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

Substâncias naturais de plantas: relação com a defesa em infecções virais e aplicação na agricultura sustentável DOI Open Access
L. M. L. Duarte, M. A. V. Alexandre, Alexandre Levi Rodrigues Chaves

et al.

Revisão Anual de Patologia de Plantas, Journal Year: 2023, Volume and Issue: unknown, P. 79 - 105

Published: March 5, 2023

During evolution, plants developed a complex set of morphological, biochemical and molecular, preformed inducible defense mechanisms that allowed them to live in stressful conditions. In addition, the ability synthesize organic compounds (primary secondary metabolites plant hormones) has ensure success colonizing challenging environments. With practice intensive monoculture, aiming feed an increasingly numerous population, incidence viruses increased almost same proportion. Thus, aggressive control practices environment human health such as use pesticides began be recommended uncontrolled way, which encouraged search for more sustainable agriculture. Therefore, understanding used by viroses interfere with metabolism compatible incompatible interactions, well those overcome or not infection, is fundamental can help clarify important points plant-virus enabling recommendation ecologically friendly crop management. this review, molecular aspects metabolic changes induced viruses, natural products application these agriculture will addressed.

Language: Английский

Citations

1
Using a handful of transcriptomes to detect sex-linked markers in a lizard with homomorphic sex chromosomes DOI Creative Commons
Paul A. Saunders, Carles Ferre-Ortega, Peta Hill

et al.

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

Published: March 15, 2023

Abstract To understand the biology of a species it is often crucial to be able differentiate males and females. Many lack distinguishable sexually dimorphic traits, but in those that possess sex chromosomes, molecular sexing offers good alternative. Designing assays typically achieved through comparison male female genomic sequences, from reduced-representation sequencing. However, many non-model chromosomes are poorly differentiated, identifying sex-limited sequences developing PCR-based challenging without additional resources. Here we highlight simple procedure for detection sex-linked markers based on transcriptomes circumvents limitations other approaches. We apply spotted snow skink Carinascincus ocellatus , lizard with homomorphic XY also experiences environmentally-induced reversal. With 3 females alone, identify thousands putative Y-linked sequences. confirm linkage alignment assembled transcripts distantly related genome, readily design PCR primers C. species. In addition providing an important tool these species, this approach facilitated valuable comparisons determining systems large taxonomic scale.

Language: Английский

Citations

1
Pollen sequencing reveals barriers and aberrant patterns of recombination in interspecific tomato hybrids DOI Open Access
Roven Rommel Fuentes, Ronald Nieuwenhuis, Jihed Chouaref

et al.

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

Published: July 3, 2022

Abstract Tomato is the most consumed vegetable in world. Increasing its natural resistance and resilience key for ensuring food security within a changing climate. Plant breeders improve those traits by generating crosses of cultivated tomatoes with their wild relatives. Specific allele introgression relying on meiotic recombination, hampered structural divergence between parental genomes. However, previous studies interspecific tomato hybridization focused single cross or lacked resolution due to prohibitive sequencing costs large segregating populations. Here, we used pooled-pollen reveal unprecedented details recombination patterns five hybrids. We detected hybrid-specific coldspots that underscore influence shaping landscape. Crossover regions show strong association specific TE superfamilies exhibiting differentially accessible chromatin somatic cells. also found gene complexes associated metabolic processes, stress domestication syndrome traits, revealing undesired consequences suppression phenotypes. Finally, demonstrate using resequencing data domesticated populations, can screen alternative genomes overcome barriers. Overall, our results will allow better informed decisions disease-resistant climate-resilient tomato.

Language: Английский

Citations

2
Understanding tobamovirus-plant interactions: implications for breeding resistance to tomato brown rugose fruit virus DOI Open Access
Mario Sánchez-Sánchez, Jimena Carrillo-Tripp, Emmanuel Aispuro‐Hernández

et al.

