A Reference‐Free Algorithm Discovers Regulation in the Plant Transcriptome

Plant Direct 2026 Open access

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Authors: Elisabeth A. Meyer, Evan V. Saldivar, Marek Kokot, Bo Xue, Sebastian Deorowicz, Seung Y. Rhee, Julia Salzman
DOI: 10.1002/pld3.70061
Cited by: 0
References: 25

Abstract

Most plant genomes and their (post-)transcriptional regulation remain unknown. We used SPLASH-a new, reference genome-free sequence variation detection algorithm-to analyze transcriptional and post-transcriptional regulation from RNA-seq data. We discovered allelic variation in expression during maize pollen development and imbibition-dependent cryptic splicing in Arabidopsis seeds. SPLASH enables discovery of novel regulatory mechanisms, including differential regulation of genes from parental haplotypes of hybrids, without the use of alignment to a reference genome.

Fields of Study & Subjects

Genomics and Phylogenetic Studies RNA and protein synthesis mechanisms Molecular Biology Techniques and Applications

Publication details

Journal / source
Plant Direct
Volume
10
Issue
4
Pages
e70061–e70061
Publication date
1 April 2026
Language
EN