Transcriptome Analysis of Sea Cucumber S. nudus

Equal amounts of body wall tissues from the three groups of S. nudus were used for RNA extraction. For Illumina RNA sequencing, 3 libraries were obtained in H, M, and L. The RNA was treated with RNase-DNase to remove DNA contaminants, and then the purified RNA quality and quantity were determined using an Agilent 2100RNA Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Samples with Qubit BR results (A and B) were used to construct cDNA libraries, and the nine transcriptomic libraries were sequenced on the Illumina HiSeq 2500 platform to obtain 150 bp paired-end reads. For further analysis, the raw reads were filtered by removing the adaptor reads and low-quality reads or unknown nucleotides. The totality of the Illumina clean read mapped to the PacBio isoforms, and the unmapped reads from each library were merged together and then de novo assembled using Trinity Release v24.0 [22 (link)].