A Phytophthora Effector Suppresses Trans-Kingdom RNAi to Promote Disease Susceptibility

Cell Host & Microbe, Год журнала: 2018, Номер 25(1), С. 153 - 165.e5

Опубликована: Дек. 27, 2018

Язык: Английский

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Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics

Nature Communications, Год журнала: 2020, Номер 11(1)

Опубликована: Фев. 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.

Язык: Английский

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A Series of Fortunate Events: Introducing Chlamydomonas as a Reference Organism

The Plant Cell, Год журнала: 2019, Номер 31(8), С. 1682 - 1707

Опубликована: Июнь 12, 2019

The unicellular alga

Язык: Английский

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The Penium margaritaceum Genome: Hallmarks of the Origins of Land Plants

Cell, Год журнала: 2020, Номер 181(5), С. 1097 - 1111.e12

Опубликована: Май 1, 2020

Язык: Английский

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An N-terminal motif in NLR immune receptors is functionally conserved across distantly related plant species

eLife, Год журнала: 2019, Номер 8

Опубликована: Ноя. 27, 2019

The molecular codes underpinning the functions of plant NLR immune receptors are poorly understood. We used in vitro Mu transposition to generate a random truncation library and identify minimal functional region NLRs. applied this method NRC4-a helper that with multiple sensor NLRs within Solanaceae receptor network. This revealed NRC4 N-terminal 29 amino acids sufficient induce hypersensitive cell death. is defined by consensus MADAxVSFxVxKLxxLLxxEx (MADA motif) conserved at N-termini NRC family proteins ~20% coiled-coil (CC)-type MADA motif matches α1 helix Arabidopsis protein ZAR1, which undergoes conformational switch during resistosome activation. Immunoassays functionally across from distantly related species. NRC-dependent lack sequences indicating has degenerated over evolutionary time.

Язык: Английский

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Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions

Genome Research, Год журнала: 2018, Номер 28(4), С. 532 - 546

Опубликована: Март 12, 2018

Meiotic recombination initiates from DNA double-strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. DSB frequency varies extensively along eukaryotic chromosomes, with hotspots controlled chromatin and sequence. To map meiotic DSBs throughout a plant genome, we purified sequenced Arabidopsis thaliana SPO11-1-oligonucleotides. SPO11-1-oligos are elevated in gene promoters, terminators, introns, which is driven AT-sequence richness that excludes nucleosomes allows SPO11-1 access. A positive relationship was observed between crossovers genome-wide, although fine-scale correlations were weaker. This may reflect the influence of interhomolog polymorphism on crossover formation, downstream formation. Although H3K4me3 enriched proximity to SPO11-1-oligo at 5′ ends, levels do not correlate DSBs. Repetitive transposons thought be silenced during meiosis, prevent nonallelic interactions genome instability. Unexpectedly, found high nucleosome-depleted Helitron/Pogo/Tc1/Mariner transposons, whereas retrotransposons coldspots. High within regulatory regions immunity genes, suggesting role as enhancers. As transposon mobility genomes restricted methylation, used met1 methyltransferase mutant investigate heterochromatin distributions. Epigenetic activation centromeres occurred mutants, coincident reduced nucleosome occupancy, gain transcription, H3K4me3. Together, our work reveals complex A. genes significance for diversity evolution genomes.

Язык: Английский

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Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation

Proceedings of the National Academy of Sciences, Год журнала: 2017, Номер 114(46)

Опубликована: Окт. 30, 2017

Eukaryotic transcriptomes contain a major non-protein-coding component that includes precursors of small RNAs as well long noncoding RNA (lncRNAs). Here, we utilized the mapping ribosome footprints on to explore translational regulation coding and in roots Arabidopsis thaliana shifted from replete deficient phosphorous (Pi) nutrition. Homodirectional changes steady-state mRNA abundance translation were observed for all but 265 annotated protein-coding genes. Of translationally regulated mRNAs, 30% had one or more upstream ORF (uORF) influenced number ribosomes principal region. Nearly one-half 2,382 lncRNAs detected footprints, including 56 with significantly altered under Pi-limited The prediction translated ORFs (sORFs) by quantitation termination peptidic analysis identified produce peptides, several deeply evolutionarily conserved Pi-regulated lncRNAs. Furthermore, discovered natural antisense transcripts (NATs) frequently have actively sORFs, five low-Pi up-regulation correlated enhanced sense mRNA. data also confirmed miRNA target mimics trans-acting phased small-interfering (tasiRNA/phasiRNAs). Mutational analyses positionally sORF TAS3a linked its tasiRNA biogenesis. Altogether, this systematic ribosome-associated mRNAs demonstrates nutrient availability controls protein peptide-encoding diverse cadre regulatory RNAs.

Язык: Английский

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A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

BMC Genomics, Год журнала: 2018, Номер 19(1)

Опубликована: Апрель 16, 2018

Most published genome sequences are drafts, and most dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that not assigned to chromosomes, predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft has 164 Mb of unassigned pseudo-chromosomes, omissions have been identified in the models.A second an A. (genotype Red5) was fully sequenced. This new resulted a 554.0 assembly with all but 6 pseudo-chromosomes. Pseudo-chromosomal comparisons showed number translocation events occurred following whole duplication (WGD) event some consistent centromeric Robertsonian-like translocations. RNA sequencing from 12 tissues ab initio analysis informed genome-wide manual annotation, using WebApollo tool. In total, 33,044 loci represented 33,123 isoforms were identified, named tagged for evidential support. Of these 3114 (9.4%) identical protein within Kiwifruit Information Resource (KIR v2). Some proportion differences will be varietal polymorphisms. However, as computationally Red5 models required re-annotation this is expected small. tested 550 cloned 'Hort16A' cDNAs comparing both original revised annotation KIR v2. Only 48.9% 63.5% had match 90% identity or better respectively, compared 90.9% models.Our study highlights need take cautious approach genes. Our use tool facilitated checking correction enabling improvement utility especially relevant certain types families such EXPANSIN like Finally, high set supply kiwifruit general plant community genomics other comparative analysis.

Язык: Английский

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TERMINAL FLOWER 1-FD complex target genes and competition with FLOWERING LOCUS T

Nature Communications, Год журнала: 2020, Номер 11(1)

Опубликована: Окт. 12, 2020

Abstract Plants monitor seasonal cues to optimize reproductive success by tuning onset of reproduction and inflorescence architecture. TERMINAL FLOWER 1 (TFL1) FLOWERING LOCUS T (FT) their orthologs antagonistically regulate these life history traits, yet mechanism action, antagonism targets remain poorly understood. Here, we show that TFL1 is recruited thousands loci the bZIP transcription factor FD. We identify master regulator floral fate, LEAFY ( LFY ) as a target under dual opposite regulation FT uncover pivotal role in promoting flower fate via upregulation. provide evidence between relies on competition for chromatin-bound FD at shared loci. Direct TFL1-FD regulated genes this complex hub repressing both regulators development endogenous signalling pathways. Our data mechanistic insight into how sculpt architecture, trait important success, plant architecture yield.

Язык: Английский

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Extensive signal integration by the phytohormone protein network

Nature, Год журнала: 2020, Номер 583(7815), С. 271 - 276

Опубликована: Июль 1, 2020

Язык: Английский

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