scholarly journals Non-Target Site Mechanisms of Fungicide Resistance in Crop Pathogens: A Review

2021 ◽  
Vol 9 (3) ◽  
pp. 502
Author(s):  
Mengjun Hu ◽  
Shuning Chen
Keyword(s):  
Fungicide Resistance ◽  
Crop Production ◽  
Large Scale ◽  
Plant Pathogens ◽  
Target Genes ◽  
Target Site ◽  
Fungal Genome ◽  
Nucleotide Polymorphisms ◽  
Human Pathogens ◽  
Target Sites

The rapid emergence of resistance in plant pathogens to the limited number of chemical classes of fungicides challenges sustainability and profitability of crop production worldwide. Understanding mechanisms underlying fungicide resistance facilitates monitoring of resistant populations at large-scale, and can guide and accelerate the development of novel fungicides. A majority of modern fungicides act to disrupt a biochemical function via binding a specific target protein in the pathway. While target-site based mechanisms such as alternation and overexpression of target genes have been commonly found to confer resistance across many fungal species, it is not uncommon to encounter resistant phenotypes without altered or overexpressed target sites. However, such non-target site mechanisms are relatively understudied, due in part to the complexity of the fungal genome network. This type of resistance can oftentimes be transient and noninheritable, further hindering research efforts. In this review, we focused on crop pathogens and summarized reported mechanisms of resistance that are otherwise related to target-sites, including increased activity of efflux pumps, metabolic circumvention, detoxification, standing genetic variations, regulation of stress response pathways, and single nucleotide polymorphisms (SNPs) or mutations. In addition, novel mechanisms of drug resistance recently characterized in human pathogens are reviewed in the context of nontarget-directed resistance.

scholarly journals Global Analysis of the Genetic Variations in miRNA-Targeted Sites and Their Correlations With Agronomic Traits in Rapeseed

2021 ◽  
Vol 12 ◽  
Author(s):  
Pengfei Xu ◽  
Yantao Zhu ◽  
Yanfeng Zhang ◽  
Jianxia Jiang ◽  
Liyong Yang ◽  
...  
Keyword(s):  
Mirna Target ◽  
Target Genes ◽  
Rare Variants ◽  
Agronomic Traits ◽  
Global Analysis ◽  
Variant Calling ◽  
Genetic Variations ◽  
Nucleotide Polymorphisms ◽  
A Genome ◽  
Target Sites

MicroRNAs (miRNAs) and their target genes play vital roles in crops. However, the genetic variations in miRNA-targeted sites that affect miRNA cleavage efficiency and their correlations with agronomic traits in crops remain unexplored. On the basis of a genome-wide DNA re-sequencing of 210 elite rapeseed (Brassica napus) accessions, we identified the single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs) in miRNA-targeted sites complementary to miRNAs. Variant calling revealed 7.14 million SNPs and 2.89 million INDELs throughout the genomes of 210 rapeseed accessions. Furthermore, we detected 330 SNPs and 79 INDELs in 357 miRNA target sites, of which 33.50% were rare variants. We also analyzed the correlation between the genetic variations in miRNA target sites and 12 rapeseed agronomic traits. Eleven SNPs in miRNA target sites were significantly correlated with phenotypes in three consecutive years. More specifically, three correlated SNPs within the miRNA-binding regions of BnSPL9-3, BnSPL13-2, and BnCUC1-2 were in the loci associated with the branch angle, seed weight, and silique number, respectively; expression profiling suggested that the variation at these 3 miRNA target sites significantly affected the expression level of the corresponding target genes. Taken together, the results of this study provide researchers and breeders with a global view of the genetic variations in miRNA-targeted sites in rapeseed and reveal the potential effects of these genetic variations on elite agronomic traits.

scholarly journals De Novo Transcriptomic Resources in the Brain of Vespa velutina for Invasion Control

