Full-length transcriptome of anadromous Coilia nasus using single molecule real-time (SMRT) sequencing

Abstract This study was designed to generate the full-length transcriptome of Coilia nasus using single-molecule long read isoform sequencing (SMRT-seq) technology. RNAs of brains, ovaries, and testes of C. nasus conditioned in both seawater and freshwater except for gut which was only from the fish conditioned in freshwater, were isolated. All the RNAs were pooled together equally for SMRT sequencing. One SMRT cell produced 64.18 Gb clean data, including 765,184 circular consensus (CCS) reads and 616,126 full-length non-chimeric (FLNC) reads. Finally, 93,793 non-redundant transcripts were obtained after clustered and polished. Structural analysis of the 93,793 non-redundant transcripts predicted 8242 alternative splicing events, a total of 229,825 SSR and 72,037 complete CDS. A total of 8437 lncRNA were identified. 84,617 transcripts were annotated in NR, Swissprot, GO, COG, KOG, eggnog, Pfam and KEGG database totally. This is the first full-length transcriptome of Coilia nasus, including transcripts appeared in the case of seawater, which will facilitate exploration of genetic data and life story of Coilia nasus.