Genome-wide identification, characterization, and comparative analysis of NLR resistance genes in Coffea spp DOI Creative Commons
Mariana de Lima Santos, Mário Lúcio Vilela de Resende, Gabriel Sérgio Costa Alves

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Feb. 4, 2022

Abstract The largest family of disease resistance genes in plants are nucleotide-binding site leucine-rich repeat (NLRs). products these responsible for recognizing avirulence proteins (Avr) phytopathogens and triggering specific defense responses. Identifying NLRs plant genomes with standard gene annotation software is challenging due to their multidomain nature, sequence diversity, clustered genomic distribution. We present the results a genome-wide scan comparative analysis NLR loci three coffee species ( Coffea canephora, eugenioides interspecific hybrid arabica ). A total 1311 non-redundant were identified C. , 927 canephora 1079 which 809, 562, 695 complete loci, respectively. NLR-annotator tool used this study showed extremely high sensitivities specificities (over 99%) increased detection putative reference genomes. distributed among all chromosomes organized mostly clusters. genome presented smaller number when compared sum parental There orthologous (orthogroups) shared between coffee, tomato, potato, those that only species, provides clues about functionality evolutionary history orthogroups. Phylogenetic demonstrated possibly lost. members subdivided into two main groups: TIR-NLR (TNL) non-TNL. non-TNLs seem represent repertoire important coffee. These will support functional studies contribute more precise use breeding disease-resistant cultivars.

Language: Английский

Domestication Shapes Recombination Patterns in Tomato DOI Creative Commons
Roven Rommel Fuentes, Dick de Ridder, Aalt D. J. van Dijk

et al.

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 39(1)

Published: Sept. 30, 2021

Meiotic recombination is a biological process of key importance in breeding, to generate genetic diversity and develop novel or agronomically relevant haplotypes. In crop tomato, curtailed as manifested by linkage disequilibrium decay over longer distance reduced compared with wild relatives. Here, we domesticated populations tomato found an overall conserved landscape, local changes effective rate specific genomic regions. We also studied the dynamics hotspots resulting from domestication that loss such associated selective sweeps, most notably pericentromeric heterochromatin. detected footprints structural variants, among them transposable elements, linked hotspot divergence during domestication, likely causing fine-scale alterations patterns drag.

Language: Английский

Citations

29
Prediction of NB‐LRR resistance genes based on full‐length sequence homology DOI Creative Commons

Giuseppe Andolfo,

Juliane C. Dohm, Heinz Himmelbauer

et al.

The Plant Journal, Journal Year: 2022, Volume and Issue: 110(6), P. 1592 - 1602

Published: April 2, 2022

The activation of plant immunity is mediated by resistance (R)-gene receptors, also known as nucleotide-binding leucine-rich repeat (NB-LRR) genes, which in turn trigger the authentic defense response. R-gene identification a crucial goal for both classic and modern breeding strategies disease resistance. conventional method identifies NB-LRR genes using protein motif/domain-based search (PDS) within an automatically predicted gene set respective genome assembly. PDS proved to be imprecise since masking prior automatic annotation unwittingly prevented comprehensive detection. Furthermore, R-genes have diversified species-specific manner, so that cannot universally standardized. Here, we present full-length Homology-based Prediction (HRP) genome's repertoire. Our has substantially addressed complex genomic organization tomato (Solanum lycopersicum) loci, proving more performant than well-established RenSeq approach. HRP efficiency was tested on three differently assembled annotated Beta sp. genomes. Indeed, identified up 45% compared previous approaches. turned out refined strategy allele mining, testified hitherto undiscovered Fom-2 homologs five Cucurbita In summary, our high-performance discovery will propel novel towards development improved cultivars.

Language: Английский

Citations

13
Heterogenous transcriptomes ofNicotiana tabacumBY-2 suspension cell lines adapted to various osmoticum DOI Creative Commons
Tomasz Skrzypczak, Przemysław Wojtaszek, Anna Kasprowicz‐Maluśki

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 28, 2024

Abstract Plants abiotic stress response and adaptation belong to the most important subjects in plants biology. Here, we present Nicotiana tabacum suspension cell lines adapted during long term cultures high concentrations of NaCl, KCl, mannitol sorbitol. Obtained differ osmotic agents final media osmolarities. RNA-seq analysis revealed similarities, as well differences transcriptomes. Presented here BY-2 cells form a good model reveal molecular mechanisms adaptations salt on cellular level.

