Two-toned pygmy squid (Idiosepius pygmaeus) transcriptome assembly, and transcriptomic response of the nervous system to elevated CO2

• Other Authors: Celia Schunter (hasCollector), Jodi Thomas (hasCollector), Philip Laing Munday (hasCollector), Roger Huerlimann (hasCollector), Sue-Ann Watson (hasCollector), Timothy Ravasi (hasCollector)
• Format: Dataset
• Language: unknown
• Published: James Cook University
• Subjects: ocean acidification; carbon dioxide; transcriptomics; de novo transcriptome assembly; gene expression; central nervous system; eyes; squid; RNA-sequencing; ISO-sequencing; ARC Centre of Excellence for Coral Reef Studies; Ocean acidification
• Online Access: https://researchdata.edu.au/two-toned-pygmy-elevated-co2/2975053; https://researchdata.jcu.edu.au//published/345b77f0831e11ecbad66f177921119e; https://doi.org/10.25903/ha66-mm11

Annotated transcriptome assembly of the two-toned pygmy squid (Idiosepius pygmaeus) central nervous system and eye tissues (OmicsBox and csv files). Data for differential expression and gene set enrichment analyses: raw gene count data, all scripts used for bioinformatic analyses, all R code used for the statistical analyses, and data files to accompany the statistical analyses. Raw water sampling data. We evaluated the transcriptomic response of the central nervous system (CNS) and eyes of male two-toned pygmy squid (Idiosepius pygmaeus) exposed to elevated (~1,000 µatm) CO2 for seven days compared with current-day (~450 µatm) controls. As a reference for gene expression quantification, we assembled a high quality, annotated de novo transcriptome of I. pygmaeus CNS and eye tissues using long read PacBio Iso-sequencing data. Differential expression analysis was carried out to determine which genes were differentially expressed between current-day and elevated CO2 conditions, in the CNS and eyes. Gene set enrichment analysis was carried out to determine if sets of genes from the same gene ontology (GO) term/functional group showed significant, concordant differences between current-day and elevated CO2 conditions, in the CNS and eyes. de novo transcritpome assembly: ISO-seq data was processed using the PacBio isoseq3 pipeline: ccs (v4.2.0) with the minimum number of full passes set at three and the minimum predicted accuracy of a read at 0.9, lima (v1.11.0) with ‘--peek-guess’, isoseq3 refine (v3.3.0), isoseq3 cluster (v3.3.0) with ‘--use-qvs’. Redundancy removal: CD-HIT-EST (v4.6) with at least 99% identity. TransDecoder (v5.5.0) to identify open reading frames (ORFs): single best ORF per contig was chosen based on blast homology to known proteins in the NCBI nr database subset for mollusca (nr_mollusca, downloaded 01/2021) using BLASTp from BLAST+ (v2.10.0+) with max_target_seqs 1 and an e-value cut-off of 1-5, and then based on ORF length (minimum 100 amino acids). The entire transcript was retained for each ...