The Plant DNA Damage Response: Signaling Pathways Leading to Growth Inhibition and Putative Role in Response to Stress Conditions

Frontiers in Plant Science, Journal Year: 2019, Volume and Issue: 10

Published: May 17, 2019

Maintenance of genome integrity is a key issue for all living organisms. Cells are constantly exposed to DNA damage due replication or transcription, cellular metabolic activities leading the production Reactive Oxygen Species (ROS) even exposure damaging agents such as UV light. However, genomes remain extremely stable, thanks permanent repair lesions. One mechanism contributing stability Damage Response (DDR) that activates pathways, and in case proliferating cells, stops cell division until complete. The signalling mechanisms DDR quite well conserved between organisms including plants where they have been investigated into detail over past 20 years. In this review we summarize acquired knowledge recent advances regarding control cycle progression. Studying plant particularly interesting because their mode development lifestyle. Indeed, develop largely post-embryonically, form new organs through activity meristems which cells retain ability proliferate. addition, sessile permanently adverse conditions could potentially induce types meristems. second part discuss findings connecting responses biotic abiotic stresses.

Language: Английский

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Origin and adaptation to high altitude of Tibetan semi-wild wheat

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: Oct. 8, 2020

Abstract Tibetan wheat is grown under environmental constraints at high-altitude conditions, but its underlying adaptation mechanism remains unknown. Here, we present a draft genome sequence of semi-wild ( Triticum aestivum ssp. tibetanum Shao) accession Zang1817 and re-sequence 245 accessions, including world-wide landraces, cultivars as well landraces. We demonstrate that environments can trigger extensive reshaping genomes, also uncover accessions accumulate adapted haplotypes related genes in response to harsh constraints. Moreover, find feral form landrace, identify two associated loci, 0.8-Mb deletion region containing Brt1/2 homologs genomic with TaQ-5A gene, responsible for rachis brittleness during the de-domestication episode. Our study provides confident evidence support hypothesis de-domesticated from local extremes.

Language: Английский

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Species divergence with gene flow and hybrid speciation on the Qinghai–Tibet Plateau

New Phytologist, Journal Year: 2022, Volume and Issue: 234(2), P. 392 - 404

Published: Jan. 12, 2022

Summary The Qinghai–Tibet Plateau (QTP) sensu lato ( sl ), comprising the platform, Himalaya and Hengduan Mountains, is characterized by a large number of endemic plant species. This evolutionary cradle may have arisen from explosive species diversification because geographic isolation. However, gene flow has been widely detected during speciation processes all groups examined, suggesting that natural selection also played an important role divergence in this region. In addition, hybrids recovered almost species‐rich genera. suggests numerous region are still ‘on pathway to complete reproductive isolation (RI)’. Such could directly develop into new through hybrid polyploidization homoploid (HHS). HHS take place more easily than previously thought alternate inheritance alleles parents at multiple RI loci. Therefore, isolation, hybridization together promoted genera on QTP . We emphasize need for identification functional analysis major genes speciation, especially encourage investigations parallel adaptive causing across different lineages within similar but specific habitats

Language: Английский

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Genome sequences of horticultural plants: past, present, and future

Horticulture Research, Journal Year: 2019, Volume and Issue: 6(1)

Published: Oct. 7, 2019

Horticultural plants play various and critical roles for humans by providing fruits, vegetables, materials beverages, herbal medicines acting as ornamentals. They have also shaped human art, culture, environments thereby influenced the lifestyles of humans. With advent sequencing technologies, there has been a dramatic increase in number sequenced genomes horticultural plant species past decade. The are highly diverse complex, often with high degree heterozygosity ploidy due to their long complex history evolution domestication. Here we summarize advances genome plants, reconstruction pan-genomes, development databases. We discuss past, present, future studies related sequencing, data storage, quality, sharing, visualization provide practical guidance genomic plants. Finally, propose project well roadmap technical details toward three goals project.

Language: Английский

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Evolutionary origin of species diversity on the Qinghai–Tibet Plateau

Journal of Systematics and Evolution, Journal Year: 2021, Volume and Issue: 59(6), P. 1142 - 1158

Published: Aug. 25, 2021

Abstract The Qinghai–Tibet Plateau (QTP) sensu lato ( sl ) houses an exceptional species diversity in Asia. To develop a comprehensive understanding of this fascinating region, we reviewed recent progress from biogeographic, paleogeographic, paleontological and genomic research both plants animals the QTP . Numerous studies have been conducted to examine whether uplift triggered production rich there, Quaternary “unified ice sheet” eliminated on central plateau how high‐altitude developed extreme environment adaptations. Major disputes arose about first issue, mainly different circumscriptions related uplift, inaccurate dating molecular phylogenetic trees, non‐causal correlations between diversification. is spatially temporally heterogeneous, abundant fossils reported recently similarly support such asynchronous upheaval model across entire region. Available phylogeographic alpine suggested their glacial refugia , rejecting unified sheet during Last Glacial Maximum. Genomic evidence limited number has identified numerous candidate genes for adaptation. In future, more should be focused speciation adaptation mechanisms based cutting‐edge methods.

Language: Английский

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Application of a novel haplotype-based scan for local adaptation to study high-altitude adaptation in rhesus macaques

Evolution Letters, Journal Year: 2021, Volume and Issue: 5(4), P. 408 - 421

Published: May 23, 2021

Abstract When natural populations split and migrate to different environments, they may experience selection pressures that can lead local adaptation. To capture the genomic patterns of a selective sweep, we develop XP-nSL, scan for adaptation compares haplotype between two populations. We show XP-nSL has power detect ongoing recently completed hard soft sweeps, then apply this statistic search evidence high altitude in rhesus macaques. analyze whole genomes 23 wild macaques captured at (mean > 4000 m above sea level) 22 low < 500 find high-altitude population or near 303 known genes several unannotated regions. strongest signal EGLN1, classic target convergent evolution species living oxygen environments. Furthermore, many are involved processes related hypoxia, regulation ROS, DNA damage repair, synaptic signaling, metabolism. These results suggest that, beyond adapting via beneficial mutation one single gene, is polygenic spread across numerous important biological systems.

