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Title: Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales

Abstract

Over the past years, metagenomics has revolutionized our view of microbial diversity. Furthermore, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through the mcrA gene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads.

Authors:
 [1];  [1]
  1. California Inst. of Technology (CalTech), Pasadena, CA (United States)
Publication Date:
Research Org.:
California Inst. of Technology (CalTech), Pasadena, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1503317
Grant/Contract Number:  
SC0016469
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
PeerJ
Additional Journal Information:
Journal Volume: 6; Journal ID: ISSN 2167-8359
Publisher:
PeerJ Inc.
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Marker genes; mcrA; Data mining; Methanogens; Methanomassiliicoccales

Citation Formats

Speth, Daan R., and Orphan, Victoria J.. Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales. United States: N. p., 2018. Web. doi:10.7717/peerj.5614.
Speth, Daan R., & Orphan, Victoria J.. Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales. United States. doi:10.7717/peerj.5614.
Speth, Daan R., and Orphan, Victoria J.. Mon . "Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales". United States. doi:10.7717/peerj.5614. https://www.osti.gov/servlets/purl/1503317.
@article{osti_1503317,
title = {Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales},
author = {Speth, Daan R. and Orphan, Victoria J.},
abstractNote = {Over the past years, metagenomics has revolutionized our view of microbial diversity. Furthermore, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through the mcrA gene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads.},
doi = {10.7717/peerj.5614},
journal = {PeerJ},
issn = {2167-8359},
number = ,
volume = 6,
place = {United States},
year = {2018},
month = {9}
}

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Works referenced in this record:

Search and clustering orders of magnitude faster than BLAST
journal, August 2010


MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

  • Edgar, R. C.
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