Nanopore adaptive sampling to identify the NLR gene family in melon (Cucumis melo L.)

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Feb. 10, 2025

Nanopore adaptive sampling (NAS) offers a promising approach for assessing genetic diversity in targeted genomic regions. Here we designed and validated an experiment to enrich set of resistance genes several melon cultivars as proof concept. Using the same reference guide read acceptance or rejection with NAS, successfully accurately reconstructed 15 regions two newly assembled ssp. melo genomes third agrestis cultivar. We obtained fourfold enrichment regardless tested samples, but some variations according enriched The accuracy our assembly was further confirmed by PCR discussed parameters that could influence NAS generated assemblies. Overall, demonstrated is simple efficient exploring complex regions, such clusters Nucleotide-binding site leucine-rich repeat (NLR) genes. These are characterized containing high number copy variations, presence-absence polymorphisms repetitive elements. features make accurate challenging crucial study due their central role plant immunity disease resistance. This facilitates gene characterization large individuals, required when breeding new suitable agroecological transition.

Language: Английский

---

Autoimmunity In Plants; A Powerful Weapon in Kingdom Plantae to Combat Stresses

International Journal of Agriculture and Biosciences, Journal Year: 2023, Volume and Issue: 12(3), P. 159 - 164

Published: Jan. 1, 2023

Plants possess two immunity systems, such as PAMP-triggered (PTI) and effector-triggered (ETI).PTI is the basic defense possessed by plants that evaded pathogens because of specific effectors which are not recognized plants' basal system.However, have nucleotide-binding leucine-rich repeat proteins (NLR) in their genome recognize pathogenic attack, turn activates NLR proteins, hypersensitive response (HR) activated to ingress pathogenicity.Based on a similar mechanism, lesion mimic mutants (LMMs) been identified intentionally developed induce HR absence pathogens.These LMMs only present single crop but throughout kingdom planate.Researchers produced many treating germplasm with EMS or other sources editing tools, gamma rays, X-rays.Owing simple Mendelian inheritance these LMMs, conventional novel plant breeding techniques can be exploited introduce causative genes keep them safe against biotic abiotic stresses.

Language: Английский

---

Bioinformatics and expression analysis of the NRL gene family in Populus trichocarpa

Genetic Resources and Crop Evolution, Journal Year: 2024, Volume and Issue: unknown

Published: May 11, 2024

Language: Английский

---

Genomic Insights into Cobweb Disease Resistance in Agaricus bisporus: A Comparative Analysis of Resistant and Susceptible Strains

Journal of Fungi, Journal Year: 2025, Volume and Issue: 11(3), P. 200 - 200

Published: March 4, 2025

Agaricus bisporus, a globally cultivated edible fungus, faces significant challenges from fungal diseases like cobweb disease caused by Cladobotryum mycophilum, which severely impacts yield. This study aimed to explore the genetic basis of resistance in A. bisporus comparing genomes susceptible strain (AB7) and resistant (AB58). Whole-genome sequencing AB7 was performed using PacBio Sequel SMRT technology, comparative genomic analyses were conducted alongside AB58 other hosts C. mycophilum. Comparative revealed distinct features AB58, including enriched regulatory elements, specific deletions affecting carbohydrate-active enzymes (CAZymes), unique cytochrome P450 (CYP) profiles. Notably, harbored more genes related fatty acid metabolism NI-siderophore synthetase genes, contributing its enhanced environmental adaptability resistance. Pan-genome analysis highlighted diversity, with strain-specific pathways aflatoxin biosynthesis ether lipid metabolism, suggesting evolutionary adaptations. These findings provide valuable insights into underlying offering foundation for future breeding strategies improve crop resilience.

Language: Английский

---

Comparative genomic analysis reveals the difference of NLR immune receptors between anthracnose-resistant and susceptible sorghum cultivars

Phytopathology Research, Journal Year: 2025, Volume and Issue: 7(1)

Published: April 3, 2025

Abstract Anthracnose, caused by Colletotrichum sublineola , is a prevalent disease that noticeably affects global sorghum production. Nucleotide-binding leucine-rich repeat receptors (NLRs) are crucial for resistance. Here, we report the differences in number, expression profile, and gene structure of NLRs between anthracnose-resistant susceptible cultivars. Through systematic anthracnose assay on 365 accessions, identified American improved cultivar BTx623 as resistant Chinese glutinous Guojiaohong1 (GJH1) cultivar. Then sequenced genome GJH1 239 NLRs, substantially fewer than 302 BTx623. Although collinear highly conserved BTx623, more half non-collinear showed notable mutations or structural variations. During C. infection, exhibited higher number expressed inducible NLR genes did. Moreover, some candidate resistance potentially valuable disease-resistant breeding. Therefore, our data provide genetic resources developing sorghum.

