“The great scallop Pecten maximus is a bivalve mollusc, wh


“The great scallop Pecten maximus is a bivalve mollusc, which occurs over a wide latitudinal gradient, from Spain to Norway, inhabiting depths from 0 m to 500 m ( Chauvaud et al., 2005). This is an economically important species, comprising almost 80% of European wild harvested scallops. Furthermore, aquaculture is expanding, especially in France and Ireland where hatchery-produced seed is used to enhance the production in the wild. The transcriptome data were generated as part of a more detailed Panobinostat ic50 study, investigating the effect of temperature on growth and development. One year old scallops (average length: 34.0 ± 4.1 mm) were obtained from the Tinduff hatchery (Bay of Brest, Dabrafenib nmr France).

They were cultured at 3 different temperatures: ambient controls at 14.8 ± 0.6 °C and also the elevated temperatures of 21.4 ± 0.2 °C and 25.2 ± 0.9 °C. Individuals in

each treatment were sampled over a time course from the beginning of the experiment and then after 3, 7, 14, 21, 27, 42 and 56 days. The scallops were dissected and mantle tissue was flash frozen in liquid nitrogen and stored at − 80 °C until further analysis. Total RNA was extracted from mantle tissue of 4 individuals per treatment at each time point using TRI Reagent® Solution (Life Technologies) according to the manufacturer’s instructions. RNA quality and concentration were determined using an Agilent 2100 RNA Nanochip (Agilent, GPX6 Santa Clara, CA, USA) and a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA), respectively. For each condition, the RNAs from the 4 individuals at each time point were then pooled for RNA-Seq. From these pooled samples, 22 cDNA libraries were produced (cf. Table 1 for details). The production of the Illumina libraries and the transcriptome sequencing using the Illumina HiSeq™ 2500 (HiSeq 100 bp pair-ends) was conducted by the Genome Analysis Centre (Norwich, UK). The RNA libraries yielded 667 million paired end reads. Raw reads were filtered and trimmed using the FASTX-toolkit (Version 0.0.13 from Assaf

Gordon Hannon lab) and rRNA contamination removed using riboPicker (Schmieder et al., 2012) and cutadapt (Version 1.1; Martin, 2011), with a final quality check performed using fastQC (Version 0.10.0; http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/). The contigs were assembled using SOAPdenovo (Luo et al., 2012), and a kmer size of 89 was used to construct the initial de novo transcriptome assembly, resulting in 1,311,367 contigs. These contigs were then used in a further assembly with CAP3 (Huang and Madan, 1999). Contigs from both rounds of assemblies that were greater than 500 bp, totaling 26,064, were used in a sequence similarity search against an in-house nr database using an e-value cutoff of 1e − 10.

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