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      Draft Genome Sequence of the Caffeine-Degrading Methylotroph Methylorubrum populi Pinkel

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          Abstract

          A pink-pigmented facultative methylotroph, Methylorubrum populi Pinkel, was isolated from compost by selective enrichment with caffeine (3,5,7-trimethylxanthine) as the sole carbon, nitrogen, and energy source. We report here its high-quality draft genome sequence, assembled in 35 contigs totaling 5,630,907 bp. We identified 5,681 protein-coding sequences, including those putatively involved in caffeine degradation.

          ABSTRACT

          A pink-pigmented facultative methylotroph, Methylorubrum populi Pinkel, was isolated from compost by selective enrichment with caffeine (3,5,7-trimethylxanthine) as the sole carbon, nitrogen, and energy source. We report here its high-quality draft genome sequence, assembled in 35 contigs totaling 5,630,907 bp. We identified 5,681 protein-coding sequences, including those putatively involved in caffeine degradation.

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          A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data.

          David Coil, Guillaume Jospin, Aaron Darling (2015)
          Open-source bacterial genome assembly remains inaccessible to many biologists because of its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina data.
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            Review of the genus Methylobacterium and closely related organisms: a proposal that some Methylobacterium species be reclassified into a new genus, Methylorubrum gen. nov.

            Peter Green, Julie Ardley (2018)
            The genus Methylobacterium, when first proposed by Patt et al. in 1976, was a monospecific genus created to accommodate a single pink pigmented facultatively methylotrophic bacterium. The genus now has over 50 validly published species, however, the percentage 16S rRNA sequence divergence within Methylobacterium questions whether or not they can still be accommodated within one genus. Additionally, several strains are described as belonging to Methylobacterium, but nodulate legumes and in some cases are unable to utilize methanol as a sole carbon source. This study reviews and discusses the current taxonomic status of Methylobacterium. Based on 16S rRNA gene, multi-locus sequence analysis, genomic and phenotypic data, the 52 Methylobacterium species can no longer be retained in one genus. Consequently, a new genus, Methylorubrum gen. nov., is proposed to accommodate 11 species previously held in Methylobacterium. The reclassified species names are proposed as: Methylorubrum aminovorans comb. nov. (type strain TH-15T=NCIMB 13343T=DSM 8832T), Methylorubrum extorquens comb. nov. (type strain NCIMB 9399T=DSM 1337T), Methylorubrum podarium comb. nov. (type strain FM4T=NCIMB 14856T=DSM 15083T), Methylorubrum populi comb. nov. (type strain BJ001T=NCIMB 13946T=ATCC BAA-705T), Methylorubrum pseudosasae comb. nov. (type strain BL44T=ICMP 17622T=NBRC 105205T), Methylorubrum rhodesianum comb. nov. (type strain NCIMB 12249T=DSM 5687T), Methylorubrum rhodinum comb. nov. (type strain NCIMB 9421T=DSM 2163T), Methylorubrum salsuginis comb. nov. (type strain MRT=NCIMB 14847T=NCCB 100140T), Methylorubrum suomiense comb. nov. (type strain F20T=NCIMB 13778T=DSM 14458T), Methylorubrum thiocyanatum comb. nov. (type strain ALL/SCN-PT=NCIMB 13651T=DSM 11490T) and Methylorubrum zatmanii comb. nov. (type strain NCIMB 12243T=DSM 5688T). The taxonomic position of several remaining species is also discussed.
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              Methylobacterium populi sp. nov., a novel aerobic, pink-pigmented, facultatively methylotrophic, methane-utilizing bacterium isolated from poplar trees (Populus deltoides x nigra DN34).

              C Peres, Jennifer Doty, Jerald Schnoor … (2004)
              A pink-pigmented, aerobic, facultatively methylotrophic bacterium, strain BJ001T, was isolated from internal poplar tissues (Populus deltoidesxnigra DN34) and identified as a member of the genus Methylobacterium. Phylogenetic analyses showed that strain BJ001T is related to Methylobacterium thiocyanatum, Methylobacterium extorquens, Methylobacterium zatmanii and Methylobacterium rhodesianum. However, strain BJ001T differed from these species in its carbon-source utilization pattern, particularly its use of methane as the sole source of carbon and energy, an ability that is shared with only one other member of the genus, Methylobacterium organophilum. In addition, strain BJ001T is the only member of the genus Methylobacterium to be described as an endophyte of poplar trees. On the basis of its physiological, genotypic and ecological properties, the isolate is proposed as a member of a novel species of the genus Methylobacterium, Methylobacterium populi sp. nov. (type strain, BJ001T=ATCC BAA-705T=NCIMB 13946T).
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                Author and article information

                Contributors
                Steven R. Gill: Role: Editor
                Journal
                Journal ID (nlm-ta): Microbiol Resour Announc
                Journal ID (iso-abbrev): Microbiol Resour Announc
                Journal ID (hwp): ga
                Journal ID (pmc): mra
                Journal ID (publisher-id): MRA
                Title: Microbiology Resource Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2576-098X
                Publication date (Electronic): 21 November 2019
                Publication date Collection: November 2019
                Volume: 8
                Issue: 47
                Electronic Location Identifier: e01300-19
                Affiliations
                [a ]Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, Davis, California, USA
                [b ]Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng Teachers University, Yancheng, China
                [c ]Department of Biology, University of St. Thomas, St. Paul, Minnesota, USA
                University of Rochester School of Medicine and Dentistry
                Author notes
                Address correspondence to Rebecca E. Parales, reparales@ 123456ucdavis.edu , or Scott C. Dawson, scdawson@ 123456ucdavis.edu .
                [*]

                Present address: Gaurav Sharma, Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India; Matthew E. Wright, Benchling, San Francisco, California, USA.

                Citation Parales RE, Sharma G, Zhang X, Subuyuj GA, Langner JT, Wright ME, Ditty JL, Dawson SC. 2019. Draft genome sequence of the caffeine-degrading methylotroph Methylorubrum populi Pinkel. Microbiol Resour Announc 8:e01300-19. https://doi.org/10.1128/MRA.01300-19.

                Author information
                https://orcid.org/0000-0002-0843-1759
                Article
                Publisher ID: MRA01300-19
                DOI: 10.1128/MRA.01300-19
                PMC ID: 6872896
                PubMed ID: 31753954
                SO-VID: 24a0a7b0-3339-4fd4-95fb-5de440006d8e
                Copyright © Copyright © 2019 Parales et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Date received : 21 October 2019
                Date accepted : 24 October 2019
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 9, Pages: 2, Words: 1223
                Categories
                Subject: Genome Sequences
                Custom metadata
                cover-date November 2019

                Data availability:

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