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

BMC Plant Biology, Journal Year: 2020, Volume and Issue: 20(1)

Published: Oct. 12, 2020

Abstract Background The immobile nature of plants means that they can be frequently confronted by various biotic and abiotic stresses during their lifecycle. Among the stresses, water stress, temperature extremities, salinity, heavy metal toxicity are major challenging overall plant growth. Plants have evolved complex molecular mechanisms to adapt under given stresses. Long non-coding RNAs (lncRNAs)—a diverse class contain > 200 nucleotides(nt)—play an essential role in adaptation Results LncRNAs play a significant as ‘biological regulators’ for developmental processes stress responses animals at transcription, post-transcription, epigenetic level, targeting stress-responsive mRNAs, regulatory gene(s) encoding transcription factors, numerous microRNAs (miRNAs) regulate expression different genes. However, mechanistic lncRNAs possible target contributing response adaptation, remain largely unknown. Here, we review types found species, with focus on understanding contribute tolerance plants. We start discussing biogenesis, type function, phylogenetic relationships, sequence conservation lncRNAs. Next, controlling including drought, heat, cold, toxicity, nutrient deficiency, relevant examples from species. Lastly, briefly discuss lncRNA databases bioinformatics predicting structural functional annotation novel Conclusions Understanding intricate is its infancy. availability comprehensive atlas across whole genomes crop plants, coupled responses, will enable us use potential biomarkers tailoring stress-tolerant future.

Language: Английский

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Genomics of Evolutionary Novelty in Hybrids and Polyploids

Frontiers in Genetics, Journal Year: 2020, Volume and Issue: 11

Published: July 28, 2020

It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically as significant speciation adaptation, recognition of the importance interspecific gene flow dramatically increased during genomics era, concomitant with an unending flood empirical examples, or without genome doubling. Interspecific is thus increasingly thought to lead evolutionary innovation diversification, via adaptive introgression, homoploid hybrid allopolyploid speciation. Less well understood, however, suite genetic genomic mechanisms set motion by merger differentiated genomes, temporal scale over which recombinational complexity mediated might be expressed exposed natural selection. We focus on these issues here, considering types molecular saltational event between two diverged species, either doubling, how various can contribute novel phenotypes. Genetic include infusion new alleles genesis structural variation including translocations inversions, homoeologous exchanges, transposable element mobilization insertional effects, presence-absence copy number variation. Polyploidy generates massive transcriptomic regulatory alteration, presumably disrupted stoichiometries factors, small RNAs other interactions cascade from single-gene expression change up through entire networks transformed modules. highlight both combinatorial possibilities range scales such generated, selection drift.

Language: Английский

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Epigenetics and the success of invasive plants

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2021, Volume and Issue: 376(1826), P. 20200117 - 20200117

Published: April 17, 2021

Biological invasions impose ecological and economic problems on a global scale, but also provide extraordinary opportunities for studying contemporary evolution. It is critical to understand the evolutionary processes that underly invasion success in order successfully manage existing invaders, prevent future invasions. As successful invasive species sometimes are suspected rapidly adjust their new environments spite of very low genetic diversity, we obliged re-evaluate genomic-level translate into phenotypic diversity. In this paper, review work supports idea trait variation, within among populations, can be created through epigenetic or other non-genetic processes, particularly clonal invaders where somatic changes persist indefinitely. We consider several have been implicated as adaptive success, focusing various forms 'genomic shock' resulting from exposure environmental stress, hybridization whole-genome duplication (polyploidy), leading patterns gene expression re-programming contribute variation even novelty. These mechanisms transgressive phenotypes, including hybrid vigour novel traits, may thus help huge successes some plant especially those genetically impoverished. This article part theme issue 'How does epigenetics influence course evolution?'

Language: Английский

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Regulatory non-coding RNAs: a new frontier in regulation of plant biology

Functional & Integrative Genomics, Journal Year: 2021, Volume and Issue: 21(3-4), P. 313 - 330

Published: May 20, 2021

Abstract Beyond the most crucial roles of RNA molecules as a messenger, ribosomal, and transfer RNAs, regulatory role many non-coding RNAs (ncRNAs) in plant biology has been recognized. ncRNAs act riboregulators by recognizing specific nucleic acid targets through homologous sequence interactions to regulate growth, development, stress responses. Regulatory ncRNAs, ranging from small long (lncRNAs), exert their control over vast array biological processes. Based on mode biogenesis function, evolved into different forms that include microRNAs (miRNAs), interfering (siRNAs), miRNA variants (isomiRs), lncRNAs, circular (circRNAs), derived ncRNAs. This article explains classes development Furthermore, applications crop improvement, targeting agriculturally important traits, have discussed.

