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Cevik, V.

Publications and source records attributed to Cevik, V..

11 recordsLinked to original sources

Presymptomatic plant disease detection with PSNet: A low-cost hyperspectral imaging and RGB fusion framework.

Plant pathogens cause yield losses worldwide, threatening food security and livelihoods. Because early infection is difficult to diagnose, management often relies on prophylactic pesticide use, increasing costs and environmental impact. Here we present PSNet, a multimodal framework that fuses hyperspectral imaging with RGB information for presymptomatic plant disease detection, together with a low-cost hyperspectral camera incorporating a 3D-printed housing, costing under {pound}500. We validate PSNet using Arabidopsis thaliana infected with the oomycete Albugo candida. Imaging at 2 and 4 days post inoculation, prior to visible symptoms, revealed spectral signatures that distinguished infected from healthy plants, while imaging at 6 days post inoculation captured the transition toward early symptom emergence. Discriminative spectral regions overlapped wavelengths associated with plant responses to biotic stress, supporting the biological plausibility of these signatures. Performance was evaluated using strict plant-level partitioning, ensuring samples from the same plant were confined to a single split. On a four-class task (healthy, 2 dpi, 4 dpi, 6 dpi), PSNet achieved 90.00% accuracy and 97.50% accuracy for binary classification. Together, these results demonstrate that presymptomatic detection is feasible under controlled conditions using low-cost hardware and multimodal learning, underscoring the potential of scalable multimodal systems for early disease monitoring.

plant biology↗

Busted: maternal modifiers of the triploid block involved in seed size control.

The triploid block leads to seed abortion in crosses involving tetraploid Col-0 pollen. The genetic basis underlying this phenomenon is established in the endosperm and attributed to parental genomic imprinting. This research utilised the genetic variation in Arabidopsis to identify the genomic regions harbouring the maternal modifiers of the triploid block to produce viable large seeds. Distinct chromosomal regions were identified in Bla-1 and Tsu-0 accessions. The Bla-1 maternal modifier maps to the TTG2 locus at the lower end of chromosome 2 to produce large viable seeds in response to a triploid block. Tsu-0 accession, on the other hand, recruits the TTG1 locus on the upper arm of chromosome 5 as a maternal modifier of the triploid block. TTG1 and TTG2 mutations significantly increased the proportion of large viable seeds in interploidy crosses. Both genes are involved in transcriptional regulation in the flavonoid biosynthesis pathway. However, to regulate seed size in diploids, TTG1 functions synergistically with auxin but does so independently of TTG2. This work contributed to the genetic framework for the TTG1 and TTG2 seed size roles. HIGHLIGHTSO_LIDifferent Arabidopsis accessions recruit maternal modifiers to repress Col-killing in F1 triploids. C_LIO_LIThese maternal modifiers may operate in the same pathway, such as the flavonoid biosynthesis pathway or other interconnected pathways such as auxin. C_LIO_LITTG1 and TTG2 generally increase F1 triploid survival but in an accession-dependent manner. C_LIO_LITTG1 differentially exhibits a strong positive additive interaction with auxin to increase diploid seed size. C_LIO_LIThe TTG1/TTG2 roles in diploid seed size control appear to have diverged somewhere in the auxin branch of the flavonoid biosynthesis pathway. C_LI

plant biology↗

ATR2Cala2 from Arabidopsis-infecting downy mildew requires 4 TIR-NLR immune receptors for full recognition

O_LIArabidopsis Col-0 RPP2A and RPP2B confer recognition of Arabidopsis downy mildew (Hyaloperonospora arabidopsidis [Hpa]) isolate Cala2, but the identity of the recognized ATR2Cala2 effector was unknown. C_LIO_LITo reveal ATR2Cala2, an F2 population was generated from a cross between Hpa-Cala2 and Hpa-Noks1. We identified ATR2Cala2 as a non-canonical RxLR-type effector that carries a signal peptide, a dEER motif, and WY domains but no RxLR motif. Recognition of ATR2Cala2and its effector function were verified by biolistic bombardment, ectopic expression and Hpa infection. C_LIO_LIATR2Cala2 is recognized in accession Col-0 but not in Ler-0 in which RPP2A and RPP2B are absent. In ATR2Emoy2 and ATR2Noks1 alleles, a frameshift results in an early stop codon. RPP2A and RPP2B are essential for the recognition of ATR2Cala2. Stable and transient expression of ATR2Cala2 under 35S promoter in Arabidopsis and Nicotiana benthamiana enhances disease susceptibility. C_LIO_LITwo additional Col-0 TIR-NLR (TNL) genes (RPP2C and RPP2D) adjacent to RPP2A and RPP2B are quantitatively required for full resistance to Hpa-Cala2. C_LIO_LIWe compared RPP2 haplotypes in multiple Arabidopsis accessions and showed that all 4 genes are present in all ATR2Cala2-recognizing accessions. C_LI

plant biology↗

Inducible TRAP RNA profiling reveals host genes expressed in Arabidopsis cells haustoriated by downy mildew

