RNA sequencing and de novo assembly of the digestive gland transcriptome in Mytilus galloprovincialis fed with toxinogenic and non-toxic strains of Alexandrium minutum

Abstract

BackgroundThe Mediterranean mussel Mytilus galloprovincialis is marine bivalve with a relevant commercial importance as well as a key sentinel organism for the biomonitoring of environmental pollution. Here we report the RNA sequencing of the mussel digestive gland, performed with the aim: a) to produce a high quality de novo transcriptome assembly, thus improving the genetic and molecular knowledge of this organism b) to provide an initial assessment of the response to paralytic shellfish poisoning (PSP) on a molecular level, in order to identify possible molecular markers of toxin accumulation.ResultsThe comprehensive de novo assembly and annotation of the transcriptome yielded a collection of 12,079 non-redundant consensus sequences with an average length of 958 bp, with a high percentage of full-length transcripts. The whole-transcriptome gene expression study indicated that the accumulation of paralytic toxins produced by the dinoflagellate Alexandrium minutum over a time span of 5 days scarcely affected gene expression, but the results need further validation with a greater number of biological samples and naturally contaminated specimens.ConclusionThe digestive gland reference transcriptome we produced significantly improves the data collected from previous sequencing efforts and provides a basic resource for expanding functional genomics investigations in M. galloprovincialis. Although not conclusive, the results of the RNA-seq gene expression analysis support the classification of mussels as bivalves refractory to paralytic shellfish poisoning and point out that the identification molecular biomarkers of PSP in the digestive gland of this organism is problematic.Electronic supplementary materialThe online version of this article (doi:10.1186/1756-0500-7-722) contains supplementary material, which is available to authorized users.

An updated molecular basis for mussel immunity

“…Moreover, mussel FREPs differ from gastropod FREPs which show a fibrinogen-like domain associated with one or two N-terminal immunoglobulin-like domains [52,56]. Considering both fulllength and partial sequences, we have detected more than 150 expressed FREPs in the transcriptome of M. galloprovincialis, a number consistent with previous preliminary data [16,55]. Overall, mussel FREPs represent the third most abundant class of secreted lectin-like molecules, after the C1qDC proteins and C-type lectins.…”

“…The abundance of CTLs in mussel appears to be in the same order of magnitude since we could detect 154 distinct CTL transcripts in the M. galloprovincialis digestive gland transcriptome [16]. Nevertheless, the specific involvement of 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 CTLs in the mussel immune response has not been yet demonstrated.…”

“…are summarized in Table 1. The first glimpse on the complex mussel immune system was provided by Sanger EST sequencing [10], an approach which was followed by 454 Life Sciences sequencing [11e15] and by high throughput Illumina sequencing, a technology allowing a better full-length reconstruction of transcripts [16]. In 2014, a non-annotated set of genomic sequences of Mytilus galloprovincialis was released, a real landmark for the progression of genomic studies in this bivalve [17].…”

Molecular analysis of the Sydney rock oyster (Saccostrea glomerata) CO2 stress response

“…Of the original 92 ERCC reference sequences and one phiX sequence, 89 ERCC's and one phiX sequence were found in the S. glomerata reference transcriptome, with all sequences close to full length. The N50 value (836 bp) of the non-redundant reference transcriptome is comparable to the N50's observed for other molluscan de novo transcriptomes [34][35][36]. Based on these results, the assembly was considered to be of suitable quality for the differential gene expression analysis.…”

The genome of the Pacific oyster Crassostrea gigas brings new insights on the massive expansion of the C1q gene family in Bivalvia

“…Following Sanger sequencing of the M. galloprovincialis transcriptome, we described at least 168 distinct C1qDC transcript sequences, but the resolution power of next generation sequencing (NGS) later suggested much larger amounts, since 524 and 232 C1qDC transcripts have been reported in M. edulis and in M. galloprovincialis, respectively (Gerdol et al, 2014;Philipp et al, 2012). The expansion of the C1qDC gene family is not restricted to Mytilus spp., as briefly outlined in the oyster genome paper and in the Crassostrea virginica transcriptome analysis (Zhang et al, , 2014.…”