Insects ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 101
Author(s):  
Miao Wang ◽  
Hanyu Li ◽  
Huoqing Zheng ◽  
Liuwei Zhao ◽  
Xiaofeng Xue ◽  
...  
Keyword(s):  
Large Scale ◽  
Target Genes ◽  
De Novo ◽  
Transcriptome Profiling ◽  
Molecular Study ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Illumina Hiseq ◽  
Vespa Velutina ◽  
Genes Encoding

The invasion of Vespa velutina presents a great threat to the agriculture economy, the ecological environment, and human health. An effective strategy for this hornet control is urgently required, but the limited genome information of Vespa velutina restricts the application of molecular-genomic tools for targeted hornet management. Therefore, we conducted large-scale transcriptome profiling of the hornet brain to obtain functional target genes and molecular markers. Using an Illumina HiSeq platform, more than 41 million clean reads were obtained and de novo assembled into 182,087 meaningful unigenes. A total of 56,400 unigenes were annotated against publicly available protein sequence databases and a set of reliable Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNP) markers were developed. The homologous genes encoding crucial behavior regulation factors, odorant binding proteins (OBPs), and vitellogenin, were also identified from highly expressed transcripts. This study provides abundant molecular targets and markers for invasive hornet control and further promotes the genetic and molecular study of Vespa velutina.

scholarly journals The Influence of 3′UTRs on MicroRNA Function Inferred from Human SNP Data

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Zihua Hu ◽  
Andrew E. Bruno
Keyword(s):  
Gene Expression ◽  
Mirna Target ◽  
Target Genes ◽  
Nucleotide Polymorphisms ◽  
Snp Data ◽  
A Genome ◽  
Local Sequence ◽  
Target Sites ◽  
Sequence Region ◽  
Microrna Function

MicroRNAs (miRNAs) regulate gene expression posttranscriptionally. Although previous efforts have demonstrated the functional importance of target sites on miRNAs, little is known about the influence of the rest of 3′ untranslated regions (3′UTRs) of target genes on microRNA function. We conducted a genome-wide study and found that the entire 3′UTR sequences could also play important roles on miRNA function in addition to miRNA target sites. This was evidenced by the fact that human single nucleotide polymorphisms (SNPs) on both seed target region and the rest of 3′UTRs of miRNA target genes were under significantly stronger negative selection, when compared to non-miRNA target genes. We also discovered that the flanking nucleotides on both sides of miRNA target sites were subject to moderate strong selection. A local sequence region of ~67 nucleotides with symmetric structure is herein defined. Additionally, from gene expression analysis, we found that SNPs and miRNA target sites on target sequences may interactively affect gene expression.

scholarly journals Rare coding variants in 35 genes associate with circulating lipid levels – a multi-ancestry analysis of 170,000 exomes

2020 ◽  
Author(s):  
George Hindy ◽  
Peter Dornbos ◽  
Mark D. Chaffin ◽  
Dajiang J. Liu ◽  
Minxian Wang ◽  
...  
Keyword(s):  
Complex Traits ◽  
Drug Target ◽  
Large Scale ◽  
Target Genes ◽  
Genome Wide Association Study ◽  
Sequence Data ◽  
Blood Lipid ◽  
Nucleotide Polymorphisms ◽  
Lipid Levels ◽  
Blood Lipid Levels

SummaryLarge-scale gene sequencing studies for complex traits have the potential to identify causal genes with therapeutic implications. We performed gene-based association testing of blood lipid levels with rare (minor allele frequency<1%) predicted damaging coding variation using sequence data from >170,000 individuals from multiple ancestries: 97,493 European, 30,025 South Asian, 16,507 African, 16,440 Hispanic/Latino, 10,420 East Asian, and 1,182 Samoan. We identified 35 genes associated with circulating lipid levels. Ten of these: ALB, SRSF2, JAK2, CREB3L3, TMEM136, VARS, NR1H3, PLA2G12A, PPARG and STAB1 have not been implicated for lipid levels using rare coding variation in population-based samples. We prioritize 32 genes identified in array-based genome-wide association study (GWAS) loci based on gene-based associations, of which three: EVI5, SH2B3, and PLIN1, had no prior evidence of rare coding variant associations. Most of the associated genes showed evidence of association in multiple ancestries. Also, we observed an enrichment of gene-based associations for low-density lipoprotein cholesterol drug target genes, and for genes closest to GWAS index single nucleotide polymorphisms (SNP). Our results demonstrate that gene-based associations can be beneficial for drug target development and provide evidence that the gene closest to the array-based GWAS index SNP is often the functional gene for blood lipid levels.

