Co‐evolution within the plant holobiont drives host performance DOI Creative Commons
Fantin Mesny, Stéphane Hacquard, Bart P. H. J. Thomma

et al.

EMBO Reports, Journal Year: 2023, Volume and Issue: 24(9)

Published: July 20, 2023

Plants interact with a diversity of microorganisms that influence their growth and resilience, they can therefore be considered as ecological entities, namely "plant holobionts," rather than singular organisms. In plant holobiont, the assembly above- belowground microbiota is ruled by host, microbial, environmental factors. Upon microorganism perception, plants activate immune signaling resulting in secretion factors modulate composition. Additionally, metabolic interdependencies antagonism between microbes are driving forces for community assemblies. We argue complex plant-microbe intermicrobial interactions have been selected during evolution may promote survival fitness associated holobionts. As part this process, evolved metabolite-mediated strategies to selectively recruit beneficial microbiota. Some these members show host-adaptation, from which mutualism rapidly arise. also co-evolved antagonistic activities restrict proliferation high pathogenic potential prevent disease development. Co-evolution within holobionts thus ultimately drives performance.

Language: Английский

Plant Immunity: Danger Perception and Signaling DOI Creative Commons
Jian‐Min Zhou, Yuelin Zhang

Cell, Journal Year: 2020, Volume and Issue: 181(5), P. 978 - 989

Published: May 1, 2020

Language: Английский

Citations

741
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes DOI
Matthew B. Hufford, Arun S. Seetharam, Margaret Woodhouse

et al.

Science, Journal Year: 2021, Volume and Issue: 373(6555), P. 655 - 662

Published: Aug. 5, 2021

We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as founders maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. results demonstrate ancient tetraploid character continues to degrade by fractionation present day. Excellent contiguity over repeat arrays complete annotation centromeres revealed additional variation major cytological landmarks. show combining structural single-nucleotide polymorphisms can improve power quantitative studies. also document at level DNA methylation unmethylated regions are enriched cis-regulatory elements contribute phenotypic variation.

Language: Английский

Citations

481
Plant pan-genomes are the new reference DOI
Philipp E. Bayer, Agnieszka A. Golicz, Armin Scheben

et al.

Nature Plants, Journal Year: 2020, Volume and Issue: 6(8), P. 914 - 920

Published: July 20, 2020

Language: Английский

Citations

398
Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics DOI Creative Commons
Wen‐Biao Jiao, Korbinian Schneeberger

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

Published: Feb. 20, 2020

Abstract Despite hundreds of sequenced Arabidopsis genomes, very little is known about the degree genomic collinearity within single species, due to low number chromosome-level assemblies. Here, we report reference-quality assemblies seven thaliana accessions selected across its global range. Each genome reveals between 13–17 Mb rearranged, and 5–6 non-reference sequences introducing copy-number changes in ~5000 genes, including ~1900 genes. Quantifying genomes ~350 euchromatic regions, where accession-specific tandem duplications destroy genomes. These hotspots rearrangements are characterized by reduced meiotic recombination hybrids genes implicated biotic stress response. This suggests that undergo altered evolutionary dynamics, as compared rest genome, which mostly based on accumulation new mutations not existing variation, thereby enable a quick response stress.

Language: Английский

Citations

214
A super pan-genomic landscape of rice DOI Creative Commons

Lianguang Shang,

Xiaoxia Li, Huiying He

et al.

Cell Research, Journal Year: 2022, Volume and Issue: 32(10), P. 878 - 896

Published: July 12, 2022

Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting 251-accession panel comprising both cultivated wild species Asian African rice. Our reveals extensive structural variations (SVs) gene presence/absence variations. Additionally, our enables the accurate identification nucleotide-binding leucine-rich repeat genes characterization their inter- intraspecific diversity. Moreover, uncovered grain weight-associated SVs which specify traits by affecting expression nearby genes. We characterized variants associated with submergence tolerance, seed shattering plant architecture found independent selection for common set that drove adaptation domestication in This facilitates pinpointing lineage-specific haplotypes trait-associated provides insights into evolutionary events have shaped various species.

Language: Английский

Citations

210
Two gap-free reference genomes and a global view of the centromere architecture in rice DOI Creative Commons
Jia‐Ming Song,

Wen‐Zhao Xie,

Shuo Wang

et al.

