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Comparative Evolutionary Genomics of Toll-like Receptors in True Geese (Anserini)

Sekar, Vaishnovi (2017) BINP41 20162
Degree Projects in Bioinformatics
Abstract
True geese are members of the bird family Anatidae which contain many waterfowl spe-cies with high relevance as natural hosts of Avian Influenza Virus (AIV). The closely re-lated mallard (Anas platyrhynchos) is the main host of AIV and has a robust immune sys-tem which is also the best understood among the Anatidae. Previous studies have shown that some species of geese are more susceptible to AIV than mallard, however, the genet-ic 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 mallard and other species of waterfowl. In this study, I investigated the evolutionary characteristics of Toll-like... (More)
True geese are members of the bird family Anatidae which contain many waterfowl spe-cies with high relevance as natural hosts of Avian Influenza Virus (AIV). The closely re-lated mallard (Anas platyrhynchos) is the main host of AIV and has a robust immune sys-tem which is also the best understood among the Anatidae. Previous studies have shown that some species of geese are more susceptible to AIV than mallard, however, the genet-ic 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 mallard and other species of waterfowl. In this study, I investigated the evolutionary characteristics of Toll-like receptors (TLRs) of all goose species. Refer-ence-based annotation for the TLR15 and TLR3 genes was performed on sequence data from 20 extant goose species obtained from a recent phylogenic study. I studied immunogenetic diversity, signatures of natural selection and evolutionary conservation of these genes among all goose species. My analyses suggest that the evolution of the goose TLR15 and TLR3 genes is dominated by purifying selection with an excess of silent nu-cleotide substitutions. Furthermore, my phylogenetic approaches suggest that the evolu-tion of TLR15 is concordant to the species tree; whereas for TLR3 some species in the Anser genus do not follow species evolution, indicating that this gene might be under dif-ferent selection pressure than the rest of the genome. TLR15 and TLR3 are conserved ir-respective of the difference with the species evolution reinforcing the idea that TLRs may be subjected to strong functional constrains. My results aid in understanding the evolu-tionary history of the immunome of geese and will benefit further comparative genomics work across more immune genes in Anatidae to arrive at a comprehensive understanding of this sub-genome. (Less)
Popular Abstract
Why are geese more susceptible to certain diseases whereas ducks are not?

Ducks and geese both share common habitat and belong to the order of waterfowl along with many other species such as swans. Aquatic habitats are ideal ecosystems for viruses and bacteria and these birds are therefore exposed to high prevalence of infectious diseases in their natural habitats. Members of waterfowl are natural host and carriers of diseases such as avian influence virus. Over the years, research and field studies have shown that ducks are more resistant to certain diseases as compared to other members of waterfowls. It is also know to have a very robust immune system, thus transmiting pathogens and rarely suffering death due to diseases. However,... (More)
Why are geese more susceptible to certain diseases whereas ducks are not?

Ducks and geese both share common habitat and belong to the order of waterfowl along with many other species such as swans. Aquatic habitats are ideal ecosystems for viruses and bacteria and these birds are therefore exposed to high prevalence of infectious diseases in their natural habitats. Members of waterfowl are natural host and carriers of diseases such as avian influence virus. Over the years, research and field studies have shown that ducks are more resistant to certain diseases as compared to other members of waterfowls. It is also know to have a very robust immune system, thus transmiting pathogens and rarely suffering death due to diseases. However, studies have shown that Geese and swans, which live in quite close proximity to ducks are slightly less resistant to such infections. However the genetic basis of this is unknown. Thus it makes an interesting group to understand the difference in the genome which might be associated with immunity to such infection.

In my study, I concentrate on Toll-like receptor (TLR) genes which play a key role in innate immunity. Innate immunity is the first line of defense in many organisms and is characterized by broad-range pathogen recognition and activation of cascading pathways which further “clear” the infection. Toll like receptors are one of the largest class of pathogen recognize receptors and have been observed to have crucial relevance for comparative immunological studies in eukaryotes. However, due to unavailability of sequence data for such analysis, the present-day knowledge about these genes are limited to few bird species with completely sequenced and documented genomes, for example from chicken.

In a recent study, 20 goose species have been sequenced to resolve their phylogenetic relationship. Availability of this sequence data has enabled exploration of the goose genomes for the functioning of specific genes, which are associated with disease resistance and susceptibility. In my study, a new workflow was developed to work with non-model genomic sequence data and two genes, TLR15 and TLR3 were analysed for evolutionary changes in these 20-goose species using this method. The sequence data is mapped to reference genome, in this case the duck and further prediction of these genes is performed using local alignment algorithm. The best alignments corresponding to the target genes are further analysed for selection pressure and amino acid conservation of these gene in all the studied goose species.

Results
My results coincided with many previous studies on avian TLRs and supports the characteristics conservative nature of the TLR genes, reinforcing the idea that these genes may be subjected to strong functional constraints and represent general pattern of pathogen recognition. Also, specific nucleotide substitutions reported in the analysis create lead for further experimental studies on understanding the functions of these genes in geese in a better manner. My results aid in understanding the evolutionary history of the immunome of geese and will benefit further comparative genomic work across more immune gene to arrive at a comprehensive understanding of this sub-genome.


Master’s Degree Project in Bioinformatics 30 credits 2017
Department of Biology, Lund University

Advisor: Dr. Robert Kraus
University of Konstanz & Max Planck Institute for Ornithology, German (Less)
Please use this url to cite or link to this publication:
author
Sekar, Vaishnovi
supervisor
organization
course
BINP41 20162
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
8925088
date added to LUP
2017-09-08 13:50:26
date last changed
2017-09-08 13:50:26
@misc{8925088,
  abstract     = {True geese are members of the bird family Anatidae which contain many waterfowl spe-cies with high relevance as natural hosts of Avian Influenza Virus (AIV). The closely re-lated mallard (Anas platyrhynchos) is the main host of AIV and has a robust immune sys-tem which is also the best understood among the Anatidae. Previous studies have shown that some species of geese are more susceptible to AIV than mallard, however, the genet-ic 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 mallard and other species of waterfowl. In this study, I investigated the evolutionary characteristics of Toll-like receptors (TLRs) of all goose species. Refer-ence-based annotation for the TLR15 and TLR3 genes was performed on sequence data from 20 extant goose species obtained from a recent phylogenic study. I studied immunogenetic diversity, signatures of natural selection and evolutionary conservation of these genes among all goose species. My analyses suggest that the evolution of the goose TLR15 and TLR3 genes is dominated by purifying selection with an excess of silent nu-cleotide substitutions. Furthermore, my phylogenetic approaches suggest that the evolu-tion of TLR15 is concordant to the species tree; whereas for TLR3 some species in the Anser genus do not follow species evolution, indicating that this gene might be under dif-ferent selection pressure than the rest of the genome. TLR15 and TLR3 are conserved ir-respective of the difference with the species evolution reinforcing the idea that TLRs may be subjected to strong functional constrains. My results aid in understanding the evolu-tionary history of the immunome of geese and will benefit further comparative genomics work across more immune genes in Anatidae to arrive at a comprehensive understanding of this sub-genome.},
  author       = {Sekar, Vaishnovi},
  language     = {eng},
  note         = {Student Paper},
  title        = {Comparative Evolutionary Genomics of Toll-like Receptors in True Geese (Anserini)},
  year         = {2017},
}