Language: Английский

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Genomic convergence underlying high‐altitude adaptation in alpine plants

Journal of Integrative Plant Biology, Journal Year: 2023, Volume and Issue: 65(7), P. 1620 - 1635

Published: March 24, 2023

Evolutionary convergence is one of the most striking examples adaptation driven by natural selection. However, genomic evidence for convergent to extreme environments remains scarce. Here, we assembled reference genomes two alpine plants, Saussurea obvallata (Asteraceae) and Rheum alexandrae (Polygonaceae), with 37,938 61,463 annotated protein-coding genes. By integrating an additional five genomes, elucidated underlying high-altitude in plants. Our results detected contractions disease-resistance genes which might be energy-saving strategy surviving hostile only a few pathogens present. We identified signatures positive selection on set involved reproduction respiration (e.g., MMD1, NBS1, HPR), revealed molecular self-incompatibility, cell wall modification, DNA repair stress resistance, may underlie cold, high ultraviolet radiation hypoxia environments. Incorporating transcriptomic data, further demonstrated that associated cuticular wax flavonoid biosynthetic pathways exhibit higher expression levels leafy bracts, shedding light genetic mechanisms adaptive "greenhouse" morphology. integrative data provide novel insights into evolution at high-taxonomic level, aiding deep understanding complex

Language: Английский

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Comparative Analysis of Chloroplast Genome of Meconopsis (Papaveraceae) Provides Insights into Their Genomic Evolution and Adaptation to High Elevation

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(4), P. 2193 - 2193

Published: Feb. 12, 2024

The Meconopsis species are widely distributed in the Qinghai-Tibet Plateau, Himalayas, and Hengduan Mountains China, have high medicinal ornamental value. diversity of plant morphology this genus poses significant challenges for identification, given their propensity highland dwelling, which makes it a question worth exploring how they cope with harsh surroundings. In study, we recently generated chloroplast (cp) genomes two species, paniculata (M. paniculata) M. pinnatifolia, compared them those ten cp to comprehend genomic features, phylogenetic relationships, what part might play plateau adaptation. These shared great deal similarities terms genome size, structure, gene content, GC codon usage patterns. were between 151,864 bp 154,997 length, contain 133 predictive genes. Through sequence divergence analysis, identified three highly variable regions (trnD-psbD, ccsA-ndhD, ycf1 genes), could be used as potential markers or DNA barcodes analysis. Between 22 38 SSRs some long repeat sequences from 12 species. Our analysis confirmed that clustered into monophyletic clade Papaveraceae, corroborated intrageneric relationships. results indicated pinnatifolia sister tree. addition, atpA ycf2 genes positively selected high-altitude functions these involved adaptation extreme environment cold low CO2 concentration conditions at plateau.

Language: Английский

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Comparative transcriptomics of 3 high-altitude passerine birds and their low-altitude relatives

Proceedings of the National Academy of Sciences, Journal Year: 2019, Volume and Issue: 116(24), P. 11851 - 11856

Published: May 24, 2019

High-altitude environments present strong stresses for living organisms, which have driven striking phenotypic and genetic adaptations. While previous studies revealed multiple adaptations in high-altitude species, how evolutionary history (i.e., phylogenetic background) contributes to similarity is largely unknown, particular a group of birds. We explored this 3 passerine birds from the Qinghai-Tibet Plateau their low-altitude relatives lowland eastern China. generated transcriptomic data 5 tissues across these species compared sequence changes expression shifts between high- pairs. Sequence comparison that all was high genes under positive selection (218 genes) but low amino acid substitutions (only 4 sharing identical substitutions). Expression profiles identified tissue-specific pattern clustered by tissue). By contrast, an altitude-related observed differentially expressed pairs associated with altitude, suggesting environment may drive similar species. Gene level, gene connectivity, interactions 2 factors altitude were correlated rates. Our results provide evidence work concerted way birds, leading evolution routes response environmental stresses.

Language: Английский

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Genomic basis of high-altitude adaptation in Tibetan Prunus fruit trees

Current Biology, Journal Year: 2021, Volume and Issue: 31(17), P. 3848 - 3860.e8

Published: July 26, 2021

The Great Himalayan Mountains and their foothills are believed to be the place of origin development many plant species. genetic basis adaptation high plateaus is a fascinating topic that poorly understood at population level. We comprehensively collected sequenced 377 accessions Prunus germplasm along altitude gradients ranging from 2,067 4,492 m in Himalayas. de novo assembled three high-quality genomes Tibetan A comparative analysis indicated remarkable expansion SINE retrotransposons occurred observed differentiation between peaches low altitudes genes associated with light stress signaling, especially UV were enriched differentiated regions. By profiling metabolomes peach fruit, we determined 379 metabolites had significant correlations particular phenylpropanoids positively correlated altitudes. identified 62 peach-specific SINEs colocalized differentially accumualted relative cultivated peach. demonstrated two inserted locus controlling accumulation 3-O-feruloyl quinic acid. SINE1 was specific SINE2 predominant These genomic metabolic data for populations native region indicate helped species adapt harsh environment plateau by promoting beneficial metabolites.

Language: Английский

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