A-ELIXIR.02: LongPolyASE: An end-to-end framework for allele-specific gene and isoform analysis in polyploids using long-read RNA-se
Authors
Marko Petek
National Instiute of Biology
Kristina Gruden
National Instiute of Biology
Keywords
plants, long-read RNA-seq, haplotype-resolved reference genomes
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Allele-specific expression analysis can reveal cis-regulatory differences (e.g., promoter variants, epigenetic changes) that cause imbalanced gene expression between haplotypes. Haplotype-resolved reference genomes and long-read RNA sequencing enable allele-specific expression analysis at gene and isoform-levels. However, existing tools are largely restricted to short-read RNA sequencing data and diploid organisms and are therefore not applicable for polyploid crop species.
We developed LongPolyASE (https://polyase.readthedocs.io/en/latest/), an end-to-end framework for allele-specific gene and isoform expression analysis in diploid and polyploid organisms using long-read RNA sequencing. It comprises three components: Syntelogfinder, for identifying syntenic genes across phased assemblies; longrnaseq, for transcript quantification, novel isoform discovery, and quality control; and PolyASE, for statistical testing of differential allelic expression, isoform usage, and haplotype-specific splicing. Applied to Oxford Nanopore RNA-seq data from diploid rice and autotetraploid potato, LongPolyASE identified cis-regulatory variation, tissue-specific trans-regulatory effects, and novel transcripts with potential relevance to plant development.
LongPolyASE addresses a methodological gap by enabling allele- and isoform-specific expression analysis in polyploid organisms. The framework is fully documented, openly available on GitHub and PyPI, and designed for FAIR and reproducible research. It directly benefits plant researchers working with complex genomes and supports the identification of regulatory variation and candidate targets in crop breeding.
Co-authors: Kristina Gruden, Marko Petek
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