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Nanopore long-read guided complete genome assembly of Hydrogenophaga intermedia, and genomic insights into 4-aminobenzenesulfonate, p-aminobenzoic acid and hydrogen metabolism in the genus Hydrogenophaga

Gan, Han Ming, Lee, Yin P. and Austin, Christopher M. 2017, Nanopore long-read guided complete genome assembly of Hydrogenophaga intermedia, and genomic insights into 4-aminobenzenesulfonate, p-aminobenzoic acid and hydrogen metabolism in the genus Hydrogenophaga, Frontiers in microbiology, vol. 8, pp. 1-9, doi: 10.3389/fmicb.2017.01880.

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Title Nanopore long-read guided complete genome assembly of Hydrogenophaga intermedia, and genomic insights into 4-aminobenzenesulfonate, p-aminobenzoic acid and hydrogen metabolism in the genus Hydrogenophaga
Formatted title Nanopore long-read guided complete genome assembly of Hydrogenophaga intermedia, and genomic insights into 4-aminobenzenesulfonate, p-aminobenzoic acid and hydrogen metabolism in the genus Hydrogenophaga
Author(s) Gan, Han MingORCID iD for Gan, Han Ming orcid.org/0000-0001-7987-738X
Lee, Yin P.
Austin, Christopher M.ORCID iD for Austin, Christopher M. orcid.org/0000-0003-1848-6267
Journal name Frontiers in microbiology
Volume number 8
Article ID 1880
Start page 1
End page 9
Total pages 9
Publisher Frontiers Media
Place of publication Lausanne, Switzerland
Publication date 2017-10
ISSN 1664-302X
Keyword(s) Hydrogenophaga
Nanopore
comparative genomics
hydrogen metabolism
phylogeny
Science & Technology
Life Sciences & Biomedicine
Microbiology
AGROBACTERIUM-RADIOBACTER S2
SULFANILIC ACID
ACTIVATED-SLUDGE
SP AH-24
SP NOV.
SP PBC
SEQUENCE
BACTERIUM
GENES
S1
Summary We improved upon the previously reported draft genome of Hydrogenophaga intermedia strain PBC, a 4-aminobenzenesulfonate-degrading bacterium, by supplementing the assembly with Nanopore long reads which enabled the reconstruction of the genome as a single contig. From the complete genome, major genes responsible for the catabolism of 4-aminobenzenesulfonate in strain PBC are clustered in two distinct genomic regions. Although the catabolic genes for 4-sulfocatechol, the deaminated product of 4-aminobenzenesulfonate, are only found in H. intermedia, the sad operon responsible for the first deamination step of 4-aminobenzenesulfonate is conserved in various Hydrogenophaga strains. The absence of pabB gene in the complete genome of H. intermedia PBC is consistent with its p-aminobenzoic acid (pABA) auxotrophy but surprisingly comparative genomics analysis of 14 Hydrogenophaga genomes indicate that pABA auxotrophy is not an uncommon feature among members of this genus. Of even more interest, several Hydrogenophaga strains do not possess the genomic potential for hydrogen oxidation, calling for a revision to the taxonomic description of Hydrogenophaga as "hydrogen eating bacteria."
Language eng
DOI 10.3389/fmicb.2017.01880
Field of Research 060408 Genomics
060503 Microbial Genetics
HERDC Research category C1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ©2017, The Authors
Free to Read? Yes
Use Rights Creative Commons Attribution licence
Persistent URL http://hdl.handle.net/10536/DRO/DU:30103335

Document type: Journal Article
Collections: School of Life and Environmental Sciences
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Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.