# Advances of Long Non-Coding RNA in Perennial Plants: Development and Stress Responses

**Authors:** Yayu Guo, Danni Guo, Yunqing Wang, Jinhuan Yin, Guijun Liu, Huimin Xu

PMC · DOI: 10.3390/plants14213280 · 2025-10-27

## TL;DR

This paper reviews how long non-coding RNAs influence growth and stress responses in perennial plants.

## Contribution

The paper provides a systematic summary of lncRNA classification and regulation in woody plants, highlighting recent advances and challenges.

## Key findings

- lncRNAs regulate plant growth and development through multiple signaling pathways.
- Recent studies show lncRNAs play roles in perennial plant responses to abiotic and biotic stresses.
- The paper identifies current challenges in lncRNA research for plant ontogeny and stress responses.

## Abstract

Long non-coding RNAs (lncRNAs), which have RNA transcripts over 200 nucleotides long and do not usually code for proteins, play an important role in plant growth and development, by interacting with multiple signaling pathways and participating in the regulation of fundamental biological processes. This review systematically summarizes the classification and regulatory mechanisms of plant lncRNAs, with a focus on recent advances in research on their regulatory roles in woody plant growth, development, and responses to abiotic and biotic stresses. Additionally, we discuss the current challenges in lncRNA research on plant ontogeny and stress responses, aiming to provide a theoretical foundation for future studies on lncRNAs in perennial plants.

