Title: Xander: employing a novel method for efficient gene-targeted metagenomic assembly

Abstract

Here, metagenomics can provide important insight into microbial communities. However, assembling metagenomic datasets has proven to be computationally challenging. Current methods often assemble only fragmented partial genes. We present a novel method for targeting assembly of specific protein-coding genes. This method combines a de Bruijn graph, as used in standard assembly approaches, and a protein profile hidden Markov model (HMM) for the gene of interest, as used in standard annotation approaches. These are used to create a novel combined weighted assembly graph. Xander performs both assembly and annotation concomitantly using information incorporated in this graph. We demonstrate the utility of this approach by assembling contigs for one phylogenetic marker gene and for two functional marker genes, first on Human Microbiome Project (HMP)-defined community Illumina data and then on 21 rhizosphere soil metagenomic datasets from three different crops totaling over 800 Gbp of unassembled data. We compared our method to a recently published bulk metagenome assembly method and a recently published gene-targeted assembler and found our method produced more, longer, and higher quality gene sequences. In conclusion, xander combines gene assignment with the rapid assembly of full-length or near full-length functional genes from metagenomic data without requiring bulk assembly or post-processingmore » to find genes of interest. HMMs used for assembly can be tailored to the targeted genes, allowing flexibility to improve annotation over generic annotation pipelines.« less

Authors:

Wang, Qiong; Fish, Jordan A.; Gilman, Mariah; Sun, Yanni; Brown, C. Titus; Tiedje, James M.; Cole, James R.

Publication Date:

Wed Aug 05 00:00:00 EDT 2015

Research Org.:

Michigan State Univ., East Lansing, MI (United States)

Sponsoring Org.:

USDOE

OSTI Identifier:

1503062

Alternate Identifier(s):

OSTI ID: 1454520

Grant/Contract Number:  

BER DE-FC02-07ER64494; FG02-99ER62848; SC0010715

Resource Type:

Published Article

Journal Name:

Microbiome

Additional Journal Information:

Journal Name: Microbiome Journal Volume: 3 Journal Issue: 1; Journal ID: ISSN 2049-2618

Publisher:

Springer Science + Business Media

Country of Publication:

United Kingdom

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; Metagenomics; Assembly; Functional gene; HMM; Nitrogen cycle; nifH; nirK; Biofuel crop