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Captured metagenomics: large-scale targeting of genes based on 'sequence capture' reveals functional diversity in soils.

Author:
  • Lokeshwaran Manoharan
  • Sandeep Kushwaha
  • Katarina Hedlund
  • Dag Ahrén
Publishing year: 2015
Language: English
Pages: 451-460
Publication/Series: DNA Research
Volume: 22
Issue: 6
Document type: Journal article
Publisher: Oxford University Press

Abstract english

Microbial enzyme diversity is a key to understand many ecosystem processes. Whole metagenome sequencing (WMG) obtains information on functional genes, but it is costly and inefficient due to large amount of sequencing that is required. In this study, we have applied a captured metagenomics technique for functional genes in soil microorganisms, as an alternative to WMG. Large-scale targeting of functional genes, coding for enzymes related to organic matter degradation, was applied to two agricultural soil communities through captured metagenomics. Captured metagenomics uses custom-designed, hybridization-based oligonucleotide probes that enrich functional genes of interest in metagenomic libraries where only probe-bound DNA fragments are sequenced. The captured metagenomes were highly enriched with targeted genes while maintaining their target diversity and their taxonomic distribution correlated well with the traditional ribosomal sequencing. The captured metagenomes were highly enriched with genes related to organic matter degradation; at least five times more than similar, publicly available soil WMG projects. This target enrichment technique also preserves the functional representation of the soils, thereby facilitating comparative metagenomics projects. Here, we present the first study that applies the captured metagenomics approach in large scale, and this novel method allows deep investigations of central ecosystem processes by studying functional gene abundances.

Keywords

  • Bioinformatics and Systems Biology
  • Genetics

Other

Published
  • ISSN: 1756-1663
Katarina Hedlund
E-mail: katarina [dot] hedlund [at] biol [dot] lu [dot] se

Professor

Biodiversity

+46 46 222 37 98

+46 72 562 10 04

E-A321

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Researcher

Centre for Environmental and Climate Research (CEC)

+46 46 222 37 98

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Centre for Animal Movement Research
Evolutionary Ecology, Department of Biology
Ecology building S-223 62 Lund Sweden