Southern Ocean Reference Gene Catalogs

These data correspond to gene catalogs and matrices obtained from 218 metagenomes sampled during the Antarctic Circumpolar Expedition (ACE). The methodology and results obtained using these data are presented in the study entitled Water mass specific genes dominate the Southern Ocean microbiome, by Faure et al. (2025). Here is a description of each catalog/dataset : ACE_Unigenes_catalog.fa.gz: Catalog of all unigenes obtained from the 218 ACE metagenomes, i.e. ORFs clustered at 95% similarity and 90% coverage thresholds. Includes ORFs detected by Prodigal in the eukaryote-dominated >3µm size fraction. In FASTA format. SO-RGC.fa.gz: Catalog of unigenes that included at least one ORF from the 0.2-3µm size fraction, i.e. limited to the bacterial free-living size fraction used to build Tara Oceans and Polar Circle Reference Gene Catalogs (OM-RGC). In FASTA format. Polar_Genes.fa.gz: Catalog of ACE unigenes that were only detected in polar samples from Tara Oceans and Polar Circle (see Faure et al. for detailed methods). In FASTA format. Annotation_Table_AGN_CDH_Tax_KEGG_EGG.tsv.gz: Annotation table of all ACE ORFs (tab-separated format, one line = one non-dereplicated ORF), including (in column order): ORF ID AGNOSTOS cluster ID AGNOSTOS cluster representative ID AGNOSTOS cluster size AGNOSTOS cluster category If AGNOSTOS singleton, singleton category Unigene cluster representative ID Predicted domain (Prokaryote / Eukaryote) KEGG KO EggNOG seed ortholog EggNOG OGs EggNOG narrow OG name EggNOG narrow OG category EggNOG best OG name EggNOG best OG category EggNOG best OG description EggNOG preferred name EggNOG CAZy EggNOG BiGG Reaction EggNOG PFAMs AGNOSTOS_CLSTRLVL_GENE_MAT_COV.tsv.gz: AGNOSTOS cluster-level matrix of coverage. Columns correspond to samples and lines to AGNOSTOS clusters, with ID matching those of the Annotation table. Cell values correspond to ORF-level DESeq2-normalized per-base pair coverage values, summed by AGNOSTOS cluster. AGNOSTOS_CLSTRLVL_GENE_MAT_DET_Maximum.tsv.gz: AGNOSTOS cluster-level matrix of Detection. Detection is calculated at ORF-level after mapping: proportion of the ORF covered at at least 1X. In this matrix, the maximum detection value observed for each AGNOSTOS cluster in each sample is given. EnrichmentPolar_CDHitLevel_EggNogDesc.tsv.gz: Functional enrichment test outputs for polar unigenes (i.e. genes present in Polar_Genes.fa.gz) versus the rest of ACE unigenes. Contig_GTDBlineage_kraken.tsv.gz: Taxonomic annotation of ACE contigs based on the Genome Taxonomy DataBase (GTDB) using Kraken2, please refer to the study for more details on the methodology. ACEsamples_CorrespondanceTable.xlsx: Table of correspondance linking the different IDs given to ACE samples accross different steps, including BioSamples and ENA run and experiment