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

Abstract

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] .

Examination of gammarid transcriptomes reveals a widespread occurrence of key metabolic genes from epibiont bdelloid rotifers in freshwater species

“…The present study aimed to clarify the origin and occurrence of sequences of LC-PUFA biosynthesizing genes, such as elovl2/5 and further biosynthetic gene components including Fed and ωx in freshwater gammarids. To do so, we conducted a systematic search of diagnostic motifs characteristic of each three LC-PUFA biosynthetic enzyme families within publicly available transcriptomes from both freshwater and marine gammarids [48][49][50][51][52][53][54][55]. Our results confirmed that sequences encoding putative Elovl2/5, Fed and ωx are widespread in transcriptomic databases from freshwater gammarids but absent in those from marine species.…”

“…As opposed to whole individuals [50], the transcriptome built from G. pulex hepatopancreas [48] did not result in any positive hit against any of the LC-PUFA biosynthesis gene markers assessed, confirming that internal body parts of the gammarid are free from epibiotic rotifers. Unlike freshwater species, marine gammarids such as E. marinus [50,52] and G. locusta [54] did not have any of the diagnostic LC-PUFA biosynthesis genes, consistent with the fact that the above described epibiotic relationship between gammarids (host) and bdelloid rotifers (epibiont) is restricted to freshwater environments [64]. Our data further support that the abundance of rotifers in the gammarid samples used for RNA sequencing was not negligible according to the presence of a remarkable amount of rotifer-derived mitochondrial genes ( cox ) in some of the available RNA sequencing data [50].…”

“…Sequences from functionally characterized LC-PUFA biosynthetic desaturases and elongases from aquatic invertebrates including annelids, molluscs and arthropods were used as queries for BLAST searches (tblastn) within transcriptomes from a variety of gammarids, including freshwater and marine species [48][49][50][51][52][53][54][55]. Hits were only selected for further analysis when they contained the full-length open reading frame (ORF) and their predicted protein sequences (https:// www.ncbi.nlm.nih.gov/orffinder) contained specific features according to Hashimoto et al [56].…”

Transcriptome Analysis to Identify Genes Related to Flowering Reversion in Tomato

“…The clean reads were mapped to the S. lycopersicum reference genome sequence (tomato genome version SL 4.0 and annotation ITAG 4.0) using HISAT2 (v2.0.4) [ 68 ]. Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, and the expression levels of the genes were calculated by RSEM (v1.2.12) [ 69 ]. DEGs were identified using DESeq2 (v1.4.5) according to a Q-value ≤ 0.05 and |log2FC| ≥ 2 [ 70 ].…”

Robust and rapid pipeline for the development of mRNA vaccine for the fast-emerging SARS-CoV-2 variants

“…Based on the FASTQc report, the reads were trimmed using a command line utility Trimmomatic-0.39 to remove the low-quality reads 16 . The parameters selected for trimming were LEADING:5, TRAILING:5, SLIDINGWINDOW:4:15, and MINLEN:36 17 .…”