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dc.contributor.advisorLycett, Samantha
dc.contributor.advisorBurt, David
dc.contributor.authorMason, Andrew Stephen
dc.date.accessioned2018-04-17T10:55:23Z
dc.date.available2018-04-17T10:55:23Z
dc.date.issued2018-06-30
dc.identifier.urihttp://hdl.handle.net/1842/29549
dc.description.abstractLong terminal repeat (LTR) retrotransposons are autonomous eukaryotic repetitive elements which may elicit prolonged genomic and immunological stress on their host organism. LTR retrotransposons comprise approximately 10 % of the mammalian genome, but previous work identified only 1.35 % of the chicken genome as LTR retrotransposon sequence. This deficit appears inconsistent across birds, as studied Neoaves have contents comparable with mammals, although all birds contain only one LTR retrotransposon class: endogenous retroviruses (ERVs). One group of chicken-specific ERVs (Avian Leukosis Virus subgroup E; ALVEs) remain active and have been linked to commercially detrimental phenotypes, such as reduced lifetime egg count, but their full diversity and range of phenotypic effects are poorly understood. A novel identification pipeline, LocaTR, was developed to identify LTR retrotransposon sequences in the chicken genome. This enabled the annotation of 3.01 % of the genome, including 1,073 structurally intact elements with replicative potential. Elements were depleted within coding regions, and over 40 % of intact elements were found in clusters in gene sparse, poorly recombining regions. RNAseq analysis showed that elements were generally not expressed, but intact transcripts were identified in four cases, supporting the potential for viral recombination and retrotransposition of non-autonomous repeats. LocaTR analysis of seventy-two additional sauropsid genomes revealed highly lineage-specific repeat content, and did not support the proposed deficit in Galliformes. A second, novel bioinformatic pipeline was constructed to identify ALVE insertions in whole genome resequencing data and was applied to eight elite layer lines from Hy-Line International. Twenty ALVEs were identified and diagnostic assays were developed to validate the bioinformatic approach. Each ALVE was sequenced and characterised, with many exhibiting high structural intactness. In addition, a K locus revertant line was identified due to the unexpected presence of ALVE21, confirmed using BioNano optic maps. The ALVE identification pipeline was then applied to ninety chicken lines and 322 different ALVEs were identified, 81 % of which were novel. Overall, broilers and non-commercial chickens had a greater number of ALVEs than were found in layers. Taken together, these two analyses have enabled a thorough characterisation of both the abundance and diversity of chicken ERVs.en
dc.contributor.sponsorBiotechnology and Biological Sciences Research Council (BBSRC)en
dc.language.isoenen
dc.publisherThe University of Edinburghen
dc.relation.hasversionMason, A. S. et al. (2016) A new look at the LTR retrotransposon content of the chicken genome, BMC Genomics. BMC Genomics, 17(1), p. 688.en
dc.relation.hasversionWragg D, Mason AS, Yu L, Kuo R, Lawal RA, Desta TT, Mwacharo JM, Cho CY, Kemp S, Burt DW & Hanotte O (2015), Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken, BMC Genomics, 16: 784.en
dc.relation.hasversionWarren WC, Hillier LW, Tomlinson C, Minx P, Kremitzki M, Graves T, Markovic C, Bouk N, Pruitt KD, Thibaud-Nissen F, Schneider V, Mansour TA, Brown CT, Zimin A, Hawken R, Abrahamsen M, Pyrkosz AB, Morisson M, Fillon V, Vignal A, Chow W, Howe K, Fulton JE, Miller MM, Lovell P, Mello CV, Wirthlin M, Mason AS, Kuo R, Burt DW, Dodgson JB & Cheng HH (2017), A New Chicken Genome Assembly Provides Insight into Avian Genome Structure, G3: Genes, Genomes, Genetics, 7(1): 109-117.en
dc.subjectendogenous retrovirusen
dc.subjectALVEsen
dc.subjectALVE diversityen
dc.subjectchickenen
dc.subjectdiagnostic testsen
dc.subjectdatasetsen
dc.titleAbundance and diversity of endogenous retroviruses in the chicken genomeen
dc.typeThesis or Dissertationen
dc.type.qualificationlevelDoctoralen
dc.type.qualificationnamePhD Doctor of Philosophyen


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