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In silico analysis of Treponema and Brachyspira genomes

assembly, annotation and phylogeny

Mushtaq, Mamoona (2015). In silico analysis of Treponema and Brachyspira genomes. Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2015:21
ISBN 978-91-576-8240-6
eISBN 978-91-576-8241-3
[Doctoral thesis]

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Abstract

Spirochaetal bacteria are highly diverse in terms of life style, growth requirements and virulence, but they all belong to a monophyletic ancient lineage. Many spirochaetes are difficult to culture or have fastidious growth requirements. Genus Brachyspira and genus Treponema, are two important members of phylum spirochetes that include well known pathogens, such as T.pallidum subsp. pallidum and B. hyodysenteriae.

Other members of the phylum include T.pedis, associated with both bovine digital dermatitis (BDD) in cattle and necrotic skin lesions in pigs, T.phagedenis associated with BDD, and "B.suanatina", which has been reported in connection with swine dysentery-like enteric disease in pigs. All these bacteria are thus associated with significant health problems in farm animals leading to economic losses. The aims of this thesis were to identify and characterize potential pathogenic factors in T.pedis and T. phagedenis and to study the genomic characteristics of B. suanatina for a complete species validation and description.

Assembly, annotation and bioinformatics analysis of the genome sequence of T. phagedenis strain V1 and T. pedis strain TA4 were performed. The complete genome of T. pedis strain TA4 was compared to that of T. denticola, a species associated with human periodontal disease. Results of the analysis showed close relatedness between these two bacterial species. Some of the pathogenicity related genes that are already known in T. denticola were also found in T. pedis strain TA4. In the genome of T. phagedenis strain V1, homologous proteins to known pathogenicity factors in T. denticola and T. pallidum were found and a locus encoding antigenic lipoproteins with potential for antigenic variation was characterized

To identify the taxonomical position of B. suanatina, we performed assembly, annotation and phylogenetic analysis of the B. suanatina strain AN4859/03 genome along with its comparison with B. hyodysenteriae and other Brachyspira species. Comparative analysis suggested that B. suanatina is a novel species, though phenotypically it showed no difference from B. hyodysenteriae.

Authors/Creators:Mushtaq, Mamoona
Title:In silico analysis of Treponema and Brachyspira genomes
Subtitle:assembly, annotation and phylogeny
Series/Journal:Acta Universitatis agriculturae Sueciae (1652-6880)
Year of publishing :2 January 2015
Depositing date:2 January 2015
Volume:2015:21
Number of Pages:54
Papers/manuscripts:
NumberReferences
ISvartström O, Mushtaq M, Pringle M, Segerman B (2013). Genome-wide relatedness of Treponema pedis, from gingiva and necrotic skin lesions of pigs, with the human oral pathogen Treponema denticola. PLoS One 8(8), e71281.
IIMushtaq M, Manzoor S, Pringle M. Rosander A, Bongcam-Rudloff E (2014). Draft genome sequence of ‘Treponema phagedenis’ strain V1, isolated from bovine digital dermatitis. (Submitted to Standards in Genomic Sciences).
IIIMushtaq M, Loftsdottir L, Pringle M, Segerman B, Rosander A. Genetic analysis of a Treponema phagedenis locus encoding antigenic lipoproteins with potential for antigenic variation. (Manuscript).
IVMushtaq M, Zubair S, Råsbäck T, Bongcam-Rudloff E, Jansson D.S. Brachyspira suanatina sp. nov., an enteropathogenic intestinal spirochaete isolated from pigs and mallards: genomic and phenotypic characteristics. (Manuscript).
Place of Publication:Uppsala
Publisher:Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences
ISBN for printed version:978-91-576-8240-6
ISBN for electronic version:978-91-576-8241-3
ISSN:1652-6880
Language:English
Publication Type:Doctoral thesis
Full Text Status:Public
Agris subject categories.:L Animal production > L10 Animal genetics and breeding
L Animal production > L73 Animal diseases
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 102 Computer and Information Science > 10203 Bioinformatics (Computational Biology) (applications to be 10610)
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 403 Veterinary Science > Pathobiology
Agrovoc terms:treponema, brachyspira, pathogens, pathogenicity, genomes, bioinformatics, phylogeny, genetic techniques, animal diseases, cattle, swine, skin diseases, swine dysentery
Keywords:Bioinformatics, Genome assembly, Phylogeny
URN:NBN:urn:nbn:se:slu:epsilon-e-2350
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-2350
ID Code:11835
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
External funders:Higher Education Commission, Pakistan
Deposited By: Ms Mamoona Mushtaq
Deposited On:02 Feb 2015 11:15
Metadata Last Modified:22 Apr 2016 07:35

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