Molecular Plant, Journal Year: 2021, Volume and Issue: 14(10), P. 1757 - 1767

Published: June 24, 2021

Language: Английский

Citations

206
Shaping the leaf microbiota: plant–microbe–microbe interactions DOI Creative Commons
Vasvi Chaudhry, Paul Runge, Priyamedha Sengupta

et al.

Journal of Experimental Botany, Journal Year: 2020, Volume and Issue: 72(1), P. 36 - 56

Published: Sept. 7, 2020

The aerial portion of a plant, namely the leaf, is inhabited by pathogenic and non-pathogenic microbes. leaf's physical chemical properties, combined with fluctuating often challenging environmental factors, create surfaces that require high degree adaptation for microbial colonization. As consequence, specific interactive processes have evolved to establish plant leaf niche. Little known about impact host immune system on phyllosphere colonization These organisms can trigger basal defenses benefit priming enhanced resistance pathogens. In most disease responses, signals are recognized extra- or intracellular receptors. interactions tend be species it unclear how they shape communities. natural habitats, microbe-microbe also important shaping To protect resources, colonizers developed direct antagonistic manipulation strategies fight competitors. Phyllosphere-colonizing microbes respond abiotic biotic fluctuations therefore an resource adaptive protective traits. Understanding complex regulatory host-microbe-microbe networks needed transfer current knowledge biotechnological applications such as plant-protective probiotics.

Language: Английский

Citations

175
Prokaryotic innate immunity through pattern recognition of conserved viral proteins DOI
Linyi Gao, Max E. Wilkinson, Jonathan Strecker

et al.

Science, Journal Year: 2022, Volume and Issue: 377(6607)

Published: Aug. 11, 2022

Many organisms have evolved specialized immune pattern-recognition receptors, including nucleotide-binding oligomerization domain-like receptors (NLRs) of the STAND superfamily that are ubiquitous in plants, animals, and fungi. Although roles NLRs eukaryotic immunity well established, it is unknown whether prokaryotes use similar defense mechanisms. Here, we show antiviral (Avs) homologs bacteria archaea detect hallmark viral proteins, triggering Avs tetramerization activation diverse N-terminal effector domains, DNA endonucleases, to abrogate infection. Cryo-electron microscopy reveals sensor domains recognize conserved folds, active-site residues, enzyme ligands, allowing a single receptor wide variety viruses. These findings extend paradigm pattern recognition pathogen-specific proteins across all three life.

Language: Английский

Citations

174
Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar DOI Creative Commons
Hequan Sun, Wen‐Biao Jiao, Kristin S Krause

et al.

Nature Genetics, Journal Year: 2022, Volume and Issue: 54(3), P. 342 - 348

Published: March 1, 2022

Abstract Potato is the most widely produced tuber crop worldwide. However, reconstructing four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly potato cultivar ‘Otava’ based on high-quality long reads, single-cell sequencing 717 pollen genomes and Hi-C data. Unexpectedly, ~50% was identical-by-descent due to recent inbreeding, which contrasted by highly abundant structural rearrangements involving ~20% genome. Among 38,214 genes, only 54% were present in all with average 3.2 copies per gene. Taking leaf transcriptome as example, 11% genes differently expressed at least one haplotype, where 25% them likely regulated through allele-specific DNA methylation. Our work sheds light breeding history potato, functional organization tetraploid has potential strengthen future genomics-assisted breeding.

Language: Английский

Citations

163
Plant NLRs: The Whistleblowers of Plant Immunity DOI Creative Commons

Solveig van Wersch,

Lei Tian, Ryan Hoy

et al.

Plant Communications, Journal Year: 2019, Volume and Issue: 1(1), P. 100016 - 100016

Published: Dec. 18, 2019

The study of plant diseases is almost as old agriculture itself. Advancements in molecular biology have given us much more insight into the immune system and how it detects many pathogens plants may encounter. Members primary family resistance (R) proteins, NLRs, contain three distinct domains, appear to use several different mechanisms recognize pathogen effectors trigger immunity. Understanding process NLR recognition activation has been greatly aided by advancements structural studies, with ZAR1 recently becoming first full-length be visualized. Genetic biochemical analysis identified critical components for homeostasis control. increased helper NLRs also provided insights downstream signaling pathways NLRs. This review summarizes progress last decades on research, focusing mechanistic understanding that achieved.

Language: Английский

Citations

159