Large-scale metagenomic and metatranscriptomic data analyses are often restricted by their gene-centric approach, limiting the ability to understand organismal and community biology. De novo assembly of large and mosaic eukaryotic genomes from complex meta-omics data remains a challenging task, especially in comparison with more straightforward bacterial and archaeal systems. Here, we use a transcriptome reconstruction method based on clustering co-abundant genes across a series of metagenomic samples. We investigated the co-abundance patterns of ∼37 million eukaryotic unigenes across 365 metagenomic samples collected during the Tara Oceans expeditions to assess the diversity and functional profiles of marine plankton. We identified ∼12,000 co-abundant gene groups (CAGs), encompassing ∼7 million unigenes, including 924 metagenomics-based transcriptomes (MGTs, CAGs larger than 500 unigenes). We demonstrated the biological validity of the MGT collection by comparing individual MGTs with available references. We identified several key eukaryotic organisms involved in dimethylsulfoniopropionate (DMSP) biosynthesis and catabolism in different oceanic provinces, thus demonstrating the potential of the MGT collection to provide functional insights on eukaryotic plankton. We established the ability of the MGT approach to capture interspecies associations through the analysis of a nitrogen-fixing haptophyte-cyanobacterial symbiotic association. This MGT collection provides a valuable resource for analyses of eukaryotic plankton in the open ocean by giving access to the genomic content and functional potential of many ecologically relevant eukaryotic species.

中文翻译：

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转录组重建和通过高通量宏基因组学和元转录组学对真核生物海洋浮游生物进行功能分析。

大规模宏基因组学和超转录组学数据分析通常受限于其以基因为中心的方法，从而限制了对生物体和群落生物学的理解。从复杂的元组学数据重新组装大型和镶嵌真核生物基因组仍然是一项艰巨的任务，特别是与更直接的细菌和古细菌系统相比。在这里，我们使用转录组重建方法，该方法基于跨一系列宏基因组学样本的共丰基因聚类。我们调查了塔拉海洋探险期间收集的365个宏基因组样本中约3700万真核单基因的共丰模式，以评估海洋浮游生物的多样性和功能特征。我们确定了约12,000个共同丰富的基因组（CAG），其中包含约700万个单基因，包括924个基于宏基因组学的转录组（MGT，大于500个单基因的CAG）。我们通过将各个MGT与现有参考文献进行比较，证明了MGT集合的生物学有效性。我们确定了几个重要的真核生物，它们参与了不同海洋省份的二甲基磺丙酸二甲酯（DMSP）生物合成和分解代谢，从而证明了MGT收集的潜力可为真核浮游生物提供功能性见解。我们通过分析固氮触媒植物-蓝细菌共生关联建立了MGT方法捕获种间关联的能力。