ArticleBMC research notes2021
Decontamination, pooling and dereplication of the 678 samples of the Marine Microbial Eukaryote Transcriptome Sequencing Project.
Article in BMC research notes, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Conserved genetic markers reveal widespread diatom sexual reproduction in the global ocean.Nature communications · 2025Article
- Unveiling the functional nature of retrogenes in dinoflagellates.Open biology · 2025Article
- What Does It Mean to Be(Come) Arctic? Functional and Genetic Traits of Arctic- and Temperate-Adapted Diatoms.Global change biology · 2025Article
- Latitude- and depth-driven divergence in protist trophic strategies revealed by a machine learning model.Frontiers in microbiology · 2025Article
- TIdeS: A Comprehensive Framework for Accurate Open Reading Frame Identification and Classification in Eukaryotic Transcriptomes.Genome biology and evolution · 2024Article
- Microalgae biofuels: illuminating the path to a sustainable future amidst challenges and opportunities.Biotechnology for biofuels and bioproducts · 2024Review
- MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes.Scientific data · 2023Article
- Identification of Incomplete Annotations of Biosynthesis Pathways in Rhodophytes Using a Multi-Omics Approach.Marine drugs · 2023Article
- Replitrons: A major group of eukaryotic transposons encoding HUH endonuclease.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- The molecular basis for pore pattern morphogenesis in diatom silica.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- CHD Chromatin Remodeling Protein Diversification Yields Novel Clades and Domains Absent in Classic Model Organisms.Genome biology and evolution · 2022Article
- Contamination detection in genomic data: more is not enough.Genome biology · 2022Review
- Article
- Decontamination, pooling and dereplication of the 678 samples of the Marine Microbial Eukaryote Transcriptome Sequencing Project.BMC research notes · 2021Article
- A Mitochondrially Related Plastidial Transporter Regulates Photosynthesis in the Diatom Phaeodactylum tricornutum.Physiologia plantarumArticle
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Authors and funding
4 authors.
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Abstract
objectivesComplex algae are photosynthetic organisms resulting from eukaryote-to-eukaryote endosymbiotic-like interactions. Yet the specific lineages and mechanisms are still under debate. That is why large scale phylogenomic studies are needed. Whereas available proteomes provide a limited diversity of complex algae, MMETSP (Marine Microbial Eukaryote Transcriptome Sequencing Project) transcriptomes represent a valuable resource for phylogenomic analyses, owing to their broad and rich taxonomic sampling, especially of photosynthetic species. Unfortunately, this sampling is unbalanced and sometimes highly redundant. Moreover, we observed contaminated sequences in some samples. In such a context, tree inference and readability are impaired. Consequently, the aim of the data processing reported here is to release a unique set of clean and non-redundant transcriptomes produced through an original protocol featuring decontamination, pooling and dereplication steps. DATA DESCRIPTION: We submitted 678 MMETSP re-assembly samples to our parallel consolidation pipeline. Hence, we combined 423 samples into 110 consolidated transcriptomes, after the systematic removal of the most contaminated samples (186). This approach resulted in a total of 224 high-quality transcriptomes, easy to use and suitable to compute less contaminated, less redundant and more balanced phylogenies.
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