DOI: 10.5281/zenodo.14207414
title: Metagenome-assembled genomes from Stordalen Mire, Sweden (2019) (MAGs from long-read, short-read, & hybrid assemblies)

description: METHODS:

Soil samples (6 total) were collected at the Stordalen Mire site in 2019 from two depths (1-5 & 20-24 cm below ground) across three habitats (Palsa, Bog, and Fen). DNA was extracted based on the protocol described by Li et al. (2024). For short reads, libraries were prepared at the Joint Genome Institute (JGI) with the KAPA Hyperprep kit, and sequenced with Illumina NovaSeq 6000. For long reads, libraries were prepared with the SMRTbell Express Template Prep Kit 2.0 (PacBio), then sequenced using PacBio Sequel IIe at JGI. PacBio data was processed at JGI to form filtered CCS (Circular Consensus Sequencing) reads. 

Assemblies were generated with short-only, long-only, and hybrid read sources: Short-only was assembled with metaSPAdes (v3.15.4) using Aviary (v0.5.3) with default parameters. Long-only was assembled with metaFlye (v2.9-b1768) using Aviary (v0.5.3) with default parameters. Hybrid assembly was performed using Aviary v0.5.3 with default parameters. This involved a step-down procedure with long-read assembly through metaFlye (v2.9-b1768), followed by short-read polishing by Racon (v1.4.3), Pilon (v1.24) and then Racon again. Next, reads that didn't map to high-quality metaFlye contigs were hybrid assembled with SPAdes (--meta option) and binned out with MetaBAT2 (v2.1.5). For each bin, the reads within the bin were hybrid assembled using Unicycler (v0.4.8). The high-coverage metaFlye contigs and Unicycler contigs were then combined to form the assembly fasta file. Genome recovery was performed using Aviary v0.5.3 with samples chosen for differential abundance binning by Bin Chicken (v0.4.2) using SingleM metapackage S3.0.5. This involved initial read mapping through CoverM (v0.6.1) using minimap2 (v2.18) and binning by MetaBAT, MetaBAT2 (v2.1.5), VAMB (v3.0.2), SemiBin (v1.3.1), Rosella (v0.4.2), CONCOCT (v1.1.0) and MaxBin2 (v2.2.7). Genomes were analyzed using CheckM2 (v1.0.2) and clustered at 95% ANI using Galah (v0.4.0).

 

FILES:



EMERGE_MAGs_2019_long-short-hybrid.tar.gz - Archive containing the MAG files (.fna).

metadata_MAGs_2019_EMERGE.tsv - Table containing source sample names and accessions, GTDB classifications, CheckM2 quality information, NCBI GenomeBatch- and MIMAG(6.0)-formatted attributes, and other metadata for the MAGs.


 

FUNDING:

This research is a contribution of the EMERGE Biology Integration Institute (https://emerge-bii.github.io/), funded by the National Science Foundation, Biology Integration Institutes Program, Award # 2022070.

This study was also funded by the Genomic Science Program of the United States Department of Energy Office of Biological and Environmental Research, grant #s DE-SC0004632. DE-SC0010580. and DE-SC0016440.

We thank the Swedish Polar Research Secretariat and SITES for the support of the work done at the Abisko Scientific Research Station. SITES is supported by the Swedish Research Council's grant 4.3-2021-00164.

Data from the Joint Genome Institute (JGI) was collected under BER Support Science Proposal 503530 (DOI: 10.46936/10.25585/60001148), conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.