LongPolyASE: an end-to-end framework for allele-specific gene and isoform analysis in polyploids using long-read...

Area of Science:

• Genomics and Bioinformatics
• Plant Molecular Biology
• Computational Biology

Background:

• Allele-specific expression (ASE) analysis reveals cis-regulatory differences impacting gene expression between haplotypes.
• Long-read RNA sequencing and haplotype-resolved genomes enable gene and isoform-level ASE analysis.
• Existing tools are limited to diploid organisms and short-read sequencing data.

Purpose of the Study:

• To develop an end-to-end computational framework for ASE analysis in diploid and polyploid organisms using long-read RNA sequencing.
• To enable haplotype-level gene and isoform quantification and statistical testing of allelic imbalance.

Main Methods:

• Development of LongPolyASE, a three-component framework: Syntelogfinder, longrnaseq, and PolyASE.
• Application of LongPolyASE to diploid rice, autotetraploid potato, allotetraploid rapeseed, and allooctoploid strawberry.
• Utilized Oxford Nanopore and PacBio long-read RNA sequencing data.

Main Results:

• Identified cis-regulatory variation, tissue-specific trans-regulatory effects, and differential isoform usage in polyploid plants.
• Discovered haplotype-specific splicing differences and novel transcripts with potential functional relevance.
• Demonstrated the framework's capability in diverse plant species with complex genomes.

Conclusions:

• LongPolyASE fills a methodological gap for ASE analysis in polyploid organisms using long-read RNA sequencing.
• Provides a reproducible workflow for haplotype-aware quantification and isoform-level resolution.
• Supports identification of regulatory variation and candidate genes for crop improvement and plant breeding.