## Full-text entities

- **Genes:** FLC (K-box region and MADS-box transcription factor family protein) [NCBI Gene 830878] {aka AGAMOUS-like 25, AGL25, FLF, FLOWERING LOCUS C, FLOWERING LOCUS F, MADS BOX PROTEIN FLOWERING LOCUS F}, PR1 (pathogenesis-related protein 1) [NCBI Gene 815949] {aka ATPR1, PATHOGENESIS-RELATED GENE 1, PATHOGENESIS-RELATED PROTEIN 1, PR 1, T6B13.15, T6B13_15}, PIL6 (phytochrome interacting factor 3-like 6) [NCBI Gene 825075] {aka PHYTOCHROME-INTERACTING FACTOR 5, PIF5, phytochrome interacting factor 3-like 6}, IPS1 (induced by phosphate starvation1) [NCBI Gene 820152] {aka A. THALIANA INDUCED BY PHOSPHATE STARVATION1, ATIPS1, INDUCED BY PHOSPHATE STARVATION1}, LAX3 (uncharacterized protein) [NCBI Gene 844105] {aka T32E8.2, T32E8_2, like AUX1 3}, SPL9 (squamosa promoter binding protein-like 9) [NCBI Gene 818820] {aka AtSPL9, T24P15.11, T24P15_11, squamosa promoter binding protein-like 9}, WOX5 (WUSCHEL related homeobox 5) [NCBI Gene 820297] {aka WOX5B, WUSCHEL related homeobox 5, WUSCHEL related homeobox 5B}, MIR5021 (ncRNA) [NCBI Gene 28717917], AT2G46690 (SAUR-like auxin-responsive protein family) [NCBI Gene 819281] {aka SAUR32, SMALL AUXIN UPREGULATED RNA 32, T3A4.7}, AZG2 (Xanthine/uracil permease family protein) [NCBI Gene 835095] {aka ARABIDOPSIS THALIANA AZA-GUANINE RESISTANT2, ATAZG2, AZA-GUANINE RESISTANT2, K6A12.16, K6A12_16}, MIR156a (ncRNA) [NCBI Gene 28718303] {aka microRNA156A, p_MI0000178}, GRP7 (cold, circadian rhythm, and rna binding 2) [NCBI Gene 816705] {aka ''cold, ATGPR7, ATGRP7, CCR2, F2G1.4, GLYCINE RICH PROTEIN 7}, RDR2 (RNA-dependent RNA polymerase 2) [NCBI Gene 826714] {aka AtRDR2, RNA-dependent RNA polymerase 2, SILENCING MOVEMENT DEFICIENT 1, SMD1, T22B4.110, T22B4_110}, MYB46 (myb domain protein 46) [NCBI Gene 831127] {aka ATMYB46, MYB DOMAIN PROTEIN 46, T24H18.40, T24H18_40, myb domain protein 46}, WOX11 (WUSCHEL related homeobox 11) [NCBI Gene 821196] {aka T12J13.6, T12J13_6, WUSCHEL related homeobox 11}, WAG2 (Protein kinase superfamily protein) [NCBI Gene 820658], NERD (GW repeat- and PHD finger-containing protein NERD) [NCBI Gene 816147] {aka F16F14.1, F16F14_1, Needed for RDR2-independent DNA methylation}, PID (Protein kinase superfamily protein) [NCBI Gene 818030] {aka ABR, ABRUPTUS, PINOID, PROTEIN KINASE PINOID, T31E10.1, T31E10_1}, MYB114 (myb domain protein 114) [NCBI Gene 842956] {aka AtMYB114, T27F4.13, T27F4_13, myb domain protein 114}, CBF1 (C-repeat/DRE binding factor 1) [NCBI Gene 828653] {aka ATCBF1, C-repeat/DRE binding factor 1, DRE BINDING PROTEIN 1B, DREB1B, T30C3.11, TRANSCRIPTIONAL ACTIVATOR CBF1}, DOG1 (delay of germination 1) [NCBI Gene 834623] {aka ATDOG1, DELAY OF GERMINATION 1, GAAS5, GLUCOSE SENSING QTL 5, GSQ5, K15I22.3}, MIR399f (ncRNA) [NCBI Gene 5007930] {aka MIR399, microRNA399F, p_MI0001025}, WRKY7 (WRKY DNA-binding protein 7) [NCBI Gene 828525] {aka ATWRKY7, T22A6.70, T22A6_70, WRKY DNA-binding protein 7}, HSP18.2 (heat shock protein 18.2) [NCBI Gene 836093] {aka MTH12.7, MTH12_7, heat shock protein 18.2}, PIF4 (phytochrome interacting factor 4) [NCBI Gene 818903] {aka AtPIF4, MFL8.13, MFL8_13, SRL2, phytochrome interacting factor 4}, MED19A (mediator of RNA polymerase II transcription subunit 19a-like protein) [NCBI Gene 831097] {aka MXC9.19, MXC9_19}
- **Diseases:** injury to (MESH:D014947), Drought (MESH:C536747), Nutrient Deficiency (MESH:D007153), citrus greening disease (OMIM:614156), infection (MESH:D007239), iron deficiency (MESH:D000090463)
- **Chemicals:** reactive oxygen species (MESH:D017382), Heavy Metal (MESH:D019216), poly(A) (MESH:D011061), uronic acid (MESH:D014574), auxin (MESH:D007210), phosphate (MESH:D010710), H2O2 (MESH:D006861), NaCl (MESH:D012965), chlorophyll (MESH:D002734), lead (MESH:D007854), gibberellin (MESH:D005875), flavonoid (MESH:D005419), salicylic acid (MESH:D020156), Salt (MESH:D012492), xylan (MESH:D014990), glucose (MESH:D005947), ABA (MESH:D000040), nitrogen (MESH:D009584), flavonol (MESH:C041477), anthocyanin (MESH:D000872), Lignin (MESH:D008031), phosphorus (MESH:D010758), ascorbic acid (MESH:D001205), Flavonols (MESH:D044948), carotenoids (MESH:D002338), Fe (MESH:D007501), sulfur (MESH:D013455), cellulose (MESH:D002482), Cd (MESH:D002104), Ca2+ (-), hemicelluloses (MESH:C007916)
- **Species:** Ginkgo biloba (ginkgo, species) [taxon 3311], Populus tomentosa (Chinese white poplar, species) [taxon 118781], P. chinensis [taxon 255799], Manihot esculenta (cassava, species) [taxon 3983], Malus pumila (paradise apple, species) [taxon 283210], Populus euphratica (Euphrates poplar, species) [taxon 75702], Populus qiongdaoensis (species) [taxon 1903715], Ziziphus jujuba (Chinese jujube, species) [taxon 326968], Hippophae rhamnoides (sallowthorn, species) [taxon 193516], Pinus sylvestris (Scotch pine, species) [taxon 3349], Morus alba (white mulberry, species) [taxon 3498], Vitis vinifera (wine grape, species) [taxon 29760], Populus simonii (species) [taxon 295327], Actinidia chinensis (golden kiwifruit, species) [taxon 3625], Betula platyphylla (Asian white birch, species) [taxon 78630], Candidatus Liberibacter asiaticus (species) [taxon 34021], Medicago truncatula (barrel medic, species) [taxon 3880], Homo sapiens (human, species) [taxon 9606], Phytophthora infestans (potato late blight agent, species) [taxon 4787], Populus trichocarpa (black cottonwood, species) [taxon 3694], Pseudomonas syringae (species) [taxon 317], Oryza sativa (Asian cultivated rice, species) [taxon 4530], Picea glauca (white spruce, species) [taxon 3330], Catalpa bungei (Manchurian catalpa, species) [taxon 265496], Hevea brasiliensis (jebe, species) [taxon 3981], Malus domestica (apple, species) [taxon 3750], Pistacia vera (pistachio, species) [taxon 55513], Pyrus pyrifolia (Asian pear, species) [taxon 3767], Arabidopsis thaliana (mouse-ear cress, species) [taxon 3702], Populus x canadensis (Canadian poplar, species) [taxon 3690], Liriodendron chinense (species) [taxon 3414]

## Figures

3 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12610617/full.md

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Source: https://tomesphere.com/paper/PMC12610617