Analysis of Transcripts and Splice Isoforms in Red Claw Crayfish (cherax Quadricarinatus) Using Single-Molecule Long-Read Sequencing

Red claw crayfish (Cherax quadricarinatus) has recently attracted widespread attention as an emerging candidate for sustainable aquaculture production in Australia and abroad. Although they are of great economic importance, few full-length transcriptomes are available. Here, transcripts of C. quadricarinatus were generated by using Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology. With SMRT, 289,232 full-length nonchimeric reads were identified, resulting in 14,089 unigene, with an N50 length of 4363 bp and a mean read length of 3913 bp. The error rate of SMRT sequences by comparison with Illumina-produced short reads was only 0.011%. A total of 13,449 transcripts (95.4%) were annotated against the protein database. Across all transcripts, 4952 long noncoding RNAs (lncRNAs), 1090 putative TF members and 21,108 simple sequence repeats (SSRs) were identified. After Vibrio alginolyticus infection, a total of 252 DEGs were screened out after a comparative analysis between samples. Of the 252 DEGs, Hsps, IAPs and Gpx were upregulated during V. alginolyticus infection, many genes were associated with V. cholerae infection, the NF-kappa B signalling pathway, apoptosis-multiple species, the TNF signalling pathway and antigen processing and presentation pathways. Our study provides a rich set of full-length cDNA sequences for C. quadricarinatus, which will greatly facilitate crayfish transcriptome research.