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]
![]() |
PDF
938kB |
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 Name/Journal: | Acta Universitatis Agriculturae Sueciae | ||||||||||
Year of publishing : | 2 January 2015 | ||||||||||
Depositing date: | 2 January 2015 | ||||||||||
Number: | 2015:21 | ||||||||||
Number of Pages: | 54 | ||||||||||
Papers/manuscripts: |
| ||||||||||
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: | 10 Sep 2020 13:41 |
Repository Staff Only: item control page