DOI: 10.5061/dryad.xwdbrv1dm
title: Pinna nobilis RNA-Seq and Transcriptome

description: 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.
description: 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).
description: No missing values &gt; 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
 &gt; 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.