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The Mycobacterium phlei Genome: Expectations and Surprises
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Chemical Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Chemical Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Chemical Biology.ORCID iD: 0000-0002-8810-6066
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Chemical Biology.
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2016 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 8, no 4, p. 975-985Article in journal (Refereed) Published
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Abstract [en]

Mycobacterium phlei, a nontuberculosis mycobacterial species, was first described in 1898-1899. We present the complete genome sequence for the IV, phlei CCUG21000(T) type strain and the draft genomes for four additional strains. The genome size for all five is 5.3 Mb with 69.4% Guanine-Cytosine content. This is approximate to 0.35 Mbp smaller than the previously reported M. phlei RIVM draft genome. The size difference is attributed partly to large bacteriophage sequence fragments in the M. phlei RIVM genome. Comparative analysis revealed the following: 1) A CRISPR system similar to Type 1E (cas3) in M. phiei RIVM; 2) genes involved in polyamine metabolism and transport (potAD, potT) that are absent in other mycobacteria, and 3) strain specific variations in the number of sigma-factor genes. Moreover, M. phlei has as many as 82 mce (mammalian cell entry) homologs and many of the horizontally acquired genes in M. phlei are present in other environmental bacteria including mycobacteria that share similar habitat. Phylogenetic analysis based on 693 Mycobacterium core genes present in all complete mycobacterial genomes suggested that its closest neighbor is Mycobacterium smegmatis JS623 and Mycobacterium rhodesiae NBB3, while it is more distant to M. smegmatis mc2 155.

Place, publisher, year, edition, pages
2016. Vol. 8, no 4, p. 975-985
Keywords [en]
Mycobacterium phlei genome sequence, mycobacterial growth, comparative genome analysis, mycobacterial phylogeny
National Category
Medical Genetics
Identifiers
URN: urn:nbn:se:uu:diva-298249DOI: 10.1093/gbe/evw049ISI: 000376126400002PubMedID: 26941228OAI: oai:DiVA.org:uu-298249DiVA, id: diva2:945450
Funder
Swedish Research CouncilSida - Swedish International Development Cooperation AgencySwedish Research Council FormasSwedish National Infrastructure for Computing (SNIC), b2011072Available from: 2016-07-01 Created: 2016-07-01 Last updated: 2018-01-10Bibliographically approved

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Das, SarbashisPettersson, B. M. FredrikBehra, Phani Rama KrishnaRamesh, MalavikaDasgupta, SantanuKirsebom, Leif A.

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