Genomes

Genomes

5.  Genomes

Genome sequences are now available for a variety of methanotrophs, either as complete or gapped sequences (Table 5.1).  Those listed as JGI/DOE that have not yet been submitted to GenBank are available on the JGI website through the IMG browser. Those with accession numbers can be accessed through the NCBI Microbial Genomes site. Note that several of these genomes have been analyzed under the auspices of OMeGA (Organization of Methanotroph Genome Analysis), a consortium focused on the sequencing and annotation of multiple methanotroph genomes.

Table 5.1.  Genome Sequences for Methanotrophs

Strain Contact person Sequencing center(leading group/ organization) AccessionGenBankIMG Status References
Alpha-proteobacteria  
Methylocapsa acidiphila B2 Murrell C. JGI/DOE ABLP0100000 Complete (Chen, 2010)
Methylocystis sp. strain Rockwell Stein L. JGI/DOE AEVM00000000 Final draft (Stein et al., 2011)
Methylocystis sp. SC2 Liesack W. Max Planck Institute NC_018485 Complete (Dam et al., 2012)
Methylocystis rosea SV97T Svenning M.M. JGI/DOE(OMeGA) ARCT0100000 Final draft
Methylocystis parvus OBBP García J. Centro de Investigaciones Biológicas AJTV00000000 Final draft (del Cerro et al., 2012)
Methylosinus trichosporium OB3b Stein L. JGI/DOE(OMeGA) ADVE00000000 Final draft (Stein et al., 2010)
Methylosinus sp. LW4 Chistoserdova L. JGI/DOE(University of Washington) ARAB00000000 Final draft
Methylosinus sp. LW8 Chistoserdova L. JGI/DOE (University of Washington) in progress
Methylosinus sp. LW3 Chistoserdova L. JGI/DOE(University of Washington) Final draft
Methylosinus sp. PW1 Chistoserdova L. JGI/DOE(University of Washington) in progress
Methylosinus sporium sp.5T Stein L. JGI/DOE(OMeGA) in progress
Methylocystis sp. LW5 Chistoserdova L. JGI/DOE(University of Washington) in progress
Methyloferula stellata AR4T Dedysh S. JGI/DOE(OMeGA) ARWA01000000 Final draft
Methylocapsa aurea KYG T Dedysh S. JGI/DOE(OMeGA) in progress
Gamma-proteobacteria  
Methylococcus capsulatus BATH TIGR TIGR AE017282.2 Complete sequence (Ward et al., 2004)
Methylococcus capsulatus TexasATCC19069 Kleiveland C.R. Norwegian University of Life Sciences AMCE00000000 Draft (Kleiveland et al., 2012)
Methylocaldum szegediense O-12 Kalyuzhnaya M.G.Khmelenina V.N. JGI/DOE(OMeGA) SRX030733 Final draft
Methylomonas methanica MC09 Murrell J.C. JGI/DOE(OMeGA) NC_015572 Complete sequence (Boden et al., 2011)
Methylomonas LW13 Kalyuzhnaya M.G University of Washington Draft
Methylomonas MK1 Kalyuzhnaya M.G JGI/DOE(University of Washington) AQOV00000000 Final draft
Methylomonas 11b Kalyuzhnaya M.G. JGI/DOE(University of Washington PRJNA157071 Final draft
Methylobacter tundripaludum SV96 Svenning M.M. JGI/DOE(OMeGA) AEGW00000000 Final draft (Svenning et al., 2011)
Methylohalobius crimeensis 10KiT Dunfield P. JGI/DOE(OMeGA) ATXB01000000 Annotation in progress
Methylosarcina lacus LW14 Kalyuzhnaya M.G. JGI/DOE(University of Washington) Final draft
Methylosarcina fibrata AML-C10T Kalyuzhnaya M.G. JGI/DOE(OMeGA) ARCU01000000 in progress
Methylobacter marinus A45 Kalyuzhnaya M.G. JGI/DOE(University of Washington) ARVS00000000 Final draft
Methylobacter luteus (synonym M. bovis) IMV-B-3098T Kalyuzhnaya M.G. JGI/DOE(OMeGA) ATYJ01000000 Final draft
Methylobacter whittenburyi (synonym M. vinelandii) ACM 3586T Kalyuzhnaya M.G. JGI/DOE(OMeGA) in progress
Methylobacter sp. BBA5 (synonym UW 659-2-H10) Kalyuzhnaya M.G. JGI/DOE(OMeGA) AQVZ01000000 in progress
Methylobacter BB5 Murrell J.C. University of East Anglia in progress
Methylobacter 31-32 Kalyuzhnaya M.G.Beck D. University of Washington/ Calysta Draft
Methylococaceae 12 Kalyuzhnaya M.G.Beck D. University of Washington Draft
Methylomicrobium pelagicum sp. D100#4 Kalyuzhnaya M.G. JGI/DOE(OMeGA) in progress
Methylomicrobium alcaliphilum 20Z Kalyuzhnaya M.G. Genoscope NC_016112 Complete sequence (Vuilleumier et al., 2012)
Methylomicrobium buryatense 5G Kalyuzhnaya M.G. JGI/DOE(OMeGA) AOTL00000000 Final draft (Khmelenina et al., 2013)
Methylomicrobium album BG8 Stein L. JGI/DOE(OMeGA) CM001475 Final draft (Kits et al., 2013)
Methylomicrobium agile Kalyuzhnaya M.G. JGI/DOE(OMeGA) in progress
Methylomonas sp. LWB Murrell J.C. University of East Anglia in progress
Methylovulum miyakonense  HT12T Sakai Y. JGI/DOE(OMeGA) AQZU01000000 Draft
Methylomarinum vadi Hirayama H./ Kalyuzhnaya M.G. JGI/DOE(OMeGA) In progress
Methylocaldum sp. 175 Knief C. JGI/DOE(OMeGA) in progress
Methanotrophic bacteria Type 1b” strain 73a (representing the RPC-1 cluster) Knief C. JGI/DOE(OMeGA) in progress
Verrucomicrobia  
Methylacidiphilum infernorum V4 Dunfield P. University of Hawaii CP000975.1 Final draft (Hou et al., 2008)
Methylacidiphilum fumariolicum SolV Huub J.M., Op den Camp H.J. Radbaoud University Nijmegen, CAHT00000000 Draft
Methylacidiphilum kamchatkense Kam1 University of Bergen 169117 In progress
Verrucomicrobium sp. LP2A Dunfield , P. JGI/DOE(OMeGA) Assembly in progress
Verrucomicrobium sp. 3C Jetten M.S; Huub J.M.; Op den Camp H.J. JGI/DOE(OMeGA) ARAS01000000 Final draft