Decontamination, pooling and dereplication of the 678 samples of the Marine Microbial Eukaryote Transcriptome Sequencing Project
Van Vlierberghe, M.; Di Franco, A.; Philippe, H.; Baurain, D. (2021). Decontamination, pooling and dereplication of the 678 samples of the Marine Microbial Eukaryote Transcriptome Sequencing Project. Bmc Research Notes 14(1): 306. https://dx.doi.org/10.1186/s13104-021-05717-2
In: BMC Research Notes. BIOMED CENTRAL LTD: London. e-ISSN 1756-0500, more
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Bioinformatics; Decontamination; Transcriptomes; Gene phylogenies; Phylogenomics; MMETSP; Algae; Eukaryotic evolution; Endosymbiotic gene transfer (EGT); Kleptoplastidy |
| Authors | | Top |
- Van Vlierberghe, M., more
- Di Franco, A.
- Philippe, H.
- Baurain, D., more
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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 descriptionWe 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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