subtypes of the virus. Flu viruses typically do not affect ducks, though a recent H5N1 strain caused an outbreak in poultry and in people, with a 59 percent mortality rate in humans.

"The exceptional virulence of avian influenza viruses in humans, in combination with their ongoing evolution in birds, motivates us to better understand host immune responses to avian influenza viruses," the researchers wrote.

Using the Illumina Genome Analyzer platform, the researchers generated 77 gigabases of paired-end reads that averaged 50 base pairs in length, getting about 64-fold coverage of the genome. With SOAPdenovo, they then assembled those short reads into nearly 78,500 scaffolds that they then constructed into 47 superscaffolds.

By aligning duck transcriptome data — generated from muscle and brain tissue —as well as chicken and human genes to the duck genome assembly, the researchers predicted some 19,150 protein-coding duck genes. Nearly 10,000 of those mapped to Gene Ontology categories.

By comparing the duck gene set with those from other organisms, the researchers saw that while fish, mammals, and reptiles, as well as ducks and turkeys, had more gene contractions than gene expansions, chickens and zebra finches had more expansions than contractions.

Further, immune genes in birds appeared to be subject to this contraction. For example, 3,116 duck genes, 3,294 chicken genes, and 3,355 zebra finch genes cluster in immune-related gene families, compared to more than 6,000 human and 5,700 mouse genes. In addition, the researchers identified 150 duck cytokines — similar to the number found in other birds, but much lower than the number found in humans or mice — and 16 defensins, which are thought to be part of the immune response to avian flu in mammals.

However, there were also lineage-specific duplications, with the duck containing 76 such duplications, including in the BTNL family, which has been implicated in immune response in mammals. The chicken and zebra finch had a higher number of duplication events.

In addition, about 5 percent of the duck genome was calculated to be under positive selection, with enrichment for genes involved in cellular assembly and organization, function and maintenance, and signaling.

To identify genes that respond to flu infection, the researchers examined the lung transcriptomes of ducks infected with a highly pathogenic or a weakly pathogenic influenza A virus strain and control ducks. From this, they identified 74 cytokines whose expression levels changed one to three days after inoculation with either virus. Those cytokines include a number of growth factors, interferons, and interleukins.

In addition, they noted that eight avian defensin genes — two of which had lineage specific duplications — showed a marked increase of expression, and 11 of the 17 BTNL genes —including eight lineage-specific duplications — were also expressed at increased levels.

"[W]e found that many genes (for example, BTNLs and defensins) were independently duplicated in the duck but not in the chicken genome," the researchers wrote. "These results suggest that gene gain and loss have influenced the divergence of the four avian genomes and the evolution of their respective immune systems."

"Our future ability to assess the functions of genes showing significantly different expression induced by highly pathogenic H5N1 viruses compared with weakly pathogenic H5N1 viruses, using genetic manipulations and co-evolutionary analyses, will certainly extend knowledge of the avian genes related to influenza in birds," they added.