Skip to main content
Dryad

Pinna nobilis RNA-Seq and Transcriptome

Cite this dataset

Salis, Pauline et al. (2022). Pinna nobilis RNA-Seq and Transcriptome [Dataset]. Dryad. https://doi.org/10.5061/dryad.xwdbrv1dm

Abstract

With the intensification of maritime traffic, recently emerged infectious diseases have become major drivers in the decline and extinction of species. Since 2016, mass mortality events have decimated the endemic Mediterranean Sea bivalve Pinna nobilis, affecting ca. 100% of individuals. These events have largely been driven by Haplosporidium pinnae’s infection, an invasive species which was likely introduced by shipping. While monitoring wild populations of P. nobilis, we observed individuals that survived such a mass mortality event during the summer of 2018 (France). We considered these individuals resistant, as they did not show any symptoms of the disease, while the rest of the population in the area was devastated. Furthermore, the parasite was not detected when we conducted a PCR amplification of a species-specific fragment of the small subunit ribosomal DNA. In parallel, the transcriptomic analysis showed evidence of some parasite RNA indicating that the resistant individuals had been exposed to the parasite without proliferating. To understand the underlying mechanisms of resistance in these individuals, we compared their gene expression with that of susceptible individuals. We performed de novo transcriptome assembly and annotated the expressed genes. A comparison of the transcriptomes in resistant and susceptible individuals highlighted a gene expression signature of the resistant phenotype. We found significant differential expressions of genes involved in immunity and cell architecture. This data provides the first insights into how individuals escape the pathogenicity associated with infection.

Methods

For each Pinna nobilis individual, a biopsy of ~ 1 cm3 of mantle tissue was collected in situ by SCUBA diving. Biopsy were put directly in RNAlater (RNAlater R0901; Sigma-Aldrich). Lysis of tissue was done using MP Biomedicals™ Instrument FastPrep-24™ 5G (fisher scientific- reference: 15260488). The RNA was automatly extracted using Maxwell® RSC Instrument (Promega, reference: AS4500) using Maxwell® RSC simplyRNA Tissue Kit (Promega- reference: AS1340).

RNA‐Seq libraries were generated with TruSeq Stranded mRNA Sample Preparation Kit (Illumina) from 400 ng of total RNA according to manufacturer's instructions. Surplus PCR primers were removed using AMPure XP beads (Beckman Coulter). Final cDNA libraries were checked for quality and quantified using capillary electrophoresis. Libraries were loaded in the flow cell at 2 nM. Clusters were generated in the Cbot and sequenced on an Illumina HiSeq 4000 as paired‐end 2X100 base reads (stranded protocol).

The score of assembly of this final transcriptome according to TransRate becomes 0.355. It consists of 269 285 transcripts (for a total of 451 934 494 bases, with a GC content of 37.4 %), with lengths ranging from 132 to 59 616 (average: 1 678, 521 transcripts under 200 bases, 118 667 over 1 000 bases, and 2 278 over 10 000 bases). 80 790 are estimated to have an open reading frame (covering, on average, 35.6 % of the transcript) (full method of transcriptome assembly is described in the manuscript).

Usage notes

No missing values

> Raw RNAseq Data are in fastq.gz (22 files)

PLSS1 corresponds to RS-1, PLSS2 to RS-2, PLSS3 to RS-3

PLSS4 corresponds to SL-1, PLSS5 to SL-2, PLSS6 to SL-3, PLSS7 to SL-4

PLSS8 corresponds to SS-1, PLSS9 to SS-2, PLSS10 to SS-3 and PLSS11 to SS-4

> PN_transcriptome.fasta corresponds to Pinna nobilis transcriptome with :

"transcript_" (Number of the transcript); "len=" (size of transcript); "homologies=" in SwissProt, UNIREF90 and OrthoDB databases: numbers correspond to the start and end positions of the part of the transcript for which the homology has been found (part of the sequence aligned with the ortholog); transcript sequence.