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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Publications at this Location » Publication #341233

Research Project: Genomics and Bioinformatics Research in Agriculturally Important Organisms

Location: Genomics and Bioinformatics Research

Title: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Author
item BOWERS, ROBERT - Joint Genome Institute
item KYRPIDES, NIKOS - Joint Genome Institute
item STEPANAUSKAS, RAMUNAS - Bigelow Laboratory For Ocean Sciences
item HARMON-SMITH, MIRANDA - Joint Genome Institute
item SCHULZ, FREDERIK - Joint Genome Institute
item DOUD, DEVIN - Joint Genome Institute
item REDDY, T.B. - Joint Genome Institute
item JARETT, JESSICA - Joint Genome Institute
item Rivers, Adam
item ELOE-FADROSH, EMILEY - Joint Genome Institute
item TRINGE, SUSANNAH - Joint Genome Institute
item IVANOVA, NATALIA - Joint Genome Institute
item COPELAND, ALEX - Joint Genome Institute
item CLUM, ALICIA - Joint Genome Institute
item BECRAFT, ERIC - Bigelow Laboratory For Ocean Sciences
item MALMSTROM, REX - Joint Genome Institute
item BIRREN, BRUCE - Broad Institute Of Mit/harvard
item SCHRIML, LYNN - National Cancer Institute (NCI, NIH)
item PODAR, MIRCEA - Oak Ridge National Laboratory
item BORK, PEER - European Molecular Biology Laboratory
item WEINSTOCK, GEORGE - National Center For Agriculture And Forestry Technologies (CENTA)
item BANFIELD, JILLIAN - University Of California
item GARRITY, GEROGE - Michigan State University
item HUGENHOLTZ, PHILIP - University Of Queensland
item PARKS, DONOVAN - University Of Queensland
item TYSON, GENE - University Of Queensland
item RINKE, CHRISTIAN - University Of Queensland
item DODSWORTH, JEREMY - California State University
item YOOSEPH, SHIBU - University Of Queensland
item SUTTON, GRANGER - J Craig Venter Institute
item YILMAZ, PELIN - Max Planck Society
item GLÖCKNER, FRANK - Max Planck Society
item MEYER, FOLKER - University Of Chicago
item GILBERT, JACK - University Of Chicago
item NELSON, WILLIAM - Pacific Northwest National Laboratory
item HALLAM, STEVEN - University Of British Columbia
item JUNGBLUTH, SEAN - Energy Joint Genome Institute
item ETTEMA, THIJS - Uppsala University
item TIGHE, SCOTT - University Of Vermont
item KONSTANTINIDIS, KONSTANTINOS - Georgia Institute Of Technology
item LIU, WEN-TSO - University Of Illinois
item BAKER, BRETT - University Of Texas At Austin
item RATTEI, THOMAS - University Of Vienna
item EISEN, JONATHAN - University Of California
item HEDLUND, BRIAN - University Of Nevada Las Vegas, Las Vegas, Nv
item MCMAHON, KATHERINE - University Of Wisconsin
item FIERER, NOAH - University Of Colorado
item KNIGHT, ROB - University Of California
item FINN, ROB - European Bioinformatics Institute
item KARSCH-MIZRACHI, ILENE - National Institutes Of Health (NIH)
item EREN, A - University Of Chicago
item WOYKE, TANJA - Energy Joint Genome Institute

Submitted to: Nature Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/27/2017
Publication Date: 8/8/2017
Publication URL: http://handle.nal.usda.gov/10113/5801851
Citation: Bowers, R.M., Kyrpides, N.C., Stepanauskas, R., Harmon-Smith, M., Schulz, F., Doud, D., Reddy, T.K., Jarett, J., Rivers, A.R., Eloe-Fadrosh, E.A., Tringe, S.G., Ivanova, N., Copeland, A., Clum, A., Becraft, E.D., Malmstrom, R.R., Birren, B., Schriml, L., Podar, M., Bork, P., Weinstock, G.W., Banfield, .F., Garrity, G.M., Hugenholtz, P., Parks, D.H., Tyson, G.W., Rinke, C., Dodsworth, J.A., Yooseph, S., Sutton, G., Yilmaz, P., Glöckner, F.O., Meyer, F., Gilbert, J.A., Nelson, W.C., Hallam, S.J., Jungbluth, S.P., Ettema, T.J., Tighe, S., Konstantinidis, K.T., Liu, W., Baker, B.J., Rattei, T., Eisen, J.A., Hedlund, B., Mcmahon, K.D., Fierer, N., Knight, R., Finn, R., Karsch-Mizrachi, I., Eren, A.M., Woyke, T. 2017. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology. 35, 725–731. doi:10.1038/nbt.3893.

Interpretive Summary: Most microorganisms cannot be grown in the laboratory. Having the genome of these organisms would reveal their role in the environment, but conventional genome sequencing requires growth in the laboratory. To sequence the genomes on these uncultivated organisms two alternative methods are used: singe cell sequencing and metagenome sequencing followed by the computational construction of “metagenome assembled genomes”. Because of the technical challenges of doing this, these genomes are often missing some components and the quality can vary greatly. This paper puts forth official Genomic Standards Consortium standards for what constitutes a Finished, High Quality Draft, Medium Quality Draft or Low Quality Draft single cell genome or metagenome assembled genome. This standardization is important because it will allow scientists to rapidly compare their data to other genomes derived from single cells or metagenomes.

Technical Abstract: We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the minimum information about any (x) sequence (MIxS). The standards are the minimum information about a single amplified genome (MISAG) and the minimum information about a metagenome-assembled genome (MIMAG), including (but not limited to) assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists including the minimum information about a genome sequence (MIGS), minimum information about a metagenomic sequence (MIMS) and minimum information about a marker gene sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.