Language: Английский

Citations

2
Genome-wide characterization of the NLR gene family in tomato (Solanum lycopersicum) and their relatedness to disease resistance DOI Creative Commons

Sehrish Bashir,

Nazia Rehman,

Fabia Fakhar Zaman

et al.

Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13

Published: Dec. 5, 2022

Nucleotide-binding leucine-rich-repeat receptors (NLR), the largest group of genes associated with plant disease resistance (R), have attracted attention due to their crucial role in protecting plants from pathogens. Genome-wide studies NLRs revealed conserved domains annotated tomato genome. The 321 NLR identified genome been randomly mapped 12 chromosomes. Phylogenetic analysis and classification that 211 share full-length categorized into three major clades (CNL, TNL, RNL); remaining 110 partial are classified CN, TN, N according motifs gene structures. cis-regulatory elements exhibit maximum number these involved response biotic abiotic stresses, pathogen recognition, resistance. Analysis phylogenetic relationship between orthologs other species has shown conservation among Solanaceae members variation A. thaliana. Synteny Ka/Ks analyses Solanum lycopersicum tuberosum underscored importance diversification ancestral millions years ago. RNA-seq data qPCR early late blight diseases tomatoes consistent expression patterns, including upregulation infected compared control (with some exceptions), suggesting as key regulators Moreover, levels (Solyc04g007060 [NRC4] Solyc10g008240 [RIB12]) suggested they regulate S. P. infestans. These findings provide important fundamental knowledge for understanding evolution diversity will empower broader characterization pyramiding through speed cloning develop disease-tolerant varieties.

Language: Английский

Citations

9
Genome-Wide Identification, Characterization, and Comparative Analysis of NLR Resistance Genes in Coffea spp. DOI Creative Commons
Mariana de Lima Santos,

M. L. V. Resende,

Gabriel Sérgio Costa Alves

et al.

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: July 7, 2022

The largest family of disease resistance genes in plants are nucleotide-binding site leucine-rich repeat (NLRs). products these responsible for recognizing avirulence proteins (Avr) phytopathogens and triggering specific defense responses. Identifying NLRs plant genomes with standard gene annotation software is challenging due to their multidomain nature, sequence diversity, clustered genomic distribution. We present the results a genome-wide scan comparative analysis NLR loci three coffee species (Coffea canephora, Coffea eugenioides interspecific hybrid arabica). A total 1311 non-redundant were identified C. arabica, 927 1079 eugenioides, which 809, 562, 695 complete loci, respectively. NLR-Annotator tool used this study showed extremely high sensitivities specificities (over 99%) increased detection putative reference genomes. distributed among all chromosomes organized mostly clusters. arabica genome presented smaller number when compared sum parental (C. eugenioides). There orthologous (orthogroups) shared between coffee, tomato, potato, those that only species, provides clues about functionality evolutionary history orthogroups. Phylogenetic demonstrated possibly lost. members subdivided into two main groups: TIR-NLR (TNL) non-TNL. non-TNLs seem represent repertoire important coffee. These will support functional studies contribute more precise use breeding disease-resistant cultivars.

Language: Английский

Citations

8
Genomic structural variation in tomato and its role in plant immunity DOI Creative Commons

Emma M. Jobson,

R. H. Roberts

Molecular Horticulture, Journal Year: 2022, Volume and Issue: 2(1)

Published: March 10, 2022

Abstract It is well known that large genomic variations can greatly impact the phenotype of an organism. Structural Variants (SVs) encompass any variation larger than 30 base pairs, and include changes caused by deletions, inversions, duplications, transversions, other genome modifications. Due to their size complex nature, until recently, it has been difficult truly capture these variations. Recent advances in sequencing technology computational analyses now permit more extensive studies SVs plant genomes. In tomato, have allowed researchers sequence hundreds genomes from tomatoes, tomato relatives. These identified related fruit flavor, as disease response, resistance/susceptibility, ability plants detect pathogens (immunity). this review, we discuss implications for structural with a focus on its role immunity. We also how led new discoveries genomes, current evidence biotic abiotic stress responses, outlook genetic modification advance breeding objectives.

Language: Английский

Citations

7
Large-scale gene gains and losses molded the NLR defense arsenal during the Cucurbita evolution DOI Creative Commons

Giuseppe Andolfo,

Cristina S. Sánchez,

Joaquı́n Cañizares

et al.

