Broad-scale phylogenomics reveals insights into retroviral origin and gammaretrovirus-host evolution

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Title: Broad-scale phylogenomics reveals insights into retroviral origin and gammaretrovirus-host evolution
Authors: Yu, Ling-Shan
Item Type: Thesis or dissertation
Abstract: The Retroviridae is a family of single-stranded positive-sense animal viruses united by a unique mechanism of replication. Numerous studies have demonstrated the host diversity and host–retrovirus evolutionary history of the Retroviridae. However, in the past it has been difficult to gain a deeper understanding owing to the lack of sufficient host genomic data. Recent advances in whole-genome sequencing and bioinformatics technologies have enabled the collection of high-quality vertebrate genomic data. Broad-scale in silico screening of vertebrate genomes provides numerous opportunities to analyse retroviral origin and evaluate the risks and limitations of horizontal transmissions between different host species. In Chapters 2 and 3, I expand our current understanding of retroviral diversity in lower vertebrates and identify the host range boundary of the Retroviridae. I report the discovery of a basal retrovirus within the genome of the lamprey (Petromyzon marinus). No retroviruses were identified within other basal chordates, such as hagfishes, molluscs and sponges. This suggests that members of the Retroviridae are restricted to the lamprey and other phylogenetically higher vertebrates, and the host range boundary of this virus family has been potentially identified. In addition, this study identified extensive retroviral diversity in the basal vertebrates. The phylogenetic results show that at least three independent invasions have occurred in cartilaginous fish and the coelacanth. In Chapter 4, I investigate the gammaretroviral diversity and evolutionary history of mammalian genomes by combining the data of viral hosts and viral sequences. The study provides insights into the retrovirus–host evolution history. Six horizontal transmission hotspots have been identified, and rodents are suggested to be the major retroviral reservoir of type II gammaretroviruses. In addition, by mapping host species onto viral phylogenies, it is shown that cross-species horizontal transmissions of gammaretroviruses are frequent between closely related species.
Content Version: Open Access
Issue Date: Dec-2015
Date Awarded: Aug-2016
URI: http://hdl.handle.net/10044/1/67568
Copyright Statement: Creative Commons Attribution Non-Commercial No Derivatives licence
Supervisor: Tristem, Michael
Department: Life Sciences
Publisher: Imperial College London
Qualification Level: Doctoral
Qualification Name: Doctor of Philosophy (PhD)
Appears in Collections:Life Sciences PhD theses



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