The downy mildew oomycete Hyaloperonospora arabidopsidis, an obligate filamentous pathogen, infects Arabidopsis by forming feeding structures called haustoria inside host cells. Previous transcriptome analyses revealed host genes are specifically induced during infection; however, RNA profiling from infected tissues may fail to capture key transcriptional events occurring exclusively in haustoriated host cells where the pathogen injects virulence effectors to modulate host immunity. To determine interactions between Arabidopsis and H. arabidopsidis at the cellular level, we devised a new translating ribosome affinity purification system applicable to inducible, including pathogen-responsive, promoters thus enabling haustoriated cell-specific RNA profiling. Among the host genes specifically expressed in H. arabidopsidis-haustoriated cells, we found genes that promote either susceptibility or resistance to the pathogen, providing new insights into the Arabidopsis/downy mildew interaction. We propose that our novel protocol for profiling cell-specific transcripts will be applicable to several stimulus-specific contexts and other plant-pathogen interactions.

plant biology↗

The integrated LIM-peptidase domain of the CSA1/CHS3 paired immune receptor detects changes in DA1 family peptidase inhibitors to confer Albugo candida resistance in Arabidopsis.

White blister rust, caused by the oomycete Albugo candida, is a widespread disease of Brassica crops. The Arabidopsis CSA1/DAR4 (also known as CSA1/CHS3) paired immune receptor carries an Integrated Domain (ID) with homology to the DA1 family of peptidases. Using domain swaps with DA1 family members, we show that the DAR4 ID acts as an integrated decoy for DAR3, which interacts with and inhibits the peptidase activities of DA1, DAR1 and DAR2 family members. Albugo infection rapidly lowered DAR3 levels and activates DA1 peptidase activity. This promotes endoreduplication of host tissues to support pathogen growth. We propose that DAR4/CSA1 senses the actions of a putative Albugo effector that reduces DAR3 levels and initiates defense.

plant biology↗

Allelic variation in the Arabidopsis TNL CHS3/CSA1 immune receptor pair reveals two functional regulatory modes

Some plant NLR immune receptors are encoded in head-to-head pairs that function together. Alleles of the NLR pair CHS3/CSA1 form three clades. The clade 1 sensor CHS3 contains an integrated domain (ID) with homology to regulatory domains, which is lacking in clades 2 and 3. We defined two regulatory modes for CHS3/CSA1 pairs. One is likely mediated by effector binding to the clade 1 ID of CHS3 and the other relies on CHS3/CSA1 pairs from all clades detecting effector modification of an associated pattern recognition receptor. We suggest that an ancestral Arabidopsis CHS3/CSA1 pair gained a second recognition specificity and regulatory mechanism through ID acquisition, while retaining its original specificity as a Guard against perturbation of pattern recognition receptor targeting by a pathogen effector. This likely comes with a cost, since both ID and non-ID alleles of the pair persist in diverse Arabidopsis populations through balancing selection. SummaryWe dissect a novel case where two regulatory modes emerged across three clades of the co-evolved CHS3/CSA1 plant immune receptor pairs, which features recruitment of an integrated domain (ID) into the clade 1 CHS3 alleles. Pre- and post-ID integration alleles maintain functionality; balancing selection maintains both in the Arabidopsis pan-genome.

plant biology↗

The TIR-NBS-LRR protein CSA1 is required for autoimmune cell death in Arabidopsis pattern recognition co-receptor bak1 and bir3 mutants

The BRI1-associated kinase BAK1/SERK3 is a positive regulator of multiple leucine rich receptor kinase-mediated signaling pathways including pattern triggered immunity (PTI). Absence or overexpression of BAK1 leads to spontaneous cell death formation. BAK1-interacting receptors (BIR) constitutively interact with BAK1, and plants lacking or overexpressing BIR proteins phenocopy the cell death symptoms observed in bak1 knock outs or overexpressors. In the interactome of BIR3, the TIR-NBS-LRR protein CONSTITUTIVE SHADE-AVOIDANCE 1 (CSA1) was identified by mass spectrometry. CSA1 physically interacts with BIR proteins and can be detected in complexes with BAK1. Direct interaction was shown only for CSA1 with BIR proteins but not BAK1. Double mutant bak1 bir3 genotypes develop strong dwarfism and cell death symptoms that are dependent on EDS1 and salicylic acid. Loss of CSA1 blocks bak1 and bak1 bir3-mediated cell death formation thus demonstrating that CSA1 is causal for this type of cell death. We propose that CSA1 guards BIR proteins and initiates autoimmune cell death that is observed when BAK1 BIR complexes are impaired. Our findings reveal how cell death in the absence of BAK1 and BIR3 is executed and links BAK1, a common co-receptor of many pattern recognition receptors, to NLR proteins typically implicated in effector-triggered immunity.