scholarly journals Plant and Fungal Genome Editing to Enhance Plant Disease Resistance Using the CRISPR/Cas9 System

2021 ◽  
Vol 12 ◽  
Author(s):  
Narayan Chandra Paul ◽  
Sung-Won Park ◽  
Haifeng Liu ◽  
Sungyu Choi ◽  
Jihyeon Ma ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Disease Management ◽  
Genome Editing ◽  
Plant Disease Resistance ◽  
Crop Production ◽  
Plant Disease ◽  
Plant Pathogens ◽  
Crop Protection ◽  
Fungal Genome ◽  
Plant Disease Management

Crop production has been substantially reduced by devastating fungal and oomycete pathogens, and these pathogens continue to threaten global food security. Although chemical and cultural controls have been used for crop protection, these involve continuous costs and time and fungicide resistance among plant pathogens has been increasingly reported. The most efficient way to protect crops from plant pathogens is cultivation of disease-resistant cultivars. However, traditional breeding approaches are laborious and time intensive. Recently, the CRISPR/Cas9 system has been utilized to enhance disease resistance among different crops such as rice, cacao, wheat, tomato, and grape. This system allows for precise genome editing of various organisms via RNA-guided DNA endonuclease activity. Beyond genome editing in crops, editing the genomes of fungal and oomycete pathogens can also provide new strategies for plant disease management. This review focuses on the recent studies of plant disease resistance against fungal and oomycete pathogens using the CRISPR/Cas9 system. For long-term plant disease management, the targeting of multiple plant disease resistance mechanisms with CRISPR/Cas9 and insights gained by probing fungal and oomycete genomes with this system will be powerful approaches.

scholarly journals Alternative Polyadenylation Regulates Patient-specific Tumor Growth by Individualizing the MicroRNA Target Site Landscape

2019 ◽  
Author(s):  
Soyeon Kim ◽  
Yulong Bai ◽  
Zhenjiang Fan ◽  
Brenda Diergaarde ◽  
George C. Tseng ◽  
...  
Keyword(s):  
Tumor Growth ◽  
Target Genes ◽  
Alternative Polyadenylation ◽  
Target Site ◽  
Patient Specific ◽  
Microrna Target ◽  
Cancer Etiology ◽  
Cancer Data ◽  
Specific Tumor ◽  
Target Sites

AbstractBackgroundAlternative polyadenylation (APA) shortens or lengthens the 3’-untranslated region (3’-UTR) of hundreds of genes in cancer. While APA genes modify microRNA target sites in the 3’-UTRs to promote tumorigenesis, previous studies have focused on a subset of the modification landscape.MethodFor comprehensive understanding of the function of global APA events, we consider the total target site landscape of microRNAs that are significantly and collectively modified by global APA genes. To identify such microRNAs in spite of complex interactions between microRNAs and the APA genes, we developedProbabilisticInference ofMicroRNATarget Site Modification throughAPA(PRIMATA-APA).ResultsRunning PRIMATA-APA on TCGA breast cancer data, we identified that global APA events concentrate to modify target sites of particular microRNAs (target-site-modified-miRNAor tamoMiRNA). TamoMiRNAs are enriched for microRNAs known to regulate cancer etiology and treatments. Also, their target genes are enriched in cancer-associated pathways, suggesting that APA modifies target sites of tamoMiRNAs to progress tumors. Knockdown of NUDT21, a master 3’-UTR regulator in HeLa cells, confirmed the causal role of tamoMiRNAs for tumor growth.ConclusionsFurther, the expressions of tamoMiRNA target genes, enriched in cancer-associated pathways, vary across tumor samples as a function of patient-specific APA events, suggesting that APA is a novel regulatory axis for interpatient tumor heterogeneity.

