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: 16S.zip 16S amplicon sequencing data and site metadata for 1,112 samples (fastq files) MQ_HQ_MAGs.zip Database of 4745 Medium and High Quality MAGs (fasta files) MUCC_v2.0.0_HQMQ_genes.faa.zip MAG amino acid gene sequences derived from DRAM gene calls (fasta file) MUCC_v2.0.0_HQMQ_annotations.tsv MAG DRAM ANNOTATIONS owc_metat_table_methanoregula_genes.csv Metatranscriptomic expression per genes in Methanoregula across 133 metatranscriptomes (csv table) gtdbtk.ar53.decorated.tree newick file for GTDB de novo work flow Methanoregula MAG tree Newick_gene_trees.zip Trees used in blast identification of methylotrophic gene homologs to curate MR for methylotrophy 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 protpipeliner.py Python script is a modification of protpipeliner.rb for building RAXML trees classification_w_outgroup.txt Taxonomy and corresponding MAG ID for Methanregula used in the tree (Figure 5B) Methanoregula_metabolism_summary.xlsx The DRAM annotations of the Methanoregula MAGs from MUCC, GTDB, and JGI Methanoregula_physiology.txt Curation of Methanoregula MAGS for physliogical functions of interest Methanoregula_MAGs_list.txt Comprehensive list of all Methanoregula MAGs used and what database they were sourced from Methanoregula_MAGs_DB.zip Database of 108 Methanregula MAGs本数据集为多组学气候变化研究数据库（Multi-omics for Understanding Climate Change, MUCC database）2.0.0版本。当前版本基于对老妇溪（Old Woman Creek, OWC）、草原坑洼区域（Prairie Pothole Region, PPR7与PPR8）、让·拉菲特国家历史公园与保护区（Jean Lafitte National Historical Park and Preserve, JLA）、AmeriFlux站点US-LA2（简称LA2）、斯托达伦泥炭地（Stordalen Mire，分为STM-fen与STM-bog）、AmeriFlux站点US-Twt（简称TWI）以及变化环境下泥炭地响应实验（Peatland Responses Under Changing Environments, SPRUCE）的湿地土壤开展的扩增子测序与宏基因组测序构建。此外，本数据集还包含OWC的宏转录组测序数据。未来，本数据集将扩充上述站点及更多湿地的相关数据。 OWC、PPR、JLA与LA2的数据已存档至NCBI生物项目（BioProject）PRJNA1007388。 斯托达伦泥炭地的宏基因组组装基因组（Metagenome-Assembled Genomes, MAGs）已提交至生物项目（BioProject）PRJNA386538。 AmeriFlux站点US-Twt的数据已存档于序列读取档案（Sequence Read Archive, SRA）的SRP003022、SRP010671、SRP010730、SRP010738、SRP010741、SRP010747、SRP010748、SRP010751、SRP010862、SRP010870及SRP011309。 SPRUCE数据集已存档于生物项目（BioProject）PRJNA638786与PRJNA638601。 本数据集包含的文件与数据集如下： 1. 16S.zip：包含1112个样本的16S扩增子测序数据与站点元数据的fastq格式文件集 2. MQ_HQ_MAGs.zip：包含4745个中、高质量宏基因组组装基因组的数据库文件（fasta格式） 3. MUCC_v2.0.0_HQMQ_genes.faa.zip：基于DRAM基因预测得到的MAG氨基酸序列文件（fasta格式） 4. MUCC_v2.0.0_HQMQ_annotations.tsv：MAG的DRAM注释文件 5. owc_metat_table_methanoregula_genes.csv：133个宏转录组中产甲烷古菌属（Methanoregula）的基因转录表达谱csv表格 6. gtdbtk.ar53.decorated.tree：基于基因组分类数据库（Genome Taxonomy Database, GTDB）从头分析流程构建的Methanoregula MAG系统发育树的Newick格式文件 7. Newick_gene_trees.zip：用于通过BLAST鉴定甲基营养基因同源物，以筛选产甲烷古菌属甲基营养功能相关的系统发育树文件集 8. fasta_reference_genes.zip：用作BLAST查询序列的FASTA格式参考基因集，用于从Methanoregula MAGs中挖掘参与活性氧（Reactive Oxygen Species, ROS）解毒及甲基化合物产甲烷代谢的相关基因 9. protpipeliner.py：用于构建RAXML系统发育树的Python脚本，为protpipeliner.rb的修改版本 10. classification_w_outgroup.txt：用于构建系统发育树（图5B）的Methanoregula菌株的分类学信息及其对应的MAG ID 11. Methanoregula_metabolism_summary.xlsx：来自MUCC、基因组分类数据库（GTDB）及联合基因组研究所（Joint Genome Institute, JGI）数据库的Methanoregula MAGs的DRAM注释汇总文件 12. Methanoregula_physiology.txt：针对目标生理功能整理的Methanoregula MAGs注释文件 13. Methanoregula_MAGs_list.txt：本研究使用的所有Methanoregula MAGs的完整列表及其来源数据库 14. Methanoregula_MAGs_DB.zip：包含108个Methanoregula MAGs的数据库文件