DOI: 10.6084/m9.figshare.21663302
title: FASTA files and relevant statistics for draft MAGs generated from a methanogenic benzene-degrading enrichment culture

description: Draft and complete metagenome assembled genomes (MAGs) were created from hybrid metagenomic assemblies of DGG-B, a strictly anaerobic, stable mixed microbial consortium that degrades benzene completely to methane and CO2. Our objective was to obtain closed genome of benzene-fermenting bacteria to enable elucidation of their elusive anaerobic benzene degradation pathway. <br> Between 2016 – 2017, aliquots from two subcultures of DGG-B (DGG1A, 15 mL; DGG0, 200 mL) were extracted for DNA using the DNeasy PowerSoil kit (Qiagen). At the time of sampling, the total volumes of DGG1A and DGG0 were 15.9 L and 9.0 L, respectively, and degraded benzene at a rate of 0.8-1.5 mg/L/day. Metagenomic sequencing was performed using long-read (PacBio) and/or short-read (Illumina) methods. Raw reads were trimmed and filtered (Trimmomatic v 0.32), assembled into contigs (MEGAHIT v. 1.1.1, metsSPAdes v. 3.10.1, SPAdes v. 3.12.0), and binned (metaBAT 2 v. 2.12, MaxBin 2.0 v. 2.2.3, BinSanity v. 0.2.6.1, DAS_Tools v. 1.1). For MEGAHIT assemblies, we used both default settings and the ‘sensitive’ preset option. Bins with a pairwise average nucleotide identity (ANI) cut-off at 99%, genome completeness &gt;50%, and contamination &lt;25% were compared and dereplicated using dRep. Taxonomy was assigned to the resulting draft metagenome-assembled genomes (MAGs) using the GTDB-tk tool kit. <br> References for methodology: Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114-2120. <br> Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. 2017. metaSPAdes: a new versatile metagenomic assembler. Genome Res 27:824-834. <br> Li D, Luo R, Liu CM, Leung CM, Ting HF, Sadakane K, Yamashita H, Lam TW. 2016. MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods 102:3-11. <br> Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455-77. <br> Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, Wang Z. 2019. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7:e7359. <br> Wu YW, Simmons BA, Singer SW. 2016. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32:605-7. <br> Graham ED, Heidelberg JF, Tully BJ. 2017. BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation. PeerJ 5:e3035. <br> Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, Banfield JF. 2018. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat Microbiol 3:836-843. <br> Olm MR, Brown CT, Brooks B, Banfield JF. 2017. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J 11:2864-2868. <br> Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. 2019. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics doi:10.1093/bioinformatics/btz848.