DOI: 10.6084/m9.figshare.22637596.v3
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 first excel sheet represent 79 dereplicated MAGs from 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 as well as taxonomy information from both anvi'o v8 and GTDB-tk. Information for the MAGs that were selected for further refinement steps before being submitted the NCBI WGS genome repository can also be found within the dataset table. The MAGs/bins that were either selected to be further refined or are relevant to the final MAGs submitted to NCBI are highlighted in yellow, along with relevant information for why they were or were not selected.The second sheet represents a table containing the final state of the 10 MAGs after refinement and subsequently submitted to the Genbank repository in NCBI. In addition to the metadata from the first sheet, information on RNA located in each MAG have been added. Also, a MAG that was used for refinement and assembly of the final <i>Thermincola</i> MAG submitted to NCBI but is not present in the 79 dereplicated MAGs in the table from the first has also been appended to this table.References for methodology:Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. 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