De novo transcriptomes of 14 gammarid individuals for proteogenomic analysis of seven taxonomic groups

Cogne, Yannick; Esposti, Davide Degli; Pible, Olivier; Gouveia, Duarte; François, Adeline; Bouchez, Olivier; Eché, Camille; Ford, Alex T.; Geffard, Olivier; Armengaud, Jean; Chaumot, Arnaud; Almunia, Christine

doi:10.1038/s41597-019-0192-5

Cited by 25 publications

(37 citation statements)

References 54 publications

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“…Simulations of distributional patterns under future climatic global change underestimate the real scale of biodiversity loss when CD is not taken into account 18 . Finally, ecotoxicological and biomonitoring studies are at risk of being flawed, as some authors reported that different cryptic species might differ in their tolerance to contaminants and ecosystem deterioration [19][20][21][22][23] .…”

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confidence: 99%

Continental-scale patterns of hyper-cryptic diversity within the freshwater model taxon Gammarus fossarum (Crustacea, Amphipoda)

Wattier

Mamos

Copilaş‐Ciocianu

et al. 2020

Sci Rep

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Traditional morphological diagnoses of taxonomic status remain widely used while an increasing number of studies show that one morphospecies might hide cryptic diversity, i.e. lineages with unexpectedly high molecular divergence. This hidden diversity can reach even tens of lineages, i.e. hyper cryptic diversity. Even well-studied model-organisms may exhibit overlooked cryptic diversity. Such is the case of the freshwater crustacean amphipod model taxon Gammarus fossarum. It is extensively used in both applied and basic types of research, including biodiversity assessments, ecotoxicology and evolutionary ecology. Based on COI barcodes of 4926 individuals from 498 sampling sites in 19 European countries, the present paper shows (1) hyper cryptic diversity, ranging from 84 to 152 Molecular Operational Taxonomic Units, (2) ancient diversification starting already 26 Mya in the Oligocene, and (3) high level of lineage syntopy. Even if hyper cryptic diversity was already documented in G. fossarum, the present study increases its extent fourfold, providing a first continental-scale insight into its geographical distribution and establishes several diversification hotspots, notably south-eastern and central Europe. The challenges of recording hyper cryptic diversity in the future are also discussed.

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confidence: 99%

Continental-scale patterns of hyper-cryptic diversity within the freshwater model taxon Gammarus fossarum (Crustacea, Amphipoda)

Wattier

Mamos

Copilaş‐Ciocianu

et al. 2020

Sci Rep

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“…One animal (S0) was genotyped by amplifying and sequencing its Cytochrome c oxidase subunit I gene from DNA extracted from a single leg, as described previously. [ 26 ] Total mRNAs were extracted from this animal, polyA mRNAs were then purified and Illumina‐sequenced using HIseq3000. For the R1 and R2 files from the paired‐end sequencing, a total of 40 979 915 reads of 150 bp were obtained.…”

Section: Resultsmentioning

confidence: 99%

“…RNA‐seq was previously performed on a G. fossarum female. [ 26 ] Raw files are available from NCBI under accession number SRR8089727 (http://identifiers.org/insdc.sra:SRR8089727). The G. fossarum transcriptome is available from NCBI under accession number GHCX01000000 (https://www.ncbi.nlm.nih.gov/nuccore/GHCX01000000).…”

Section: Methodsmentioning

confidence: 99%

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Proteogenomics‐Guided Evaluation of RNA‐Seq Assembly and Protein Database Construction for Emergent Model Organisms

