Genome-scale community modelling reveals key metabolic cross-feedings in epipelagic bacterioplankton communities (Supplementary Materials)

A comprehensive catalog of 19,791 marine prokaryotic isolates (WGS), single-amplified genomes (SAGs) and metagenomic-assembled genomes (MAGs) compiled from MarRef v4.0 (N=943, mostly high-quality WGS), MarDB v4.0 (N=12,963), and the aquatic representative genomes from the ProGenomes database v1.0 (N=566). This collection of well-documented genomes was complemented by 5,319 MAGs assembled from four distinct studies, namely: Parks et al. 2017 (DOI; N=1,765; downloaded from EBI), Tully et al. 2017/2018 (DOI and DOI; N=2,597; downloaded from EBI), and Delmont et al. 2018 (DOI; N=957; downloaded from FIGSHARE). The Parks et al. study contained genomes reconstructed from non-marine biomes. Thus, a selection of 1,765 genomes was extracted by searching for specific keywords: “tara|marine|sea|ocean|mediterranean” (case insensitive). Note that depending on their study of origin, included MAGs may have been reconstructed using different assembling and binning methods. The archive includes: a metadata file describing the quality and redundancy of the genomes named `EcoSysMic_metadata.tsv` sequences of the 19,791 (redundant) genomes in `All/WGS` companion files in `All/Data` and `dRep95/Data` (see Methods in the associated paper), including predicted CDS and EggNOG functional annotations predicted GTDB taxonomy CarveMe reconstructed metabolic models and their MEMOTE quality The 7,658 non-redundant species-level genomes (delineated by a 95% ANI threshold over 60% of genome length) that were used in the associated paper are defined by the column `is_drep95` in the metadata file.本数据集为一套涵盖19791株海洋原核生物分离株全基因组测序（Whole Genome Sequencing, WGS）、单扩增基因组（Single-Amplified Genomes, SAGs）与宏基因组组装基因组（Metagenome-Assembled Genomes, MAGs）的综合目录，数据整合自三个公开来源：MarRef v4.0（样本量N=943，以高质量WGS为主）、MarDB v4.0（N=12963），以及ProGenomes数据库v1.0中的水生代表性基因组（N=566）。这套经过详实记录的基因组集合，额外补充了来自四项独立研究的5319个MAGs，具体包括：Parks等人2017年的研究（DOI；N=1765，从EBI平台下载）、Tully等人2017/2018年的两项相关研究（两篇DOI；N=2597，从EBI平台下载），以及Delmont等人2018年的研究（DOI；N=957，从FIGSHARE平台下载）。由于Parks等人的研究包含了非海洋生物群落中重建的基因组，因此本数据集通过检索不区分大小写的关键词“tara|marine|sea|ocean|mediterranean”，从其原始的1765个基因组中筛选得到符合海洋来源的子集。需注意的是，根据来源研究的不同，本次纳入的MAGs可能采用了各异的基因组组装与分箱方法。本归档文件包含以下内容： 1. 一份名为`EcoSysMic_metadata.tsv`的元数据文件，用于描述各基因组的质量与冗余度； 2. 19791个（含冗余）基因组的序列数据，存储于`All/WGS`、`All/Data`及`dRep95/Data`配套文件中（详细说明参见相关论文的方法部分），其中包含预测的编码序列（Coding Sequence, CDS）、EggNOG功能注释信息，以及基于GTDB（Genome Taxonomy Database）的分类学预测注释； 3. CarveMe工具重建的代谢模型及其MEMOTE质量评估结果。本相关论文中使用的7658个非冗余物种级基因组（以95%平均核苷酸一致性（Average Nucleotide Identity, ANI）阈值、覆盖60%基因组长度的标准划定），可通过元数据文件中的`is_drep95`列进行快速定位筛选。