TY - JOUR

T1 - BiosyntheticSPAdes

T2 - reconstructing biosynthetic gene clusters from assembly graphs

AU - Meleshko, Dmitry

AU - Mohimani, Hosein

AU - Tracanna, Vittorio

AU - Hajirasouliha, Iman

AU - Medema, Marnix H.

AU - Korobeynikov, Anton

AU - Pevzner, Pavel A.

N1 - Publisher Copyright: © 2019 Meleshko et al.

PY - 2019/8/1

Y1 - 2019/8/1

N2 - Predicting biosynthetic gene clusters (BGCs) is critically important for discovery of antibiotics and other natural products. While BGC prediction from complete genomes is a well-studied problem, predicting BGCs in fragmented genomic assemblies remains challenging. The existing BGC prediction tools often assume that each BGC is encoded within a single contig in the genome assembly, a condition that is violated for most sequenced microbial genomes where BGCs are often scattered through several contigs, making it difficult to reconstruct them. The situation is even more severe in shotgun metagenomics, where the contigs are often short, and the existing tools fail to predict a large fraction of long BGCs. While it is difficult to assemble BGCs in a single contig, the structure of the genome assembly graph often provides clues on how to combine multiple contigs into segments encoding long BGCs. We describe biosyntheticSPAdes, a tool for predicting BGCs in assembly graphs and demonstrate that it greatly improves the reconstruction of BGCs from genomic and metagenomics data sets.

AB - Predicting biosynthetic gene clusters (BGCs) is critically important for discovery of antibiotics and other natural products. While BGC prediction from complete genomes is a well-studied problem, predicting BGCs in fragmented genomic assemblies remains challenging. The existing BGC prediction tools often assume that each BGC is encoded within a single contig in the genome assembly, a condition that is violated for most sequenced microbial genomes where BGCs are often scattered through several contigs, making it difficult to reconstruct them. The situation is even more severe in shotgun metagenomics, where the contigs are often short, and the existing tools fail to predict a large fraction of long BGCs. While it is difficult to assemble BGCs in a single contig, the structure of the genome assembly graph often provides clues on how to combine multiple contigs into segments encoding long BGCs. We describe biosyntheticSPAdes, a tool for predicting BGCs in assembly graphs and demonstrate that it greatly improves the reconstruction of BGCs from genomic and metagenomics data sets.

KW - PEPTIDIC NATURAL-PRODUCTS

KW - COMPLETE GENOME SEQUENCE

KW - MASS-SPECTROMETRY

KW - DATABASE SEARCH

KW - BACTERIAL

KW - DEREPLICATION

KW - PREDICTION

KW - PARALLEL

KW - REVEALS

KW - MODEL

UR - http://www.scopus.com/inward/record.url?scp=85071055943&partnerID=8YFLogxK

UR - http://www.mendeley.com/research/biosyntheticspades-reconstructing-biosynthetic-gene-clusters-assembly-graphs

U2 - 10.1101/gr.243477.118

DO - 10.1101/gr.243477.118

M3 - Article

C2 - 31160374

AN - SCOPUS:85071055943

VL - 29

SP - 1352

EP - 1362

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 8

ER -