Journal of Plant Pathology, Journal Year: 2022, Volume and Issue: 105(1), P. 83 - 94

Published: Dec. 7, 2022

Language: Английский

Citations

2
Genomic Tools for Improving Tomato to Biotic Stress Resistance DOI
Ciro Gianmaria Amoroso, Dilip R. Panthee,

Giuseppe Andolfo

et al.

Springer eBooks, Journal Year: 2022, Volume and Issue: unknown, P. 1 - 35

Published: Jan. 1, 2022

Language: Английский

Citations

1
Isolated loss of the AUTS2 long isoform, brain-wide or targeted toCalbindin-lineage cells, generates a specific suite of brain, behavioral and molecular pathologies DOI Open Access

Yunshu Song,

Christopher H. Seward, Chih‐Ying Chen

et al.

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

Published: May 4, 2023

Abstract Rearrangements within the AUTS2 region are associated with a rare syndromic disorder intellectual disability, developmental delay and behavioral abnormalities as core features. In addition, smaller regional variants linked to wide range of neuropsychiatric disorders, underscoring gene’s essential role in brain development. Like many neurodevelopmental genes, is large complex, generating distinct long (AUTS2-l) short (AUTS2-s) protein isoforms from alternative promoters. Although evidence suggests unique isoform functions, contributions each specific AUTS2- phenotypes have not been clearly resolved. Furthermore, Auts2 widely expressed across developing brain, but cell populations most central disease presentation determined. this study, we focused on roles AUTS2-l development, behavior, postnatal gene expression, showing that brain-wide ablation leads subsets recessive pathologies C-terminal mutations disrupt both isoforms. We identify downstream genes could explain including hundreds putative direct l target genes. contrast which lead dominant hypoactivity, loss-of-function hyperactivity, phenotype exhibited by human patients. Finally, show Calbindin 1 -expressing lineages sufficient yield learning/memory deficits hyperactivity abnormal dentate gyrus granule maturation, other phenotypic effects. These data provide new clues vivo functions novel information relevant genotype-phenotype correlations region.

Language: Английский

Citations

0
Meiotic recombination in natural and experimental plant populations DOI Open Access
Roven Rommel Fuentes

Published: Aug. 28, 2023

Language: Английский

Citations

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

Surya Hembrom

et al.

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

Published: Oct. 17, 2023

Abstract Understanding the evolution of pathogen resistance genes (nucleotide-binding site-leucine-rich repeats, also known as NLRs) within a species requires comprehensive examination factors that affect gene loss and gain. We present new reference genome Solanum chilense , leads to an increased number more accurate annotation NLRs. Next, 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. Furthermore, amount not correlated with presence in clusters genome, but rather past demographic history species, NLRs diverging at distribution edges smaller sizes. Finally, redundancy analysis, find limited evidence being environmental gradients. Our results contradict classic assumptions important selective role for suggest driven by random processes (and weak selection) outcrossing plant high nucleotide diversity.

Language: Английский

Citations

0
Warmer temperatures result in maladaptive learning of sexual preferences DOI Creative Commons
Marie–Jeanne Holveck, Doriane Muller, Bertanne Visser

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2020, Volume and Issue: unknown

Published: Nov. 6, 2020

Abstract The impact of learning ability and sexual selection on the climate biodiversity crisis are currently unclear. Using African butterfly Bicyclus anynana , which shows strong phenotypic plasticity (i.e., polyphenism) in response to temperature, we tested whether affects mate preferences under warming. We first modelled warming scenarios then showed experimentally that as temperature becomes an unreliable cue onset dry season, adult butterflies displayed wet season rather than form. Experienced females were exposed different male seasonal phenotypes during maturation changed preferences. Female fertilization success was reversed for naive compared experienced females, likely reducing female fitness following Our results emphasize importance selection, learning, their consequences understanding (mal)adaptation natural populations

Language: Английский

Citations

0
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

Citations

0