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

Speth, Daan R. and Orphan, Victoria J. (2018) Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds light on metabolic versatility of the Methanomassiliicoccales. . (Unpublished) http://resolver.caltech.edu/CaltechAUTHORS:20181030-134348430

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Abstract

Over the past years, metagenomics has revolutionized our view of microbial diversity. Moreover, 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. We use our mcrA dataset to assess the environmental distribution of the Methanomassiliicoccales and reconstruct and analyze a draft genome belonging to the ′Lake Pavin cluster′, an understudied environmental clade of the Methanomassiliicoccales. Thus, we show that marker gene mining can enhance the discovery power of metagenomics, by identifying novel lineages and aiding selection of targets for in-depth analyses. Marker gene mining is less sensitive to strain heterogeneity and has a lower abundance threshold than genome-resolved metagenomics, as it only requires short contigs and there is no binning step. Additionally, it is computationally cheaper than genome resolved metagenomics, since only a small subset of reads needs to be assembled. It is therefore a suitable approach to extract knowledge from the many publicly available sequencing projects.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/328906DOIDiscussion Paper
ORCID:
AuthorORCID
Speth, Daan R.0000-0002-2361-5935
Orphan, Victoria J.0000-0002-5374-6178
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. bioRxiv preprint first posted online May. 23, 2018. We thank Woody Fischer and Connor Skennerton for helpful discussion and Grayson Chadwick for critically reading the manuscript. This manuscript is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under award number DE-SC0016469 to VJO. In addition, DRS was supported by NWO Rubicon 019.153LW.039.
Funders:
Funding AgencyGrant Number
Department of Energy (DOE)DE-SC0016469
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)019.153LW.039
Subject Keywords:Marker genes; data mining; mcrA; methanogens; metagenomics; Methanomassiliicoccales
Record Number:CaltechAUTHORS:20181030-134348430
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20181030-134348430
Official Citation:Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds light on metabolic versatility of the Methanomassiliicoccales. Daan R Speth, Victoria J Orphan. bioRxiv 328906; doi: https://doi.org/10.1101/328906
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:90518
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:30 Oct 2018 20:57
Last Modified:30 Oct 2018 20:57

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