Language: Английский

---

PlantNLRatlas: a comprehensive dataset of full- and partial-length NLR resistance genes across 100 chromosome-level plant genomes

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: April 14, 2023

Plants have evolved two layers of protection against biotic stress: PAMP-triggered immunity (PTI) and effector-triggered (ETI). The primary mechanism ETI involves nucleotide-binding leucine-rich repeat immune receptors (NLRs). Although NLR genes been studied in several plant species, a comprehensive database NLRs across diverse array species is still lacking. Here, we present thorough analysis 100 high-quality genomes (PlantNLRatlas). PlantNLRatlas includes total 68,452 NLRs, which 3,689 are full-length 64,763 partial-length NLRs. majority groups were phyletically clustered. In addition, the domain sequences found to be highly conserved within each group. Our dataset complementary RefPlantNLR, collection experimentally confirmed. should prove helpful for comparative investigations range groups, including understudied taxa. Finally, resource intended help field move past monolithic understanding structure function.

Language: Английский

---

Integrated Molecular and Bioinformatics Approaches for Disease-Related Genes in Plants

Plants, Journal Year: 2023, Volume and Issue: 12(13), P. 2454 - 2454

Published: June 26, 2023

Modern plant pathology relies on bioinformatics approaches to create novel disease diagnostic tools. In recent years, a significant amount of biological data has been generated due rapid developments in genomics and molecular biology techniques. The progress the sequencing agriculturally important crops made it possible develop better understanding plant–pathogen interactions resistance. availability host–pathogen genome offers effective assistance retrieving, annotating, analyzing, identifying functional aspects for characterization at gene levels. Physical mapping facilitates identification isolation several candidate resistance (R) genes from diverse species. A large number genetic variations, such as disease-causing mutations genome, have identified characterized using tools, these desirable were exploited Moreover, crop editing namely CRISPR (clustered regulatory interspaced short palindromic repeats)/Cas9 (CRISPR-associated) system, offer efficient strategies developing durable This review paper describes some concerning databases, techniques used characterize management.

Language: Английский

---

SMRT–AgRenSeq-d in potato (Solanum tuberosum) as a method to identify candidates for the nematode resistance Gpa5

Horticulture Research, Journal Year: 2023, Volume and Issue: 10(11)

Published: Oct. 17, 2023

Potato is the third most important food crop in world. Diverse pathogens threaten sustainable production but can be controlled, many cases, through deployment of disease resistance genes belonging to family nucleotide-binding, leucine-rich-repeat (NLR) genes. To identify effective established varieties, we have successfully SMRT-AgRenSeq tetraploid potatoes and further enhanced methodology by including dRenSeq an approach that term SMR-AgRenSeq-d. The inclusion enables filtering candidates after association analysis establishing a presence/absence matrix across resistant susceptible varieties translated into F1 score. Using SMRT-RenSeq-based sequence representation NLRome from cultivar Innovator, SMRT-AgRenSeq-d analyses reliably identified late blight benchmark Rpi-R1, Rpi-R2-like, Rpi-R3a, Rpi-R3b panel 117 with variable phenotype penetrations. All were score 1, which indicates absolute linkage panel. This method also nine strong for Gpa5 controls potato cyst nematode (PCN) species Globodera pallida (pathotypes Pa2/3). Assuming NLRs are involved controlling types resistances, readily applied diverse crops pathogen systems.

Language: Английский

---

Optimization of immune receptor-related hypersensitive cell death response assay using agrobacterium-mediated transient expression in tobacco plants

Plant Methods, Journal Year: 2022, Volume and Issue: 18(1)

Published: May 2, 2022

The study of the regulatory mechanisms evolutionarily conserved Nucleotide-binding leucine-rich repeat (NLR) resistance (R) proteins in animals and plants is increasing importance due to understanding basic immunity value various crop engineering applications NLR immune receptors. temperature also emerging when applying crops responding global climate change. In particular, studies pathogen effector recognition autoimmune activity NLRs can quickly easily determine their function tobacco using agro-mediated transient assay. However, there are conditions that should not be overlooked these cell death-related assays tobacco.Environmental play an important role response plants. system used this was establish for optimal hypertensive (HR) death analysis by paired RPS4/RRS1 AvrRps4 system. most suitable greenhouse growing fixed at 22 °C. study, RPS4/RRS1-mediated activity, RPS4 TIR domain-dependent death, HR upon perception significantly inhibited under 65% humidity. strongly activated humidity below 10%. Besides, leaf position death. Position #4 from top 4-5 weeks old showed effective death.As whole genome sequencing (WGS) or gene enrichment (RenSeq) continues, different types functions will studied. At time, if we optimize evaluating NLR-mediated it help more accurately identify NLRs. addition, possible contribute development change through engineering.

Language: Английский

---

Recent advances in the improvement of genetic resistance against disease in vegetable crops

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 196(1), P. 32 - 46

Published: May 26, 2024

 Many R genes have been cloned and functionally validated.This has contributed to our understanding of gene mechanisms while providing effective resistance. Pangenomes provide the most accurate representation a species genome by incorporating genetic diversity from range individuals.The number pangenomes for vegetable crops is growing. Developments in resistance enrichment sequencing (RenSeq), such as SMRT RenSeq, facilitated rapid identification causal genes, well characterising species-wide repertoires genes. -omics technologies provided some insights into complex quantitative (QR). Alternative biotechnologies, ncRNA, can be used enhance disease resistance.

Language: Английский

---