codes. RF_AGC_NZVuniquecut20_T60MAX_ATT_All.txt.gz: Random forest models outputs for the large size fraction. Presents for each AGC the model R-squared, mean squared error and predictors' importance. RF_AGC_NZVuniquecut20_T60MAX_FL_All.txt.gz: Random forest models outputs for the small size fraction. Presents for each AGC the model R-squared, mean squared error and predictors' importance. DMSP_Lyase.tar.gz: Folder containing the matrix of abundance of the DMSP lyase AGCs, the corresponding ORF-level annotation table and random forest outputs. contigs_virus_genomadannot.tsv.gz: Annotation of ACE viral contigs (geNomad outputs). contigs_mimiviridae.xlsx: More detailed annotation of mimivirus contigs (please refer to the study for more details on the methodology). Please note that all CAG-related files are available on Figshare at DOI 10.6084/m9.figshare.29821949.本数据集源自南极环极考察（Antarctic Circumpolar Expedition, ACE）期间采集的218份宏基因组，经分析得到基因目录与矩阵文件。使用本数据集完成的研究方法与结果已发表于Faure等人（2025年）题为《水团特异性基因主导南大洋微生物组》的论文中。 以下为各目录/数据集的详细说明： ACE_Unigenes_catalog.fa.gz：源自218份ACE宏基因组的所有非冗余基因（unigene）目录，即按照95%相似度与90%覆盖度阈值聚类得到的开放阅读框（Open Reading Frame, ORF）。包含通过Prodigal在真核生物占比>3μm的粒径分级中检测到的ORF，文件格式为FASTA。 SO-RGC.fa.gz：包含至少1条来自0.2-3μm粒径分级（即用于构建Tara大洋与极圈参考基因目录（OM-RGC）的自由生活细菌粒径分级）的ORF的非冗余基因目录，文件格式为FASTA。 Polar_Genes.fa.gz：仅在Tara大洋与极圈的极地样本中检测到的ACE非冗余基因目录（详细方法参见Faure等人的研究），文件格式为FASTA。 Annotation_Table_AGN_CDH_Tax_KEGG_EGG.tsv.gz：所有ACE ORF的注释表（制表符分隔格式，每行对应1个未去冗余的ORF），列顺序依次为：ORF编号、AGNOSTOS聚类簇编号、AGNOSTOS聚类簇代表序列编号、AGNOSTOS聚类簇大小、AGNOSTOS聚类簇类别、若为AGNOSTOS单例则标注单例类别、非冗余基因聚类簇代表序列编号、预测的结构域（原核/真核）、KEGG KO编号、EggNOG种子直系同源基因、EggNOG直系同源簇（OGs）、EggNOG细分OG名称、EggNOG细分OG类别、EggNOG最优OG名称、EggNOG最优OG类别、EggNOG最优OG描述、EggNOG首选名称、EggNOG CAZy注释、EggNOG BiGG反应注释、EggNOG PFAM家族注释。 AGNOSTOS_CLSTRLVL_GENE_MAT_COV.tsv.gz：AGNOSTOS聚类簇水平的覆盖度矩阵。列对应样本，行对应AGNOSTOS聚类簇，其ID与注释表中的ID一致。单元格数值为经DESeq2标准化的ORF水平每碱基覆盖度，按AGNOSTOS聚类簇求和得到。 AGNOSTOS_CLSTRLVL_GENE_MAT_DET_Maximum.tsv.gz：AGNOSTOS聚类簇水平的检测度矩阵。检测度通过比对后在ORF水平计算：即至少被1X覆盖的ORF碱基比例。本矩阵给出每个AGNOSTOS聚类簇在各样本中观测到的最大检测度值。 EnrichmentPolar_CDHitLevel_EggNogDesc.tsv.gz：极地非冗余基因（即Polar_Genes.fa.gz中的基因）相较于其余ACE非冗余基因的功能富集测试结果文件。 Contig_GTDBlineage_kraken.tsv.gz：基于基因组分类学数据库（Genome Taxonomy Database, GTDB）与Kraken2对ACE重叠群（contig）进行的分类注释文件，详细方法参见相关研究。 ACEsamples_CorrespondanceTable.xlsx：ACE样本在不同分析步骤中使用的各类ID对应表，包含生物样本（BioSamples）编号以及欧洲核苷酸档案库（European Nucleotide Archive, ENA）的测序运行与实验编号。 RF_AGC_NZVuniquecut20_T60MAX_ATT_All.txt.gz：大粒径分级的随机森林模型输出文件。针对每个AGC，文件中给出了模型决定系数（R²）、均方误差以及预测因子重要性。 RF_AGC_NZVuniquecut20_T60MAX_FL_All.txt.gz：小粒径分级的随机森林模型输出文件。针对每个AGC，文件中给出了模型决定系数（R²）、均方误差以及预测因子重要性。 DMSP_Lyase.tar.gz：包含二甲基巯基丙酸内盐（Dimethylsulfoniopropionate, DMSP）裂解酶AGC丰度矩阵、对应ORF水平注释表以及随机森林模型输出结果的压缩文件夹。 contigs_virus_genomadannot.tsv.gz：ACE病毒重叠群的注释文件（geNomad分析输出结果）。 contigs_mimiviridae.xlsx：拟菌病毒科（Mimiviridae）重叠群的详细注释文件，详细方法参见相关研究。 请注意，所有与CAG相关的文件可在Figshare平台获取，DOI为10.6084/m9.figshare.29821949。