Crop domestication and pathogen virulence: Interactions of tomato and Botrytis genetic diversity

2018 ◽  
Author(s):  
Nicole E. Soltis ◽  
Susanna Atwell ◽  
Gongjun Shi ◽  
Rachel Fordyce ◽  
Raoni Gwinner ◽  
...  
Keyword(s):  
Allelic Variation ◽  
Lesion Size ◽  
Resistance Mechanisms ◽  
Plant Domestication ◽  
Crop Domestication ◽  
Pathogen Virulence ◽  
Genome Wide ◽  
In The Wild ◽  
Qualitative Resistance ◽  
Overall Resistance

AbstractHuman selection during crop domestication alters numerous traits, including disease resistance. Studies of qualitative resistance to specialist pathogens typically find decreased resistance in domesticated crops in comparison to their wild relatives. However, less is known about how crop domestication affects quantitative interactions with generalist pathogens. To study how crop domestication impacts plant resistance to generalist pathogens, and correspondingly how this interacts with the pathogen’s genetics, we infected a collection of wild and domesticated tomato accessions with a genetically diverse population of the generalist pathogen Botrytis cinerea. We quantified variation in lesion size of 97 B. cinerea genotypes (isolates) on 6 domesticated Solanum lycopersicum and 6 wild S. pimpinellifolium genotypes. This showed that lesion size was significantly controlled by plant domestication, plant genetic variation, and the pathogen’s genotype. Overall, resistance was slightly elevated in the wild germplasm in comparison to domesticated tomato accessions. Genome-wide association (GWA) mapping in B. cinerea identified a highly polygenic collection of genes. This suggests that breeding against this pathogen would need to utilize a diversity of isolates to capture all possible mechanisms. Critically, we identified a discrete subset of B. cinerea genes where the allelic variation was linked to altered virulence against the wild versus domesticated tomato accessions. This indicates that this generalist pathogen already has the necessary allelic variation in place to handle the introgression of wild resistance mechanisms into the domesticated crop. Future studies are needed to assess how these observations extend to other domesticated crops and other generalist pathogens.

scholarly journals Elevated virulence of an emerging viral genotype as a driver of honeybee loss

2016 ◽  
Vol 283 (1833) ◽  
pp. 20160811 ◽  
Author(s):  
Dino P. McMahon ◽  
Myrsini E. Natsopoulou ◽  
Vincent Doublet ◽  
Matthias Fürst ◽  
Silvio Weging ◽  
...  
Keyword(s):  
Emerging Infectious Diseases ◽  
Genetic Identity ◽  
Accurate Identification ◽  
Deformed Wing Virus ◽  
Species Decline ◽  
Biodiversity Crisis ◽  
Pathogen Virulence ◽  
Population Loss ◽  
Genome Wide

Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo . The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline.

scholarly journals Population genetics of the coral Acropora millepora: Towards a genomic predictor of bleaching

2019 ◽  
Author(s):  
Zachary L. Fuller ◽  
Veronique J.L. Mocellin ◽  
Luke Morris ◽  
Neal Cantin ◽  
Jihanne Shepherd ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Genome Wide Association ◽  
Conservation Strategies ◽  
Genome Sequences ◽  
Acropora Millepora ◽  
Genome Wide ◽  
A Genome ◽  
In The Wild

AbstractAlthough reef-building corals are rapidly declining worldwide, responses to bleaching vary both within and among species. Because these inter-individual differences are partly heritable, they should in principle be predictable from genomic data. Towards that goal, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We then obtained whole genome sequences for 237 phenotyped samples collected at 12 reefs distributed along the Great Barrier Reef, among which we inferred very little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We further used 213 of the samples to conduct a genome-wide association study of visual bleaching score, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for the use of genomics-based approaches in conservation strategies.

scholarly journals ATM orchestrates the DNA-damage response to counter toxic non-homologous end-joining at broken replication forks

2018 ◽  
Author(s):  
Gabriel Balmus ◽  
Domenic Pilger ◽  
Julia Coates ◽  
Mukerrem Demir ◽  
Matylda Sczaniecka-Clift ◽  
...  
Keyword(s):  
Genetic Resistance ◽  
Resistance Mechanisms ◽  
Replication Forks ◽  
End Joining ◽  
Strand Breaks ◽  
Dna Damaging Agents ◽  
Genome Wide ◽  
Topoisomerase Poison ◽  
Recombination Repair ◽  
Non Homologous End Joining

