DOI: 10.6084/m9.figshare.22637596.v1
title: FASTA files and relevant statistics for draft MAGs generated from a nitrate-reducing benzene-degrading enrichment culture

description: Presented within are draft metagenome assembled genomes (MAGs) created from multiple genome assemblies of nitrate-reducing benzene-degrading enrichment cultures (NRBC) derived from soil samples collected from a decomissioned gas station located in Toronto, Canada. The primary objective was to obtain closed genomes of organisms from NRBC in order to understand each organism's role in the enrichment culture.The MAGs presented within the file represent dereplicated MAGs that originate from 15mL samples taken from the following four samples: CartCons19 in 2018 (paired-end sequencing; culture volume 1L), FeS-Dialysis in 2018 (paired-end sequencing; culture volume 500 mL), FeS-Dialysis in 2020 (paired-end and PacBio sequencing; culture volume 500mL), and 10L-NRBC in 2020 (paired-end and PacBio sequencing; culture volume 10L), each with a benzene degradation rate ranging from 0.5-4 mg/L/day. DNA was extracted using the DNeasy PowerSoil kit (Qiagen). First, Trimmomatic v0.32 was used to preprocess the raw sequencing data. Then, several prominent assembly tools were used for sequence assembly (Megahit v1.1.1, metaspades v3.15.3, and IDBA-UD. The assembled contigs were next binned using the following tools: MaxBIN v2.2.7, metaBAT v2.12, and CONCOCT v1.1. Finally, taxonomy for each draft MAG was classified using the GTDB-tk tool kit. Nucleotide FASTA files for 79 MAGs dereplicated from 868 using dRep v2.0.0 can be found within the attached archive file. Details for the sequencing datasets, assembly techniques, and binning techniques used for each MAG can be found within the attached dataset table. In addition, the table contains metadata for each MAG, such as completeness, contamination and read recruitment from each metagenome paired-end library from CheckM and anvi'o v8. Information for how each MAG was selected for further refinement steps before being submitted the NCBI WGS genome repository can also be found within the dataset table.References for methodology:Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114-2120.Peng, Y., et al., <i>IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.</i> Bioinformatics, 2012. <b>28</b>(11): p. 1420-1428.Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. 2017. metaSPAdes: a new versatile metagenomic assembler. Genome Res 27:824-834.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.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.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.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.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.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.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.Alneberg, J., et al., Binning metagenomic contigs by coverage and composition. Nature Methods, 2014. 11(11): p. 1144-1146.Eren, A.M., et al., Anvi'o: an advanced analysis and visualization platform for 'omics data. PeerJ, 2015. 3: p. e1319.Parks, D.H., et al., CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res, 2015. 25(7): p. 1043-55.