Aix-Marseille Université, Université de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France.
Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara Oceans-GOSEE, Paris, France.
Nucleic Acids Res. 2022 Jul 5;50(W1):W516-W526. doi: 10.1093/nar/gkac420.
Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the 'Ocean Gene Atlas' (OGA2) is a freely available intuitive online service to mine large and complex marine environmental genomic databases. OGA2 datasets available have been extended and now include, from the Tara Oceans portfolio: (i) eukaryotic Metagenome-Assembled-Genomes (MAGs) and Single-cell Assembled Genomes (SAGs) (10.2E+6 coding genes), (ii) version 2 of Ocean Microbial Reference Gene Catalogue (46.8E+6 non-redundant genes), (iii) 924 MetaGenomic Transcriptomes (7E+6 unigenes), (iv) 530 MAGs from an Arctic MAG catalogue (1E+6 genes) and (v) 1888 Bacterial and Archaeal Genomes (4.5E+6 genes), and an additional dataset from the Malaspina 2010 global circumnavigation: (vi) 317 Malaspina Deep Metagenome Assembled Genomes (0.9E+6 genes). Novel analyses enabled by OGA2 include phylogenetic tree inference to visualize user queries within their context of sequence homologues from both the marine environmental dataset and the RefSeq database. An Application Programming Interface (API) now allows users to query OGA2 using command-line tools, hence providing local workflow integration. Finally, gene abundance can be interactively filtered directly on map displays using any of the available environmental variables. Ocean Gene Atlas v2.0 is freely-available at: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.
利用 Tara Oceans 海洋宏基因组和宏转录组等大型数据资源来检验关于基因生物地理学的假设，需要大量的硬件资源和编程技能。新版本的“海洋基因图谱”（OGA2）是一个免费的直观在线服务，可以挖掘大型和复杂的海洋环境基因组数据库。OGA2 现在可提供扩展数据集，其中包括 Tara Oceans 项目中的：（i）真核生物宏基因组组装基因组（MAGs）和单细胞组装基因组（SAGs）（10.2E+6 个编码基因），（ii）海洋微生物参考基因目录的版本 2（46.8E+6 个非冗余基因），（iii）924 个元基因组转录组（7E+6 个单基因），（iv）来自北极 MAG 目录的 530 个 MAG（1E+6 个基因）和（v）1888 个细菌和古菌基因组（4.5E+6 个基因），以及 Malaspina 2010 年环球航行的另外一个数据集：（vi）317 个 Malaspina 深海宏基因组组装基因组（0.9E+6 个基因）。OGA2 支持的新型分析包括系统发育树推断，可在来自海洋环境数据集和 RefSeq 数据库的序列同源物的上下文中可视化用户查询。现在，应用程序编程接口（API）允许用户使用命令行工具查询 OGA2，从而提供本地工作流程集成。最后，用户可以使用任何可用的环境变量直接在地图显示上交互式筛选基因丰度。Ocean Gene Atlas v2.0 可在以下网址免费获得：https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/。