SummaryMutations in the ATM tumor suppressor confer hypersensitivity to DNA-damaging agents. To explore genetic resistance mechanisms, we performed genome-wide CRISPR-Cas9 screens in cells treated with the DNA topoisomerase poison topotecan. Thus, we establish that loss of terminal components of the non-homologous end-joining (NHEJ) machinery or the BRCA1-A complex specifically confers topotecan resistance to ATM-deficient cells. We show that hypersensitivity of ATM-mutant cells to topotecan or the poly-(ADP-ribose) polymerase inhibitor olaparib is due to delayed homologous recombination repair at DNA-replication-fork-associated double-strand breaks (DSBs), resulting in toxic NHEJ-mediated chromosome fusions. Accordingly, restoring legitimate repair in ATM-deficient cells, either by preventing NHEJ DNA ligation or by enhancing DSB-resection by BRCA1-A complex inactivation, markedly suppresses this toxicity. Our work suggests opportunities for patient stratification in ATM-deficient cancers and when using ATM inhibitors in the clinic, and identifies additional therapeutic vulnerabilities that might be exploited when such cancers evolve drug resistance.One Sentence SummaryATM counteracts toxic NHEJ at broken replication forks

scholarly journals Genome-Wide Analysis of Multiple Organellar RNA Editing Factor (MORF) Family in Kiwifruit (Actinidia chinensis) Reveals Its Roles in Chloroplast RNA Editing and Pathogens Stress

Plants ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 146
Author(s):  
Yuhong Xiong ◽  
Jing Fang ◽  
Xiaohan Jiang ◽  
Tengfei Wang ◽  
Kangchen Liu ◽  
...  
Keyword(s):  
Rna Editing ◽  
Chloroplast Development ◽  
Structural Features ◽  
Resistance Mechanisms ◽  
Actinidia Chinensis ◽  
Rna Seq ◽  
Good Taste ◽  
Genome Wide ◽  
Solid Foundation ◽  
Chloroplast Rna

Kiwifruit (Actinidia chinensis) is well known for its high vitamin C content and good taste. Various diseases, especially bacterial canker, are a serious threat to the yield of kiwifruit. Multiple organellar RNA editing factor (MORF) genes are pivotal factors in the RNA editosome that mediates Cytosine-to-Uracil RNA editing, and they are also indispensable for the regulation of chloroplast development, plant growth, and response to stresses. Although the kiwifruit genome has been released, little is known about MORF genes in kiwifruit at the genome-wide level, especially those involved in the response to pathogens stress. In this study, we identified ten MORF genes in the kiwifruit genome. The genomic structures and chromosomal locations analysis indicated that all the MORF genes consisted of three conserved motifs, and they were distributed widely across the seven linkage groups and one contig of the kiwifruit genome. Based on the structural features of MORF proteins and the topology of the phylogenetic tree, the kiwifruit MORF gene family members were classified into six groups (Groups A–F). A synteny analysis indicated that two pairs of MORF genes were tandemly duplicated and five pairs of MORF genes were segmentally duplicated. Moreover, based on analysis of RNA-seq data from five tissues of kiwifruit, we found that both expressions of MORF genes and chloroplast RNA editing exhibited tissue-specific patterns. MORF2 and MORF9 were highly expressed in leaf and shoot, and may be responsible for chloroplast RNA editing, especially the ndhB genes. We also observed different MORF expression and chloroplast RNA editing profiles between resistant and susceptible kiwifruits after pathogen infection, indicating the roles of MORF genes in stress response by modulating the editing extend of mRNA. These results provide a solid foundation for further analyses of the functions and molecular evolution of MORF genes, in particular, for clarifying the resistance mechanisms in kiwifruits and breeding new cultivars with high resistance.

scholarly journals Genome-wide footprints in the carob tree (Ceratonia siliqua) unveil a new domestication pattern of fruit trees in the Mediterranean

2021 ◽  
Author(s):  
Alex Baumel ◽  
Gonzalo Nieto Feliner ◽  
Frederic Medail ◽  
Stefano La Malfa ◽  
Mario Diguardo ◽  
...  
Keyword(s):  
Eastern Mediterranean ◽  
Ex Situ ◽  
Plant Domestication ◽  
Mediterranean Forests ◽  
Migration Routes ◽  
Long Distance ◽  
Genome Wide ◽  
Western Morocco ◽  
Carob Tree ◽  
The Mediterranean

Intense research efforts on phylogeography over the last two decades uncovered major biogeographical trends and renewed our understandings of plant domestication in the Mediterranean. We aim to investigate the evolutionary history and the origin of domestication of the carob tree that has been cultivated for millennia for food and fodder. We used >1000 microsatellite genotypes to identify carob evolutionary units (CEUs) based on genetic diversity structure and geography. We investigated genome-wide diversity and evolutionary patterns of the CEUs with 3557 SNPs generated by restriction-site associated DNA sequencing (RADseq). The 56 populations sampled across the Mediterranean basin, classified as natural, semi-natural or cultivated, were examined. Although, RADseq data are consistent with previous studies identifying a strong West-to-East genetic structure and considerable admixture in some geographic parts, we reconstructed a new phylogeographic scenario with two migration routes occurring from a single refugium likely located in South-Western Morocco. Our results do not favour the regionally bound or single origin of domestication. Indeed, our findings support a cultivation model of locally selected wild genotypes, albeit punctuated by long-distance westward dispersals of domesticated varieties by humans, concomitant with major cultural waves by Romans and Arabs in the regions of dispersal. Ex-situ efforts to preserve carob genetic resources should prioritize accessions from both western and eastern populations, with emphasis on the most differentiated CEUs situated in South-Western Morocco, South Spain and Eastern Mediterranean. Our study underscores the relevance of natural and seminatural habitats of Mediterranean forests and their refugia in the conservation efforts of tree crops.

