Full-Length transcriptome assembly and SSR marker development for Spinibarbus hollandi using PacBio SMRT sequencing

Spinibarbus hollandi is an economically significant subtropical fish in China, valued for both ornamental and aquaculture purposes. However, the full-length transcriptomic resources for this species remain scarce. To address this gap, we constructed the first multi-tissue, full-length transcriptome of S. hollandi using PacBio single-molecule real-time sequencing. We assembled 23,403 non-redundant transcripts, including 15,197 unigenes, with a mean length of 2,147 bp and an N50 of 2,868 bp. Among these, 14,567 unigenes (95.85%) were annotated in public databases. Our analysis identified 373 alternative splicing events, with retained intron being the most common type. We also predicted 2,397 long non-coding RNAs. Furthermore, a comprehensive screening revealed 7,449 simple sequence repeat (SSR) loci, comprising 1,198 compound and 6,251 perfect SSRs, with an occurrence frequency of 30.96%. Di- and tri-nucleotide repeats were the predominant types. Thirteen highly polymorphic SSR loci showed robust polymorphism across four geographical populations. This study provides a crucial data foundation and genetic resource for functional gene research, molecular marker-assisted breeding, and germplasm conservation in S. hollandi.