The transcriptome profile of the marine Calanoid copepod Parvocalanus crassirostris isolated from Kuwait territorial waters and generations cultured under different ocean acidification scenarios

Abstract

Copepods are primary consumers, amounting to about 70 % of the metazoans in the marine environment, and are fundamental to marine food webs. Ocean acidification (OA) and ocean warming (OW) significantly affect the copepod community leading to the severe consequences of an ecological imbalance. Molecular resources are minimal for copepods and call for transcriptome profiling to better understand their responses under changing environmental conditions. This manuscript describes the de novo transcriptome of Parvocalanus crassirostris, a common inhabitant of coastal waters. RNA sequencing (RNAseq) was performed on whole organisms. Raw reads assembled through Trinity comprised 344,652 transcripts and 249,255 unigenes. Bench-marking-universal-single-copy-orthologs (BUSCO) analysis identified 86.6 % (C:86.9 % [S: 78 %, D: 8.6 %], M: 3.5 %, F: 9.9 %) of the assembly to be complete. Approximately 40 % and 12 % of unigenes were functionally annotated against the gene ontologies (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The dominant GO categories were cellular (58.20 %) > metabolic (55.91 %) > catalytic activity (50.12 %) > binding (45.55 %) > cellular anatomical entity (39.36 %) > and intracellular binding (21.68 %). In contrast, signal transduction pathways were the dominant pathways under the environment information processing of the KEGG category. Differential gene expression analysis was performed on different generations of copepods under progressively lower pH. Over 99,117 unigenes were discovered, of which 53,044 were upregulated and 46,073 downregulated. Gene ontologies enrichment analysis revealed significantly different functional pathways at a false discovery rate (FDR) of q< 0.05 (COP1-COP2: 15; COP1-COP3: 47; COP2-COP3: 22). The KEGG enrichment informed genes associated with 17 pathways to be upregulated while 31 pathways to be downregulated. This investigation provides an important genomic resource of P. crassirostris under ambient conditions and in future climate scenarios in response to OA.