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

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.

OWC, PPR, JLA and LA2 data are deposited in NCBI Bioproject PRJNA1007388

Stordalen Mire MAGs are deposited in BioProject PRJNA386538

AmeriFlux site-ID US-Twt are deposited in SRA SRP003022, SRA SRP010671, SRP010730, SRP010738, SRP010741, SRP010747, SRP010748, SRP010751, SRP010862, SRP010870, and SRP011309. 

SPRUCE data are deposited in PRJNA638786 and PRJNA638601

Files and datasets included here: 

1. 16S.zip 16S amplicon sequencing data and site metadata for 1,112 samples (fastq files)
2. MQ_HQ_MAGs.zip Database of 4745 Medium and High Quality MAGs (fasta files)
3. MUCC_v2.0.0_HQMQ_genes.faa.zip MAG amino acid gene sequences derived from DRAM gene calls (fasta file)
4. MUCC_v2.0.0_HQMQ_annotations.tsv MAG DRAM ANNOTATIONS
5. owc_metat_table_methanoregula_genes.csv Metatranscriptomic expression per genes in Methanoregula across 133 metatranscriptomes (csv table)
6. gtdbtk.ar53.decorated.tree newick file for GTDB de novo work flow Methanoregula MAG tree
7. Newick_gene_trees.zip Trees used in blast identification of methylotrophic gene homologs to curate MR for methylotrophy
8. fasta_reference_genes.zip 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
9. protpipeliner.py Python script is a modification of protpipeliner.rb for building RAXML trees
10. classification_w_outgroup.txt Taxonomy and corresponding MAG ID for Methanregula used in the tree (Figure 5B)
11. Methanoregula_metabolism_summary.xlsx The DRAM annotations of the Methanoregula MAGs from MUCC, GTDB, and JGI
12. Methanoregula_physiology.txt Curation of Methanoregula MAGS for physliogical functions of interest
13. Methanoregula_MAGs_list.txt Comprehensive list of all Methanoregula MAGs used and what database they were sourced from
14. Methanoregula_MAGs_DB.zip Database of 108 Methanregula MAGs