Planta, Journal Year: 2021, Volume and Issue: 254(4)

Published: Sept. 24, 2021

Abstract Main conclusion Genome - wide annotation reveals that the gene birth–death process of Cucurbita R family is associated with a species-specific diversification TNL and CNL protein classes. The Cucurbitaceae includes nearly 1000 plant species known universally as cucurbits. genus many economically important worldwide crops vulnerable to more than 200 pathogens. Therefore, identification pathogen-recognition genes utmost importance for this genus. major class plant-resistance (R) encodes nucleotide-binding site leucine-rich repeat (NLR) proteins, divided into three sub-classes namely, TIR-NB-LRR (TNL), CC-NB-LRR (CNL) RPW8-NB-LRR (RNL). Although characterization NLR has been carried out in species, information still linked availability sequenced genomes. In study, we analyzed 40 de novo transcriptomes 5 genome assemblies, which were explored investigate expressed-NLR (eNLR) repertoires using an ad hoc approach. Over 1850 NLR-encoding identified, finely characterized compared 96 well-characterized R-genes. maximum likelihood analyses revealed unusual CNL/TNL strong RNL conservation. Indeed, several gain loss events have shaped family. Finally, provide first validation step , eNLRs by real-time PCR analysis. repertories 12 presented paper will be useful discover novel

Language: Английский

Citations

7
Sequence-defined oligophosphoesters for selective inhibition of the KRAS G12D/RAF1 interaction DOI Creative Commons
Bini Claringbold, Steven Vance, Alexandra R. Paul

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 14, 2024

Rat Sarcoma (RAS) genes are the most frequently mutated in cancer, with KRAS being predominant oncogene, yet they have proved extremely difficult to drug because operate primarily through protein-protein interactions (PPIs) which lack an obvious pocket for small molecules. Sequence-defined synthetic oligomers could combine precision and customisability of molecules size requirements address entire interaction surfaces. We adapted phosphoramidite chemistry oligonucleotide synthesis produce a library nearly one million non-nucleosidic oligophosphoester sequences – phosphoestamers - used fluorescent-activated bead sorting (FABS) process select that inhibit between G12D (the prevalent, undrugged, mutant) RAF, downstream effector RAS whose activation results cell proliferation. Hits were identified using tandem mass spectrometry, validation showed effective inhibition IC 50 values as low 25 nM, excellent selectivity mutant over wild type form. These findings lead new drugs against cancers driven by RAS, provided proof-of-principle phosphoestamer platform PPIs general.

Language: Английский

Citations

0
Patterns of presence–absence variation of NLRs across populations of Solanum chilense are clade‐dependent and mainly shaped by past demographic history DOI Creative Commons
Gustavo A. Silva‐Arias, Edeline Gagnon,

Surya Hembrom

et al.

New Phytologist, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 24, 2024

Summary Understanding the evolution of pathogen resistance genes (nucleotide‐binding site‐leucine‐rich repeats, NLRs) within a species requires comprehensive examination factors that affect gene loss and gain. We present new reference genome Solanum chilense , which leads to an increased number more accurate annotation NLRs. Using target capture approach, we quantify presence–absence variation (PAV) NLR loci across 20 populations from different habitats. build rigorous pipeline validate identification PAV NLRs then show is larger than between populations, suggesting maintenance diversity linked population dynamics. The amount appears not be correlated with presence in clusters genome, but rather past demographic history species, diverging (smaller) at distribution edges. Finally, using redundancy analysis, find limited evidence being environmental gradients. Our results suggest random processes (genetic drift demography) weak positive selection for local adaptation shape single nucleotide polymorphism levels outcrossing plant high diversity.

Language: Английский

Citations

0
The influence of parasite load on transcriptional activity and morphology of a cestode and its ant intermediate host DOI Creative Commons
Tom Sistermans, Juliane Hartke, Marah Stoldt

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Feb. 2, 2023

Abstract Parasites with complex life cycles are known to induce phenotypic changes in their intermediate hosts increase transmission the final host. The magnitude of these could number parasites, which would be beneficial co-infecting parasites. Yet, adverse effects high parasite load (i.e., many parasites a single host) might stress both and (e.g., through an increased immune response). We investigated consequences on transcriptional activity morphology cestode Anomotaenia brevis its host, ant Temnothorax nylanderi . demonstrated that differentially expressed host genes shifted load, functions indicate stronger response fight against oxidative heavily infected hosts. expression other responded infection all-or-nothing manner, as did workers. However, cestodes became smaller when they competed for resources from Their profile further indicated shifts avoidance, starvation resistance vesicle-mediated transport. In summary, our study reveals clear highlights specific processes traits affected by this.

Language: Английский

Citations

1