scholarly journals A Chromosome-Scale Genome Assembly for the Fusarium oxysporum Strain Fo5176 To Establish a Model Arabidopsis-Fungal Pathosystem

2020 ◽  
Vol 10 (10) ◽  
pp. 3549-3555
Author(s):  
Like Fokkens ◽  
Li Guo ◽  
Susanne Dora ◽  
Bo Wang ◽  
Kai Ye ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Large Scale ◽  
Plant Pathogens ◽  
Single Copy ◽  
Model Systems ◽  
Fungal Genome ◽  
Suitable Model ◽  
Sequencing Data ◽  
High Coverage ◽  
Phylogenomic Analyses

Plant pathogens cause widespread yield losses in agriculture. Understanding the drivers of plant-pathogen interactions requires decoding the molecular dialog leading to either resistance or disease. However, progress in deciphering pathogenicity genes has been severely hampered by suitable model systems and incomplete fungal genome assemblies. Here, we report a significant improvement of the assembly and annotation of the genome of the Fusarium oxysporum (Fo) strain Fo5176. Fo comprises a large number of serious plant pathogens on dozens of plant species with largely unresolved pathogenicity factors. The strain Fo5176 infects Arabidopsis thaliana and, hence, constitutes a highly promising model system. We use high-coverage Pacific Biosciences Sequel long-read and Hi-C sequencing data to assemble the genome into 19 chromosomes and a total genome size of 67.98 Mb. The genome has a N50 of 4 Mb and a 99.1% complete BUSCO score. Phylogenomic analyses based on single-copy orthologs clearly place the Fo5176 strain in the Fo f sp. conglutinans clade as expected. We generated RNAseq data from culture medium and plant infections to train gene predictions and identified ∼18,000 genes including ten effector genes known from other Fo clades. We show that Fo5176 is able to infect cabbage and Brussel sprouts of the Brassica oleracea, expanding the usefulness of the Fo5176 model pathosystem. Finally, we performed large-scale comparative genomics analyses comparing the Fo5176 to 103 additional Fo genomes to define core and accessory genomic regions. In conjunction with the molecular tool sets available for A. thaliana, the Fo5176 genome and annotation provides a crucial step toward the establishment of a highly promising pathosystem.

scholarly journals Introducing the first whole genomes of nationals from the United Arab Emirates

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Habiba S. AlSafar ◽  
Mariam Al-Ali ◽  
Gihan Daw Elbait ◽  
Mustafa H. Al-Maini ◽  
Dymitr Ruta ◽  
...  
Keyword(s):  
United Arab Emirates ◽  
Large Scale ◽  
Target Genes ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Genome Sequences ◽  
Therapeutic Modalities ◽  
Starting Point ◽  
Disease Associations ◽  
Medicine Quality

Abstract Whole Genome Sequencing (WGS) provides an in depth description of genome variation. In the era of large-scale population genome projects, the assembly of ethnic-specific genomes combined with mapping human reference genomes of underrepresented populations has improved the understanding of human diversity and disease associations. In this study, for the first time, whole genome sequences of two nationals of the United Arab Emirates (UAE) at >27X coverage are reported. The two Emirati individuals were predominantly of Central/South Asian ancestry. An in-house customized pipeline using BWA, Picard followed by the GATK tools to map the raw data from whole genome sequences of both individuals was used. A total of 3,994,521 variants (3,350,574 Single Nucleotide Polymorphisms (SNPs) and 643,947 indels) were identified for the first individual, the UAE S001 sample. A similar number of variants, 4,031,580 (3,373,501 SNPs and 658,079 indels), were identified for UAE S002. Variants that are associated with diabetes, hypertension, increased cholesterol levels, and obesity were also identified in these individuals. These Whole Genome Sequences has provided a starting point for constructing a UAE reference panel which will lead to improvements in the delivery of precision medicine, quality of life for affected individuals and a reduction in healthcare costs. The information compiled will likely lead to the identification of target genes that could potentially lead to the development of novel therapeutic modalities.

