RNA-Seq and differential gene expression analysis in Temora stylifera copepod females with contrasting non-feeding nauplii survival rates: an environmental transcriptomics study

Abstract

Background Copepods are fundamental components of pelagic food webs, but reports on how molecular responses link to reproductive success in natural populations are still scarce. We present a de novo transcriptome assembly and differential expression (DE) analysis in Temora stylifera females collected in the Gulf of Naples, Mediterranean Sea, where this copepod dominates the zooplankton community. High-Throughput RNA-Sequencing and DE analysis were performed from adult females collected on consecutive weeks (May 23rd and 30th 2017), because opposite naupliar survival rates were observed. We aimed at detecting key genes that may have influenced copepod reproductive potential in natural populations and whose expression was potentially affected by phytoplankton-derived oxylipins, lipoxygenase-derived products strongly impacting copepod naupliar survival. Results On the two sampling dates, temperature, salinity, pH and oxygen remained stable, while variations in phytoplankton cell concentration, oxylipin concentration and oxylipin-per-diatom-cell production were observed. T. stylifera naupliar survival was 25% on May 23rd and 93% on May 30th. De novo assembly generated 268,665 transcripts (isoforms) and 120,749 unique ‘Trinity predicted genes’ (unigenes), of which 50% were functionally annotated. Out of the 331 transcript isoforms differentially expressed between the two sampling dates, 119 sequences were functionally annotated (58 up- and 61 down-regulated). Among predicted genes (unigenes), 144 sequences were differentially expressed and 31 (6 up-regulated and 25 down-regulated) were functionally annotated. Most of the significantly down-regulated unigenes and isoforms were A5 Putative Odorant Binding Protein (Obp). Other differentially expressed sequences (isoforms and unigenes) related to developmental metabolic processes, protein ubiquitination, response to stress, oxidation-reduction reactions and hydrolase activities. DE analysis was validated through Real Time-quantitative PCR of 9 unigenes and 3 isoforms. Conclusions Differential expression of sequences involved in signal detection and transduction, cell differentiation and development offered a functional interpretation to the maternally-mediated low naupliar survival rates observed in samples collected on May 23rd. Down-regulation of A5 Obp along with higher quantities of oxylipins-per-litre and oxylipins-per-diatom-cell observed on May 23rd could suggest oxylipin-mediated impairment of naupliar survival in natural populations of T. stylifera. Our results may help identify biomarker genes explaining variations in copepod reproductive responses at a molecular level.

First De Novo Transcriptome of the Copepod Rhincalanus gigas from Antarctic Waters

“…The number of high-quality transcriptomes, especially for copepods, is still limited, although, in recent years, there has been an increase in molecular resources for metazoan zooplankton [ 31 , 32 , 33 , 34 , 35 , 36 , 37 ]. In this study, we present the first molecular resource for an eucalanoid copepod, Rhincalanus gigas .…”

Twenty‐year trends of Centropages typicus (Copepoda, Calanoida) reproduction, feeding, population abundance and structure in the Gulf of Naples (Western Mediterranean Sea)

“…Mortality of larval stages well‐explained the seasonal population dynamics of the copepod T. stylifera in the Gulf of Naples (Mazzocchi et al, 2006). More effort, therefore, should be paid on investigating natural mortality of copepod larval stages in situ, which can be at times very high (Di Capua & Mazzocchi, 2017; Russo, Lauritano, et al, 2020), to better explain copepod population dynamics on a seasonal and interannual scale. The outcomes of this two‐decadal analysis shed new light into the ecology of this widespread species, improving our understanding of the driving role of different environmental factors and highlighting the importance of studying the species reproductive biology and population dynamics in the long term.…”

Data on SSR markers and SNPs filtered from transcriptome of Parvocalanus crassirostris

“…Briefly Oligo (dT) beads were added to selectively pick the mRNA. Fragmentation was performed and first strand cDNA synthesis initiated [6] followed by second strand cDNA synthesis. The libraries were purfied through the AMPure XP beads (Beckman Coulter Genomics, Brea, CA, USA) and indexed with Illumina indices.…”