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<p><i>Spinibarbus hollandi</i> 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 <i>S. hollandi</i> 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&#xa0;bp and an N50 of 2,868&#xa0;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 <i>S. hollandi</i>.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年1月17日

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  • Sixun Li,
  • Jie Lai,
  • Mengmeng Wu,
  • Zihang Xie,
  • Min Zhang,
  • Guojun Cai,
  • Ziyan Deng,
  • Binhua Deng,
  • Chong Han,
  • Qiang Li

摘要

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.