scholarly journals miR-608 rs4919510 C>G POLYMORPHISM DECREASED THE RISK OF BREAST CANCER IN AN IRANIAN SUBPOPULATION

2016 ◽  
Vol 38 (1) ◽  
pp. 57-59 ◽  
Author(s):  
M Hashemi ◽  
S Sanaei ◽  
M Rezaei ◽  
G Bahari ◽  
S M Hashemi ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Large Scale ◽  
Target Genes ◽  
Clinicopathological Characteristics ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Noncoding Rnas ◽  
Pcr Rflp ◽  
Mirnas Expression ◽  
The Impact

Aim: MicroRNAs (miRNAs) are small noncoding RNAs that function as oncogene or tumor suppressors. The single nucleotide polymorphisms in miRNAs potentially can alter miRNA-binding sites on target genes as well as affecting miRNAs expression. The present study aimed to evaluate the impact of miR-608 rs4919510 C>G variant on breast cancer (BC) risk. Materials and Me thods: This case-control study conducted on 160 women with BC and 192 age-matched healthy women. Genotyping of miR608 rs4919510 was done using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Results: Our findings showed that GC genotype significantly decreased the risk of BC (odds ratio (OR) = 0.49, 95% confidence interval (CI) 0.28–0.88, p = 0.018) compared to CC genotype. Furthermore the G allele decreased the risk of BC (OR = 0.53, 95%CI 0.30–0.92, p = 0.024). No significant association was found between miR-609 genotypes and clinicopathological characteristics of BC patients (p > 0.05). Conclusion: Our findings indicate that miR-608 polymorphism might be associated with decreased risk of BC in an Iranian subpopulation. Further large-scale studies with different ethnicities are needed to verify our findings.

scholarly journals A chromosome-scale genome assembly for the Fusarium oxysporum strain Fo5176 to establish a model Arabidopsis-fungal pathosystem

2020 ◽  
Author(s):  
Like Fokkens ◽  
Li Guo ◽  
Susanne Dora ◽  
Bo Wang ◽  
Kai Ye ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Large Scale ◽  
Plant Pathogens ◽  
Single Copy ◽  
Model Systems ◽  
Fungal Genome ◽  
Suitable Model ◽  
Sequencing Data ◽  
High Coverage ◽  
Phylogenomic Analyses

AbstractPlant pathogens cause widespread yield losses in agriculture. Understanding the drivers of plant-pathogen interactions requires decoding the molecular dialog leading to either resistance or disease. However, progress in deciphering pathogenicity genes has been severely hampered by suitable model systems and incomplete fungal genome assemblies. Here, we report a significant improvement of the assembly and annotation of the genome of the Fusarium oxysporum (Fo) strain Fo5176. Fo comprises a large number of serious plant pathogens on dozens of plant species with largely unresolved pathogenicity factors. The strain Fo5176 infects Arabidopsis thaliana and, hence, constitutes a highly promising model system. We use high-coverage Pacific Biosciences Sequel long-read and Hi-C sequencing data to assemble the genome into 19 chromosomes and a total genome size of 67.98 Mb. The genome has a N50 of 4 Mb and a 99.1% complete BUSCO score. Phylogenomic analyses based on single-copy orthologs clearly place the Fo5176 strain in the Fo f sp. conglutinans clade as expected. We generated RNAseq data from culture medium and plant infections to train gene predictions and identified ∼18,000 genes including ten effector genes known from other Fo clades. We show that Fo5176 is able to infect cabbage and Brussel sprouts of the Brassica oleracea, expanding the usefulness of the Fo5176 model pathosystem. Finally, we performed large-scale comparative genomics analyses comparing the Fo5176 to 103 additional Fo genomes to define core and accessory genomic regions. In conjunction with the molecular tool sets available for A. thaliana, the Fo5176 genome and annotation provides a crucial step towards the establishment of a highly promising pathosystem.

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