Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) location information on samples obtained on Gould (LMG1411) in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project)

Abstract 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.

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The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

PLoS Biology ◽

10.1371/journal.pbio.1001889 ◽

2014 ◽

Vol 12 (6) ◽

pp. e1001889 ◽

Cited By ~ 498

Author(s):

Patrick J. Keeling ◽

Fabien Burki ◽

Heather M. Wilcox ◽

Bassem Allam ◽

Eric E. Allen ◽

...

Keyword(s):

Functional Diversity ◽

Transcriptome Sequencing ◽

Sequencing Project ◽

Microbial Eukaryote

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De NovoAssembly of the Pea (Pisum sativumL.) Nodule Transcriptome

International Journal of Genomics ◽

10.1155/2015/695947 ◽

2015 ◽

Vol 2015 ◽

pp. 1-11 ◽

Cited By ~ 14

Author(s):

Vladimir A. Zhukov ◽

Alexander I. Zhernakov ◽

Olga A. Kulaeva ◽

Nikita I. Ershov ◽

Alexey Y. Borisov ◽

...

Keyword(s):

Transcriptome Sequencing ◽

De Novo ◽

Transcriptome Assembly ◽

Specific Gene ◽

Its Sequencing ◽

Sequencing Data ◽

Root Tips ◽

Sequencing Project ◽

Illumina Gaiix ◽

Project Data

The large size and complexity of the garden pea (Pisum sativumL.) genome hamper its sequencing and the discovery of pea gene resources. Although transcriptome sequencing provides extensive information about expressed genes, some tissue-specific transcripts can only be identified from particular organs under appropriate conditions. In this study, we performed RNA sequencing of polyadenylated transcripts from young pea nodules and root tips on an Illumina GAIIx system, followed byde novotranscriptome assembly using the Trinity program. We obtained more than 58,000 and 37,000 contigs from “Nodules” and “Root Tips” assemblies, respectively. The quality of the assemblies was assessed by comparison with pea expressed sequence tags and transcriptome sequencing project data available from NCBI website. The “Nodules” assembly was compared with the “Root Tips” assembly and with pea transcriptome sequencing data from projects indicating tissue specificity. As a result, approximately 13,000 nodule-specific contigs were found and annotated by alignment to known plant protein-coding sequences and by Gene Ontology searching. Of these, 581 sequences were found to possess full CDSs and could thus be considered as novel nodule-specific transcripts of pea. The information about pea nodule-specific gene sequences can be applied for gene-based markers creation, polymorphism studies, and real-time PCR.

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