FRESH-MAP dataset: study on the ecological success of streamlined aquatic microorganisms

We release the FRESH-MAP dataset, a compilation of 9028 prokaryotic species-clusters (ANI >95%) detected on a set of 636 globally-distributed freshwater metagenomes after competitive mapping. The main goal of our study was to provide the first systematic evaluation of the ‘Black Queen Hypothesis’ on a global scale based on aquatic metagenomic datasets. In this repository, we provide the supplementary tables and the full set of genomes. Moreover, we include all 9028 representative genomes (FRESH-MAP dataset) as a zip file (FreshMap_dataset.zip). You can also find 12 supplementary tables that include the following information. - Table S1: Genomic statistics of all 80561 medium-to-high quality genomes (>50% completeness and <5% contamination) used in the study. We include publication reference, completeness, contamination, GTDB-tk taxonomy, type of genome, environment of origin, etc. - Table S2: Genomic information of all 24050 species-clusters (ANI >95%), including the best representative genome. We include origin of the species-clusters (freshwater, non-freshwater or mixed) and the type of genome (omics, isolate or both). Genome stats here included refer to the best representative genome of each species-cluster. - Table S3: List of all 636 freshwater genomes used for competitive mapping. We include accession numbers, reference of publication and metadata. - Table S4: Mapping statistics after trimming. We include the total number of reads, number of mapped reads, average length of the reads (bp), and GC content (%). - Table S5: Relative abundance results for each of the 24050 species-clusters (ANI >95%) across the freshwater metagenomes. - Table S6: List of 1202 representative genomes part of the co-occurrence network, including information on the degree of connectedness and cohort. - Table S7: Recruitment of species-clusters per phyla across the different cohorts. Yellow indicates phyla linked to a specific cohort. - Table S8: Completeness (ranging from 0 to 1) of all KEGG modules involved in biosynthesis of amino acids, nucleotides and vitamins for each of the 9028 species-clusters (ANI > 95%) detected on ≥1 freshwater metagenomes. - Table S9: Number of copies of each KEGG KO involved in flagellar, sigma factors, two-component systems, carbon fixation, nitrogen cycle, and sulfur cycle for each of the 9028 species-clusters (ANI > 95%) detected on ≥1 freshwater metagenomes. - Table S10: Metadata of the two newly sequenced metagenomic samples from Stadsträdgården, Uppsala (Sweden), including accession numbers. - Table S11: Metagenomic samples used for re-binning from the StratfreshDB (Buck et al., 2021), including ENA accession numbers. - Table S12: Genomic statistics, including completeness and contamination of the re-binned (n = 11146) and original (n = 7837) MAGs.

本研究发布FRESH-MAP数据集，该数据集包含经竞争性比对后，在636个全球分布的淡水宏基因组中检测得到的9028个原核物种簇（平均核苷酸同源性（ANI，Average Nucleotide Identity）>95%）。本研究的核心目标为，基于水生宏基因组数据集，首次在全球尺度上对“黑皇后假说（Black Queen Hypothesis）”开展系统性评估。在本数据仓库中，我们提供了补充表格与完整基因组集。此外，我们将全部9028条代表性基因组（即FRESH-MAP数据集）打包为压缩文件（FreshMap_dataset.zip）。
此外还包含12张补充表格，涵盖以下内容：
- 表S1：本研究使用的全部80561条中高质量基因组（完整性>50%且污染率<5%）的基因组统计信息，包含发表参考文献、基因组完整性、污染率、GTDB-tk（Genome Taxonomy Database toolkit）分类学注释、基因组类型、来源生境等内容。
- 表S2：全部24050个物种簇（ANI>95%）的基因组信息，包含各物种簇的最优代表性基因组。表格涵盖物种簇的来源生境（淡水、非淡水或混合生境）以及基因组类型（宏基因组、分离株或两者兼具），此处列出的基因组统计信息均对应各物种簇的最优代表性基因组。
- 表S3：用于竞争性比对的全部636条淡水基因组列表，包含登录号、发表参考文献与元数据信息。
- 表S4：质控过滤后的比对统计信息，包含reads总数、比对上的reads数、reads平均长度（单位：bp）以及GC含量（百分比）。
- 表S5：24050个物种簇（ANI>95%）在各淡水宏基因组中的相对丰度结果。
- 表S6：共现网络包含的1202条代表性基因组列表，包含连接度与类群分组信息。
- 表S7：不同类群分组中各菌门的物种簇招募情况，黄色标注代表与特定类群分组相关联的菌门。
- 表S8：在≥1个淡水宏基因组中检测到的9028个物种簇（ANI>95%）中，所有参与氨基酸、核苷酸与维生素生物合成的KEGG模块（KEGG modules）的完整性（取值范围0~1）。
- 表S9：在≥1个淡水宏基因组中检测到的9028个物种簇（ANI>95%）中，所有参与鞭毛结构、σ因子、双组分系统、碳固定、氮循环与硫循环的KEGG KO（KEGG Orthology）的拷贝数。
- 表S10：来自瑞典乌普萨拉市Stadsträdgården的2条新测序宏基因组样本的元数据，包含登录号信息。
- 表S11：从StratfreshDB（Buck等，2021）中获取用于重新分箱的宏基因组样本，包含欧洲核苷酸档案馆（ENA，European Nucleotide Archive）登录号。
- 表S12：重新分箱得到的（n=11146）与原始（n=7837）宏基因组组装基因组（MAGs，Metagenome-Assembled Genomes）的基因组统计信息，包含完整性与污染率。