Molecular Traits of Long Non-protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships

Abstract

Long non-coding RNAs (lncRNAs) represent a diverse class of regulatory loci with roles in development and stress responses throughout all kingdoms of life. LncRNAs, however, remain under-studied in plants compared to animal systems. To address this deficiency, we applied a machine learning prediction tool, Classifying RNA by Ensemble Machine learning Algorithm (CREMA), to analyze RNAseq data from 11 plant species chosen to represent a wide range of evolutionary histories. Transcript sequences of all expressed and/or annotated loci from plants grown in unstressed (control) conditions were assembled and input into CREMA for comparative analyses. On average, 6.4% of the plant transcripts were identified by CREMA as encoding lncRNAs. Gene annotation associated with the transcripts showed that up to 99% of all predicted lncRNAs for Solanum tuberosum and Amborella trichopoda were missing from their reference annotations whereas the reference annotation for the genetic model plant Arabidopsis thaliana contains 96% of all predicted lncRNAs for this species. Thus a reliance on reference annotations for use in lncRNA research in less well-studied plants can be impeded by the near absence of annotations associated with these regulatory transcripts. Moreover, our work using phylogenetic signal analyses suggests that molecular traits of plant lncRNAs display different evolutionary patterns than all other transcripts in plants and have molecular traits that do not follow a classic evolutionary pattern. Specifically, GC content was the only tested trait of lncRNAs with consistently significant and high phylogenetic signal, contrary to high signal in all tested molecular traits for the other transcripts in our tested plant species.

Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation

“…The highly evolved nature of lncRNAs has resulted in lower sequence conservation across plant and animal species and, thus, fewer phylogenetic relationships [38,39]. Marques and Ponting [40] reported that < 2% of lncRNAs in Arabidopsis thaliana were evolutionarily conserved across the plant kingdom, which explains the rapid evolution of lncRNA sequences.…”

Genome-wide analysis of lncRNAs points to their roles in the modulation of developmental regulator expression during plant male germline development

“…Across plant species, lncRNAs are reported to show low conservation and are mostly species-specific [47, 48]. Because lncRNAs are highly evolved, there is less sequence conservation across plant and animal taxa, resulting in fewer phylogenetic connections [47].…”

Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress

“…Thus over 60% of the lncRNAs that we detected in both Eutrema salsugineum ecotypes were also expressed in plants that we have no reason to believe were stressed. lncRNAs are notoriously difficult to identify with certainty and, not surprisingly, are generally poorly annotated in existing public plant reference genomes [38]. For this study we used an accurate ensemble machine learning program (CREMA [39]) that used validated lncRNAs for training.…”