True geese are members of the order waterfowl (Anseriformes) which contain many species with high relevance as natural hosts of avian influenza virus (AIV). The closely related waterfowl mallard (Anas platyrhynchos) is considered to be the main host of AIV and has a robust immune system which is also the best understood among the Anseriformes. Previous studies have shown that some species of geese are more susceptible to AIV than mallard, however, the genetic basis of this is not known. Geese are therefore an interesting group for discovering what differences in the genome might be associated with the differences in susceptibility to pathogens in the mallards and other species of waterfowl.
Recent studies have sequenced reference goose genomes and subsequently the phylogenetic relationships of this species group fully solved. Beyond this taxonomic assessment, further investigations on the specific genes involved in immunity have not been performed, yet. The primary focus of this research work is to study the genetic diversity in immune genes responsible for responses to avian diseases across all goose genomes.
The goose genomic data was obtained from J. Ottenburghs et al. (2016). They have sequenced 19 goose genomes consisting of two clades of species, Anser and Branta to ~15-20x depth of sequence coverage per species (Illumina technology).
My proposed method can be described in four broad steps.
- Mapping to mallard genome
- Annotate and validate
- Gene tree construction
I plan to do a de novo annotation with the duck genome (Huang et al, 2013). A possible suggestion is to use MAKER gene predictor to perform the gene prediction. Also, I plan to do a sequence-based search for the missing genes in the genome.
After I performed gene prediction, I will be able to identify a set of genes involved in immunological pathways. I plan to look for Toll-Like Receptors (TLRs) and other immune genes studied from literature initially. After identification of these genes in the goose genomes, I will construct gene trees. By comparatively analyzing the nucleotide and amino acid sequences across all species of geese I will infer sites under natural selection, their mode of selection and make inferences about their role and position in immunological pathways. I will compare the constructed gene trees to the established phylogenetic trees for the True Geese. This will help us to understand and infer the gene diversity with respect to the species evolution over the time. This eventually will lead to an improved understanding why some species of waterbirds display lower or higher susceptibility to diseases such as Avian Influenza, a globally important zoonotic disease.