Related Experiment Video
Updated: Feb 9, 2026
08:57
Amplicon Sequencing using the Long-Read Sequencing Technologies
Published on: August 29, 2025
544
A survey of transcriptome complexity in Sus scrofa using single-molecule long-read sequencing.
Yao Li1, Chengchi Fang1, Yuhua Fu1
1Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
Summary
This study reveals the complex landscape of pig transcriptome diversity through alternative splicing (AS) and fusion transcripts. DNA methylation significantly influences AS events and lncRNA expression, enhancing our understanding of pig gene models.
Area of Science:
- Genomics
- Epigenetics
- Transcriptomics
Background:
- Alternative splicing (AS) and fusion transcripts expand transcriptome and proteome diversity.
- Uncertainties in mRNA structure limit understanding of AS, fusion events, and epigenetic regulation.
Purpose of the Study:
- To characterize DNA methylation landscapes on AS, fusion isoforms, and lncRNA features in pigs.
- To unveil the complexity of the pig transcriptome.
Main Methods:
- Combined single-molecule real-time sequencing, Illumina RNA-seq, and DNA methylation data.
- Analyzed DNA methylation patterns associated with AS, fusion transcripts, and lncRNAs.
Main Results:
- Identified over 28,127 novel isoforms from 26,881 novel genes and >92,000 novel AS events, with intron retention being predominant.
- Demonstrated DNA methylation's role in regulating splicing sites, promoters, and first exons for AS isoform generation.
- Discovered numerous fusion transcripts and novel lncRNAs, with DNA methylation impacting lncRNA expression.
Conclusions:
- The study significantly improved existing pig gene models.
- Revealed a greater complexity of alternative splicing and epigenetic modifications in pigs than previously understood.
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