# Diversity of lncRNAs in the pan-transcriptome of maize inbred lines

## TL;DR

This study explores the diversity of long non-coding RNAs in maize inbred lines, revealing higher sequence variation and lineage-specific traits compared to mRNAs.

## Contribution

The study provides new insights into the evolutionary patterns and diversity of lncRNAs in maize using a pan-transcriptomic approach.

## Key findings

- The lncRNA pan-transcriptome has more sequences and higher nucleotide diversity compared to the mRNA pan-transcriptome.
- Antisense lncRNAs are the most conserved, while intergenic lncRNAs show the highest sequence diversity and line specificity.
- Nucleotide substitution rates differ systematically between coding and non-coding sequences across pan-transcriptome components.

## Abstract

Long non-coding RNAs (lncRNAs) constitute a substantial portion of the plant transcriptomes and performs important functions in numerous molecular, regulatory, growth and developmental processes and stress responses. However, functional characteristics supported by experimental evaluation are known only for a small part of lncRNAs. In this regard, evolutionary and comparative analysis of lncRNA sequences can provide additional information about the functional role of these molecules.

Analysis of RNA-seq libraries from 503 maize inbred lines obtained by Hirsch et al. (2014) enabled the assessment of sequence diversity and evolutionary patterns of maize lncRNAs within the pan-transcriptome framework and their comparison with analogous mRNA characteristics. The lncRNA pan-transcriptome comprises a greater number of representative sequences (595,198), compared to mRNA pan-transcriptome (245,436), smaller fraction of core and shell parts and larger cloud component (52.5% vs 11%). However, both pan-transcriptomes are closed according to estimates of the power-law parameters. Nucleotide diversity of the lncRNAs significantly higher compared to mRNAs. Moreover, nucleotide substitution rates estimates for coding and non-coding sequences demonstrated systematic increase of the gamma distribution shape parameter α in the order α(Ka) < α(Ks) < α(Kn) across all pan-transcriptome components (core, shell, cloud). Comparison of evolutionary characteristics also demonstrated that antisense lncRNAs are the most conserved in terms of both nucleotide substitution rates and their representation in the core; intronic lncRNAs display the highest mutation rate, while intergenic lncRNAs exhibit the greatest sequence repertoire diversity and highest line specificity.

These results allowed to evaluate the diversity of lncRNAS from the pan-transcriptomic point of view and supported their high lineage-specificity and sequence variation across maize inbred lines in comparison to mRNA sequences.

The online version contains supplementary material available at 10.1186/s12864-025-12242-0.