et al. 2020

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Proteogenomics is gaining momentum as, today, genomics, transcriptomics, and proteomics can be readily performed on any new species. This approach allows key alterations to molecular pathways to be identified when comparing conditions. For animals and plants, RNA-seq-informed proteomics is the most popular means of interpreting tandem mass spectrometry spectra acquired for species for which the genome has not yet been sequenced. It relies on high-performance de novo RNA-seq assembly and optimized translation strategies. Here, several pre-treatments for Illumina RNA-seq reads before assembly are explored to translate the resulting contigs into useful polypeptide sequences. Experimental transcriptomics and proteomics datasets acquired for individual Gammarus fossarum freshwater crustaceans are used, the most relevant procedure is defined by the ratio of MS/MS spectra assigned to peptide sequences. Removing reads with a mean quality score of less than 17-which represents a single probable nucleotide error on 150-bp reads-prior to assembly, increases the proteomics outcome. The best translation using Transdecoder is achieved with a minimal open reading frame length of 50 amino acids and systematic selection of ORFs longer than 900 nucleotides. Using these parameters, transcriptome assembly and translation informed by proteomics pave the way to further improvements in proteogenomics.

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“…transcriptomes, already published (e.g. [13] , [14] , [15] , [16] , [17] ). All versions of the transcriptome were submitted to the online Figshare repository and can be consulted in the following link: https://figshare.com/s/1110e0d14fcc6a275acb .…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

Transcriptomic data on the transgenerational exposure of the keystone amphipod Gammarus locusta to simvastatin

et al. 2020

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The use of transcriptomics data brings new insights and works as a powerful tool to explore the molecular mode of action (MoA) of transgenerational inheritance effects of contaminants of emerging concern. Therefore, in this dataset, we present the transcriptomic data of the transgenerational effects of environmentally relevant simvastatin levels, one of the most prescribed human pharmaceuticals, in the keystone amphipod species Gammarus locusta . In summary, G. locusta juveniles were maintained under simvastatin exposure up to adulthood (exposed group - F0E) and the offspring of F0E were transferred to control water for the three subsequent generations (transgenerational group - F1T, F2T and F3T). To gain insights into the biological functions and canonical pathways transgenerationally disrupted by simvastatin, a G. locusta de novo transcriptome assembly was produced and the transcriptomic profiles of three individual G. locusta females, per group, over the four generations (F0 to F3) - solvent control groups (F0.C, F1.C, F2.C and F3.C), F0 320 ng/L simvastatin exposed group (F0.320E) and F1 to F3 320 transgenerational group (F1.320T; F2.320T and F3.320T) - were analyzed. Briefly, Illumina HiSeq™ 2500 platform was used to perform RNA sequencing, and due to the unavailability of G. locusta genome, the RNA-seq datasets were assembled de novo using Trinity and annotated with Trinotate software. After assembly and post-processing steps, 106093 transcripts with N50 of 2371 bp and mean sequence length of 1343.98 bp was produced. BUSCO analyses showed a transcriptome with gene completeness of 97.5 % Arthropoda library profile. The Bowtie2, RSEM and edgeR tools were used for the differential gene expression (DEGs) analyses that allowed the identification of a high quantity of genes differentially expressed in all generations. Finally, to identify the main metabolic pathways affected by the transgenerational effects of SIM across all generations, the DGEs genes were blasted onto KEGG pathways database using the KAAS webserver. The data furnished in this article allows a better molecular understanding of the transgenerational effects produced by simvastatin in the keystone amphipod G. locusta and has major implications for hazard and risk assessment of pharmaceuticals and other emerging contaminants. This article is related to the research article entitled “Transgenerational inheritance of chemical-induced signature: a case study with simvastatin [1] .

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De novo transcriptomes of 14 gammarid individuals for proteogenomic analysis of seven taxonomic groups

Cited by 25 publications

References 54 publications

Continental-scale patterns of hyper-cryptic diversity within the freshwater model taxon Gammarus fossarum (Crustacea, Amphipoda)

Continental-scale patterns of hyper-cryptic diversity within the freshwater model taxon Gammarus fossarum (Crustacea, Amphipoda)

Proteogenomics‐Guided Evaluation of RNA‐Seq Assembly and Protein Database Construction for Emergent Model Organisms

Transcriptomic data on the transgenerational exposure of the keystone amphipod Gammarus locusta to simvastatin

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