[en] OBJECTIVES: Complex 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.
Baurain, Denis ; Université de Liège - ULiège > Département des sciences de la vie > Phylogénomique des eucaryotes
Language :
English
Title :
Decontamination, pooling and dereplication of the 678 samples of the Marine Microbial Eukaryote Transcriptome Sequencing Project.
Publication date :
2021
Journal title :
BMC Research Notes
eISSN :
1756-0500
Publisher :
BioMed Central, London, United Kingdom
Volume :
14
Issue :
1
Pages :
306
Peer reviewed :
Peer Reviewed verified by ORBi
Funders :
FRIA - Fonds pour la Formation à la Recherche dans l'Industrie et dans l'Agriculture [BE] F.R.S.-FNRS - Fonds de la Recherche Scientifique [BE] ULiège - Université de Liège [BE]
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Van Vlierberghe M, Di Franco A, Philippe H, Baurain D. Data file 1—Methods. 2021. Figshare. 10.6084/m9.figshare.14079866.v5.
Van Vlierberghe M, Di Franco A, Philippe H, Baurain D. Data set 1—Forty-Two reports and configuration files (662 individual samples). 2021. Figshare. 10.6084/m9.figshare.12362699.v1.
Van Vlierberghe M, Di Franco A, Philippe H, Baurain D. Data file 2—Consolidation table. 2021. Figshare. 10.6084/m9.figshare.14727411.v3.
Van Vlierberghe M, Di Franco A, Philippe H, Baurain D. Data file 3—Sample consolidation report. 2021. Figshare. 10.6084/m9.figshare.12154824.v3.
Van Vlierberghe M, Di Franco A, Philippe H, Baurain D. Data file 4—Redundancy drop analysis. 2021. Figshare. 10.6084/m9.figshare.12213731.v3.
Van Vlierberghe M, Di Franco A, Philippe H, Baurain D. Data set 2—Transcriptomes. 2021. Figshare. 10.6084/m9.figshare.13634840.v1.
Van Vlierberghe M, Di Franco A, Philippe H, Baurain D. Data file 5—Sobek analysis summary. 2021. Figshare. 10.6084/m9.figshare.12410522.v3.
Van Vlierberghe M, Di Franco A, Philippe H, Baurain D. Data set 3—Forty-Two reports and configuration files (260 transcriptomes). 2021. Figshare. 10.6084/m9.figshare.13006622.v1.
Van Vlierberghe M, Di Franco A, Philippe H, Baurain D. Data file 6—Consolidated sample purity (cross-contaminations). 2021. Figshare. 10.6084/m9.figshare.12173235.v3.
Van Vlierberghe M, Di Franco A, Philippe H, Baurain D. Data file 7—Consolidated sample purity (contaminations). 2021. Figshare. 10.6084/m9.figshare.12998726.v3.
Van Vlierberghe M, Di Franco A, Philippe H, Baurain D. Data file 8—Completeness analysis. 2021. Figshare. 10.6084/m9.figshare.12154833.v3.
Van Vlierberghe M, Di Franco A, Philippe H, Baurain D. Data set 4—Taxonomic samplings. 2021. Figshare. 10.6084/m9.figshare.12401639.v1.
Van Vlierberghe M, Di Franco A, Philippe H, Baurain D. Data set 5—GAPDH phylogenies. 2021. Figshare. 10.6084/m9.figshare.13096208.v2.