scholarly journals Allelic variation contributes to bacterial host specificity

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Min Yue ◽  
Xiangan Han ◽  
Leon De Masi ◽  
Chunhong Zhu ◽  
Xun Ma ◽  
...  
Keyword(s):  
Allelic Variation ◽  
Multinomial Logistic Regression ◽  
Gene Gain ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Serovar Typhimurium ◽  
Functional Analyses ◽  
High Degree

Abstract Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.

scholarly journals Genome-wide identification and characterization of mRNAs and lncRNAs involved in cold stress in the wild banana (Musa itinerans)

PLoS ONE ◽  
2018 ◽  
Vol 13 (7) ◽  
pp. e0200002 ◽  
Author(s):  
Weihua Liu ◽  
Chunzhen Cheng ◽  
Yuling Lin ◽  
Xu XuHan ◽  
Zhongxiong Lai
Keyword(s):  
Cold Stress ◽  
Genome Wide ◽  
In The Wild ◽  
Wild Banana ◽  
Musa Itinerans ◽  
Identification And Characterization

scholarly journals Using historical genome‐wide DNA to unravel the confused taxonomy in a songbird lineage that is extinct in the wild

2020 ◽  
Author(s):  
Pratibha Baveja ◽  
Kritika M. Garg ◽  
Balaji Chattopadhyay ◽  
Keren R. Sadanandan ◽  
Dewi M. Prawiradilaga ◽  
...  
Keyword(s):  
Genome Wide ◽  
In The Wild

Resistance mechanism development to the topoisomerase-I inhibitor Hoechst 33342 byLeishmania donovani

Parasitology ◽  
2005 ◽  
Vol 131 (2) ◽  
pp. 197-206 ◽  
Author(s):  
J.-F. MARQUIS ◽  
I. HARDY ◽  
M. OLIVIER
Keyword(s):  
Mammalian Cells ◽  
Topoisomerase I ◽  
Resistance Mechanism ◽  
Resistance Mechanisms ◽  
Drug Accumulation ◽  
Wild Type ◽  
Hoechst 33342 ◽  
In The Wild ◽  
Energy Dependent

The bisbenzimidazole compound Hoechst 33342 (Ho342) has been identified as a specific Topoisomerase-I (Topo-I) inhibitor in mammalian cells. More recently, we have reported the ability of Ho342 to targetL. donovaniTopo-I, leading to parasite growth inhibitionin vitroby mechanisms involving DNA breakage and apoptosis-like phenomenon. As the Ho342 lead molecule (2,5′-Bi-1H-benzimidazole) can be used as a starting structure for derivative compounds more effective againstLeishmania, defining the Ho342 resistance mechanism(s) inLeishmaniarepresents an important strategic tool. In the present study, we selected resistant parasites to Ho342 (LdRHo.300). While we observed an increase of the Topo-I gene expression correlated by a higher Topo-I DNA relaxation activity, the Topo-I genes (LdTOP1AandLdTOP1B) sequencing did not reveal any mutation for the resistant parasites. Moreover, our results on Ho342 cellular accumulation suggested the presence of a potential energy-dependent Ho342 transporter in the wild-type parasite, and that an alteration of this transporter has occurred inLdRHo.300, leading to an altered drug accumulation. Collectively, Ho342 resistance characterization provided results supporting that the resistance developed byLdRHo.300involves complex mechanisms, most likely dominated by an altered drug accumulation, providing new insight in the Ho342 resistance mechanisms.

scholarly journals A genome-wide association study unravels cytokinin as a major component in the root defense responses against Ralstonia solanacearum

2021 ◽  
Author(s):  
Alejandro Alonso-Díaz ◽  
Santosh B Satbhai ◽  
Roger de Pedro-Jové ◽  
Hannah M Berry ◽  
Christian Göschl ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Allelic Variation ◽  
Defense Responses ◽  
Genome Wide Association ◽  
Root Growth Inhibition ◽  
Future Research ◽  
Cytokinin Signaling ◽  
Genome Wide ◽  
A Genome

Abstract Bacterial wilt caused by the soil-borne pathogen Ralstonia solancearum is economically devastating, with no effective methods to fight the disease. This pathogen invades plants through their roots and colonizes their xylem, clogging the vasculature and causing rapid wilting. Key to preventing colonization are the early defense responses triggered in the host’s root upon infection, which remain mostly unknown. Here, we have taken advantage of a high-throughput in vitro infection system to screen natural variability associated to the root growth inhibition phenotype caused by R. solanacearum in Arabidopsis during the first hours of infection. To analyze the genetic determinants of this trait, we have performed a Genome-Wide Association Study, identifying allelic variation at several loci related to cytokinin metabolism, including genes responsible for biosynthesis and degradation of cytokinin. Further, our data clearly demonstrate that cytokinin signaling is induced early during the infection process and cytokinin contributes to immunity against R. solanacearum. This study highlights a new role of cytokinin in root immunity, paving the way for future research that will help understanding the mechanisms underpinning root defenses.

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