Genome-wide identification and tissue-specific profiling of microRNAs in lentil (Lens culinaris Medik.)

Abstract

MicroRNAs (miRNAs) are key post-transcriptional regulators involved in plant development, metabolism, and stress adaptation. Despite the agronomic importance of lentil ( Lens culinaris Medik.), its miRNA landscape remains relatively underexplored. This study aimed to generate a comprehensive, tissue-specific conserved and novel miRNA dataset to support future investigationsof gene regulation in lentil. Small RNA libraries from seven tissues—root, shoot, stem, mature leaf, flower, flower bud, and young pod—were sequenced using the Illumina HiSeq platform, generating over 432 million reads. A total of 1,490 miRNA candidates were identified, comprising 415 conserved and 1,075 novel miRNAs. Among 370 miRNAs with sufficient expression levels for analysis, a substantial proportion showed differential accumulation across tissues, indicating spatial variation in miRNA profiles. Conserved miRNAs displayed broadly distributed expression patterns, while many novel candidates were detected in a more limited number of tissues. Computational target prediction and functional enrichment analyses suggested associations of conserved miRNAs with transcriptional regulation and hormone signaling pathways, whereas predicted targets of novel miRNAs were linked to diverse metabolic and stress-related processes. This study provides the first comprehensive, multi-tissue overview of miRNA populations in lentil and substantially expands the currently available repertoire of both conserved and candidate novel miRNAs. The dataset offers a valuable resource for future studies aimed at functional characterization, experimental validation, and integration of miRNA-mediated regulation into lentil biology and crop improvement efforts.