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Doctoral thesis, 2015

In silico analysis of Treponema and Brachyspira genomes

Mushtaq, Mamoona

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.

Keywords

Bioinformatics; Genome assembly; Phylogeny

Published in

Acta Universitatis Agriculturae Sueciae
2015, number: 2015:21
ISBN: 978-91-576-8240-6, eISBN: 978-91-576-8241-3
Publisher: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences

Authors' information

Mushtaq, Mamoona
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics

UKÄ Subject classification

Bioinformatics (Computational Biology)
Pathobiology

URI (permanent link to this page)

https://res.slu.se/id/publ/64205