Multi-omics for Understanding Climate Change (MUCC) database v2.0.0

<p>This is the Multi-omics for Understanding Climate Change (MUCC database) version 2.0.0. This current version is based on amplicon and metagenomic sequencing of Old Woman Creek (OWC), Prairie Pothole Region(PPR7 and PPR8), Jean Lafitte National Historical Park and Preserve (JLA), AmeriFlux site US-LA2 (LA2), Stordalen Mire (STM-fen and STM-bog), AmeriFlux site-ID US-Twt (TWI), and Peatland Responses Under Changing Environments (SPRUCE) and wetland soils. Additionally, this includes metatranscriptome sequencing from OWC. In the future, this will be expanded to include more data from these sites and from additional wetlands.</p> <p>OWC, PPR, JLA and LA2 data are deposited in NCBI Bioproject PRJNA1007388</p> <p>Stordalen Mire MAGs are deposited in BioProject PRJNA386538</p> <p>AmeriFlux site-ID US-Twt are deposited in SRA SRP003022, SRA SRP010671, SRP010730, SRP010738, SRP010741, SRP010747, SRP010748, SRP010751, SRP010862, SRP010870, and SRP011309.&nbsp;</p> <p>SPRUCE data are deposited in PRJNA638786 and PRJNA638601</p> <p>&nbsp;</p> <p>Files and datasets included here:&nbsp;</p> <ol> <li><strong>16S.zip&nbsp;</strong>16S amplicon sequencing data and site metadata for 1,112 samples (fastq files)</li> <li><strong>MQ_HQ_MAGs.zip&nbsp;</strong>Database of 4745 Medium and High Quality MAGs (fasta files)</li> <li><strong>MUCC_v2.0.0_HQMQ_genes.faa.zip </strong>MAG amino acid gene sequences derived from DRAM gene calls (fasta file)</li> <li><strong>MUCC_v2.0.0_HQMQ_annotations.tsv&nbsp;</strong>MAG DRAM ANNOTATIONS</li> <li><strong><strong>owc_metat_table_methanoregula_genes.csv&nbsp;</strong></strong>Metatranscriptomic expression per genes in <em>Methanoregula</em> across 133 metatranscriptomes (csv table)</li> <li><strong>gtdbtk.ar53.decorated.tree&nbsp;</strong>newick file for GTDB de novo work flow <em>Methanoregula</em> MAG tree</li> <li><strong>Newick_gene_trees.zip&nbsp;</strong>Trees used in blast identification of methylotrophic gene homologs to curate MR for methylotrophy</li> <li><strong>fasta_reference_genes.zip </strong>FASTA reference files of genes used as BLAST query to mine Methanoregula MAGs for genes involved in detoxification of reactive oxygen species (ROS) and methanogenic metabolism of methylated compounds</li> <li><strong>protpipeliner.py&nbsp;</strong>Python script is a modification of protpipeliner.rb for building RAXML trees</li> <li><strong>classification_w_outgroup.txt&nbsp;</strong>Taxonomy and corresponding MAG ID for&nbsp;<em>Methanregula&nbsp;</em>used in the tree (Figure 5B)</li> <li><strong>Methanoregula_metabolism_summary.xlsx&nbsp;</strong>The DRAM annotations of the&nbsp;<em>Methanoregula&nbsp;</em>MAGs from MUCC, GTDB, and JGI</li> <li><strong>Methanoregula_physiology.txt&nbsp;</strong>Curation of&nbsp;<em>Methanoregula</em> MAGS for physliogical functions of interest</li> <li><strong>Methanoregula_MAGs_list.txt </strong>Comprehensive list of all&nbsp;<em>Methanoregula </em>MAGs used and what database they were sourced from</li> <li><strong>Methanoregula_MAGs_DB.zip </strong>Database of 108&nbsp;<em>Methanregula</em> MAGs</li> </ol>