Language: Английский

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Long non-coding RNAs in plants: emerging modulators of gene activity in development and stress responses

Planta, Journal Year: 2020, Volume and Issue: 252(5)

Published: Oct. 24, 2020

Abstract Main conclusion Long non-coding RNAs modulate gene activity in plant development and stress responses by various molecular mechanisms. (lncRNAs) are transcripts larger than 200 nucleotides without protein coding potential. Computational approaches have identified numerous lncRNAs different species. Research the past decade has unveiled that participate a wide range of biological processes, including regulation flowering time morphogenesis reproductive organs, as well abiotic biotic responses. LncRNAs execute their functions interacting with DNA, RNA molecules, modulating expression level targets through epigenetic, transcriptional, post-transcriptional or translational regulation. In this review, we summarize characteristics lncRNAs, discuss recent progress on understanding lncRNA functions, propose an experimental framework for functional characterization.

Language: Английский

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Interplay between miRNAs and lncRNAs: Mode of action and biological roles in plant development and stress adaptation

Computational and Structural Biotechnology Journal, Journal Year: 2021, Volume and Issue: 19, P. 2567 - 2574

Published: Jan. 1, 2021

Plants employ sophisticated mechanisms to control developmental processes and cope with environmental changes at transcriptional post-transcriptional levels. MicroRNAs (miRNAs) long noncoding RNAs (lncRNAs), two classes of endogenous RNAs, are key regulators gene expression in plants. Recent studies have identified the interplay between miRNAs lncRNAs as a novel regulatory layer On one hand, target for production phased small interfering (phasiRNAs). other serve origin or regulate accumulation activity transcription Theses lncRNA-miRNA interplays crucial plant development, physiology responses biotic abiotic stresses. In this review, we summarize recent advances biological roles, interaction computational predication methods

Language: Английский

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Genetic and molecular mechanisms underlying mangrove adaptations to intertidal environments

iScience, Journal Year: 2021, Volume and Issue: 25(1), P. 103547 - 103547

Published: Nov. 30, 2021

Language: Английский

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A fungal effector suppresses the nuclear export of AGO1–miRNA complex to promote infection in plants

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(12)

Published: March 15, 2022

Communication between interacting organisms via bioactive molecules is widespread in nature and plays key roles diverse biological processes. Small RNAs (sRNAs) can travel host plants filamentous pathogens to trigger transkingdom RNA interference (RNAi) recipient cells modulate plant defense pathogen virulence. However, how fungal counteract antifungal RNAi has rarely been reported. Here we show that a secretory protein VdSSR1 (secretory silencing repressor 1) from Verticillium dahliae, soil-borne phytopathogenic fungus causes wilt diseases wide range of hosts, required for virulence plants. translocate nucleus serve as general suppressor sRNA nucleocytoplasmic shuttling. We further reveal sequesters ALY family proteins, adaptors the TREX complex, interfere with nuclear export AGO1–microRNA (AGO1–miRNA) leading great attenuation cytoplasmic AGO1 levels. With this mechanism, V. dahliae suppress accumulation mobile miRNAs succedent genes, thereby increasing its Our findings mechanism by which fungi antagonize RNAi-dependent immunity expand understanding on complex interaction pathogens.

Language: Английский

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Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: April 7, 2022

All extant core-eudicot plants share a common ancestral genome that has experienced cyclic polyploidizations and (re)diploidizations. Reshuffling of the generates abundant genomic diversity, but role this diversity in shaping hierarchical architecture, such as chromatin topology gene expression, remains poorly understood. Here, we assemble chromosome-level genomes one diploid three tetraploid Panax species conduct in-depth comparative epigenomic analyses. We show chromosomal interactions within each duplicated chromosome largely maintain species, albeit experiencing ca. 100-150 million years evolution from shared ancestor. Biased genetic fractionation epigenetic regulation divergence during polyploidization/(re)diploidization processes generate remarkable biochemical secondary metabolites genus. Our study provides paleo-polyploidization perspective how reshuffling leads to highly dynamic metabolic diversification eudicot plants.

Language: Английский

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Molecular evolution and functional modification of plant miRNAs with CRISPR

Trends in Plant Science, Journal Year: 2022, Volume and Issue: 27(9), P. 890 - 907

Published: Feb. 11, 2022

Language: Английский

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