plant biology↗

The Arabidopsis WRR4A and WRR4B paralogous NLR proteins both confer recognition of multiple Albugo candida effectors

The oomycete Albugo candida causes white blister rust, an important disease of Brassica crops. Distinct races of A. candida are defined by their specificity for infecting different host species. The White Rust Resistance 4 (WRR4) locus in Col-0 accession of Arabidopsis thaliana contains three genes that encode TIR-NLR resistance proteins. The Col-0 alleles of WRR4A and WRR4B confer resistance to at least four A. candida races (2, 7 and 9 from B. juncea, B. rapa and B. oleracea, respectively, and Race 4 from Capsella bursa-pastoris). Resistance mediated by both paralogs can be overcome by Col-0-virulent isolates of Race 4. After comparing repertoires of candidate effectors in resisted and resistance-breaking strains, we used transient co-expression in tobacco or Arabidopsis to identify effectors recognized by WRR4A and WRR4B. A library of CCG effectors from four A. candida races was screened for WRR4A- or WRR4B- dependent elicitation of hypersensitive response (HR). These CCG genes were validated for WRR-dependent HR by bombardment assays in wild type Col-0, wrr4A or wrr4B mutants. Our analysis revealed eight WRR4A-recognized CCGs and four WRR4B-recognized CCGs. Remarkably, the N-terminal region of 100 amino acids after the secretion signal is sufficient for WRR4A recognition of these eight recognized effectors. This multiple recognition capacity potentially explains the broad-spectrum resistance to many A. candida races conferred by WRR4 paralogs.

plant biology↗

An improved assembly of the Albugo candida Ac2V genome reveals the expansion of the "CCG" class of effectors

Albugo candida is an obligate oomycete pathogen that infects many plants in the Brassicaceae family. We re-sequenced the genome of isolate Ac2V using PacBio long reads and constructed an assembly augmented by Illumina reads. The Ac2VPB genome assembly is 10% larger and more contiguous compared to a previous version. Our annotation of the new assembly, aided by RNASeq information, revealed a dramatic 250% expansion (40 to 110) in the CHxC effector class, which we redefined as "CCG" based on motif analysis. This class of effectors consist of arrays of phylogenetically related paralogs residing in gene sparse regions, and shows signatures of positive selection and presence/absence polymorphism. This work provides a resource that allows the dissection of the genomic components underlying A. candida adaptation and particularly the role of CCG effectors in virulence and avirulence on different hosts.

plant biology↗

Evolutionary trade-offs at the Arabidopsis WRR4A resistance locus underpin alternate Albugo candida recognition specificities

The oomycete Albugo candida causes white rust of Brassicaceae, including vegetable and oilseed crops, and wild relatives such as Arabidopsis thaliana. Novel White Rust Resistance (WRR)-genes from Arabidopsis enable new insights into plant/parasite co-evolution. WRR4A from Arabidopsis accession Col-0 provides resistance to many but not all white rust races, and encodes a nucleotide-binding (NB), leucine-rich repeat (LRR) (NLR) immune receptor protein. Col-0 WRR4A resistance is broken by a Col-0-virulent isolate of A. candida race 4 (AcEx1). We identified an allele of WRR4A in Arabidopsis accession Oy-0 and other accessions that confers full resistance to AcEx1. WRR4AOy-0 carries a C-terminal extension required for recognition of AcEx1, but reduces recognition of several effectors recognized by the WRR4ACol-0 allele. WRR4AOy-0 confers full resistance to AcEx1 when expressed as a transgene in the oilseed crop Camelina sativa. SignificanceA C-terminal extension in an allele of the Arabidopsis resistance-protein WRR4A changes effector recognition specificity, enabling the WRR4AOy-0 allele to confer immunity to Albugo candida races that overcome the WRR4ACol-0 allele. This resistance can be transferred to the oil-producing crop Camelina sativa. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/437434v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@a68de6org.highwire.dtl.DTLVardef@ae0addorg.highwire.dtl.DTLVardef@4b3384org.highwire.dtl.DTLVardef@12330b2_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

The Arabidopsis thaliana pan-NLRome

Disease is both among the most important selection pressures in nature and among the main causes of yield loss in agriculture. In plants, resistance to disease is often conferred by Nucleotide-binding Leucine-rich Repeat (NLR) proteins. These proteins function as intracellular immune receptors that recognize pathogen proteins and their effects on the plant. Consistent with evolutionarily dynamic interactions between plants and pathogens, NLRs are known to be encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define the majority of the Arabidopsis thaliana species-wide "NLRome". From NLR sequence enrichment and long-read sequencing of 65 diverse A. thaliana accessions, we infer that the pan-NLRome saturates with approximately 40 accessions. Despite the high diversity of NLRs, half of the pan-NLRome is present in most accessions. We chart the architectural diversity of NLR proteins, identify novel architectures, and quantify the selective forces that act on specific NLRs, domains, and positions. Our study provides a blueprint for defining the pan-NLRome of plant species.

plant biology↗