Plant long noncoding RNAs: why do we not know more?

Abstract

Analysis of plant and animal genomes is essential for understanding their biological function, adaptation, and evolution. Human genomic databases are the most advanced due to extensive research on the genetic basis of disease and personalized medicine. Key resources include GenBank, Ensembl, the 1000 Genomes Project, and GTEx, which provide detailed information on genome sequences, genetic variation, and gene expression in different tissues. Similarly, genomic and transcriptome databases for animals are relatively well-developed, particularly for model organisms such as Mus musculus, Drosophila melanogaster, and Danio rerio. In contrast, plant genomic databases are developing rapidly but remain less comprehensive than those for humans and animals. This discrepancy is primarily due to the high species diversity and complexity of plant genomes, which are often characterized by gene duplication and significant structural variability. Databases such as Phytozome, TAIR (The Arabidopsis Information Resource), Gramene, and Planteome focus mainly on model plants and agriculturally important species. Another crucial factor is the lower funding for plant-related projects, despite the substantial investment required due to the large size and complexity of plant genomes. This disparity is also evident in the study of long non-coding RNAs (lncRNAs), which play a key role in the growth and development of organisms. In plants, genome complexity-driven by factors such as considerable length, polyploidy, and epigenetic modifications-poses significant challenges for research. Despite these obstacles, understanding lncRNAs in plants, particularly in forest trees, is of paramount importance. lncRNAs hold great potential for applications in agriculture and forestry, especially in the context of climate change. For example, they could enhance our ability to develop resilient tree species capable of withstanding environmental stressors. To achieve this, a comprehensive understanding of lncRNA functions at the molecular and biological levels, as well as the development of robust and complete databases, is urgently needed. In the near future, computational analyses are expected to play a key role in overcoming these challenges. In this article, we review the current state of knowledge about lncRNAs in plants, highlight the obstacles to their study, and explore how advances in this field could revolutionize agriculture and forestry. By focusing on the unique challenges and opportunities presented by forest trees, we emphasize the crucial role of lncRNA research in addressing global environmental challenges.

Keywords: Coexpression; Computational analyses; Epitranscriptome; Genome duplication; Genome size; Plants; Polyploidization; Species range; lncRNA; miRNA.

Fig. 1

Genome size (logarithmic scale) in different taxonomic groups according to the NCBI data (only ;‘reference’’ and ‘‘representative’’ genomes). The data were visualized with the ‘ggstatsplot’ package [30]. Most animals, especially mammals, have similar-sized genomes (3–7 Gbp). However, in plants, the sizes of the genomes vary much more between species, reaching very large values (1–148 Gbp). Tree genomes typically contain tens of billions of base pairs (10–30 Gbp)

Fig. 2

Occurrence of ploidy. A—percentage of polyploids (green and blue colours) and diploids (grey colour) in plants and animals; the size of the chart is proportional to the logarithm of the number of species in each group. B—correlation between the ploidy level and chromosome number in the plants; data according to the plant RNA database [44], plot prepared in JMP© software. R2 and p-value calculated using function lm in the R environment (R Core Team. 2021. R: A language and environment for statistical. https://www.R-project.org/) for two datasets: full and without outliers (red lines)

Fig. 3

Examples of the action of long ncRNAs in different anatomical parts of the plant

Fig. 4

Changing of the potential range of two woody species according to [111]. A—Potential range of Picea abies in current conditions; B—Potential range of Picea abies in 2095 (RCP 8.5), C—Potential range of Populus tremula in current conditions; D—Potential range of Populus tremula in 2095 (RCP 8.5). Maps were prepared using QGIS software (QGIS Geographic Information System. QGIS Association. 2023. http://www.qgis.org)

Fig. 5

Minimum Free Energy (MFE) and Centroid secondary structures for the lncRNA and its target: A—COOLAIR lncRNA (full length, noncoding primary transcript from TAIR database (The Arabidopsis Information Resource, on www.arabidopsis.org, 08.03.2024); accession number: 6533802487, name: AT5G01675.1). B—FLOWERING LOCUS C gene, sequence according to NCBI database: NC_003076.8. Structures were prepared using the RNAfold tool [142, 143]