20.500.12556/DiRROS-31455 LongPolyASE: an end-to-end framework for allele-specific gene and isoform analysis in polyploids using long-read RNA-seq Background 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. Results We developed LongPolyASE, an end-to-end computational framework for allele-specific gene and isoform expression analysis in diploid and polyploid organisms using long-read RNA sequencing, consisting of three components: Syntelogfinder, for identifying syntenic gene relationships and annotation inconsistencies; longrnaseq, for novel isoform discovery and haplotype-level quantification; and PolyASE, for statistical testing and visualization of allelic imbalance and isoform usage. We applied LongPolyASE to diploid rice, autotetraploid potato, allotetraploid rapeseed, and allooctoploid strawberry using Oxford Nanopore and PacBio long-read RNA-seq. The framework enabled identification of cis-regulatory variation, tissue-specific trans-regulatory effects, differential isoform usage, and haplotype-specific splicing differences. In addition, it facilitated the discovery of novel transcripts and genes with potential functional relevance in plant development. Conclusions LongPolyASE addresses a key methodological gap by enabling allele-specific expression analysis in polyploid organisms using long-read RNA sequencing. By combining haplotype-aware quantification with isoform-level resolution in a reproducible workflow, the framework provides a practical tool for plant researchers working with complex genomes. Its application to crop species highlights its potential to support the identification of regulatory variation and candidate targets for plant breeding. allele-specific expression analysis polyploids long-read RNA-seq isoform expression gene expression true false false Angleški jezik Ni določen Neznano 2026-08-03 10:21:30 2026-08-03 10:21:30 2026-08-04 03:53:11 0000-00-00 00:00:00 2026 0 0 Nasl. z nasl. zaslona; Opis vira z dne 3. 8. 2026; Str. 1-24 21. Jul. 2026 0000-00-00 PreprintVObjavi VTisku apc 0000-00-00 0000-00-00 2026-07-21 577.2 1746-4811 10.1186/s13007-026-01569-8 267622659 https://doi.org/10.1186/s13007-026-01569-8 1 57857bd4-8f14-11f1-a7fa-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=48727 RAZ_Nolte_Nadja_Franziska_2026.pdf RAZ_Nolte_Nadja_Franziska_2026.pdf 1 61F5B1B6B5E2478249086500EF9A79EF 9c7a2b84d89a1f1318d762d59fdabf45b8d9a3b2a49f82700acb9b16adfc6b0e 6c6db924-8f14-11f1-a7fa-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=48728 Nacionalni inštitut za biologijo 0 0 0