scholarly journals Genome Sequencing of Cladobotryum protrusum Provides Insights into the Evolution and Pathogenic Mechanisms of the Cobweb Disease Pathogen on Cultivated Mushroom

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 124 ◽  
Author(s):  
Frederick Sossah ◽  
Zhenghui Liu ◽  
Chentao Yang ◽  
Benjamin Okorley ◽  
Lei Sun ◽  
...  
Keyword(s):  
Single Molecule ◽  
Molecular Mechanisms ◽  
Divergence Time ◽  
Edible Mushrooms ◽  
Economic Losses ◽  
Phylogenomic Analysis ◽  
Evolutionary Divergence ◽  
Cytochrome P450 Enzymes ◽  
Sequencing Platform ◽  
Cobweb Disease

Cladobotryum protrusum is one of the mycoparasites that cause cobweb disease on cultivated edible mushrooms. However, the molecular mechanisms of evolution and pathogenesis of C. protrusum on mushrooms are largely unknown. Here, we report a high-quality genome sequence of C. protrusum using the single-molecule, real-time sequencing platform of PacBio and perform a comparative analysis with closely related fungi in the family Hypocreaceae. The C. protrusum genome, the first complete genome to be sequenced in the genus Cladobotryum, is 39.09 Mb long, with an N50 of 4.97 Mb, encoding 11,003 proteins. The phylogenomic analysis confirmed its inclusion in Hypocreaceae, with its evolutionary divergence time estimated to be ~170.1 million years ago. The genome encodes a large and diverse set of genes involved in secreted peptidases, carbohydrate-active enzymes, cytochrome P450 enzymes, pathogen–host interactions, mycotoxins, and pigments. Moreover, C. protrusum harbors arrays of genes with the potential to produce bioactive secondary metabolites and stress response-related proteins that are significant for adaptation to hostile environments. Knowledge of the genome will foster a better understanding of the biology of C. protrusum and mycoparasitism in general, as well as help with the development of effective disease control strategies to minimize economic losses from cobweb disease in cultivated edible mushrooms.

scholarly journals Genome Sequencing of Paecilomyces Penicillatus Provides Insights into Its Phylogenetic Placement and Mycoparasitism Mechanisms on Morel Mushrooms

Pathogens ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 834
Author(s):  
Xinxin Wang ◽  
Jingyu Peng ◽  
Lei Sun ◽  
Gregory Bonito ◽  
Yuxiu Guo ◽  
...  
Keyword(s):  
Single Molecule ◽  
Molecular Mechanisms ◽  
Draft Genome ◽  
Gene Clusters ◽  
Single Copy ◽  
Dual Culture ◽  
Edible Fungi ◽  
Fungal Cell ◽  
Sequencing Platform ◽  
Phylogenetic Placement

Morels (Morchella spp.) are popular edible fungi with significant economic and scientific value. However, white mold disease, caused by Paecilomyces penicillatus, can reduce morel yield by up to 80% in the main cultivation area in China. Paecilomyces is a polyphyletic genus and the exact phylogenetic placement of P. penicillatus is currently still unclear. Here, we obtained the first high-quality genome sequence of P. penicillatus generated through the single-molecule real-time (SMRT) sequencing platform. The assembled draft genome of P. penicillatus was 40.2 Mb, had an N50 value of 2.6 Mb and encoded 9454 genes. Phylogenetic analysis of single-copy orthologous genes revealed that P. penicillatus is in Hypocreales and closely related to Hypocreaceae, which includes several genera exhibiting a mycoparasitic lifestyle. CAZymes analysis demonstrated that P. penicillatus encodes a large number of fungal cell wall degradation enzymes. We identified many gene clusters involved in the production of secondary metabolites known to exhibit antifungal, antibacterial, or insecticidal activities. We further demonstrated through dual culture assays that P. penicillatus secretes certain soluble compounds that are inhibitory to the mycelial growth of Morchella sextelata. This study provides insights into the correct phylogenetic placement of P. penicillatus and the molecular mechanisms that underlie P. penicillatus pathogenesis.

scholarly journals Integrated analysis of full-length transcriptome and secondary metabolism reveals novel regulation in Paulownia fortunei infected with phytoplasma

2019 ◽  
Author(s):  
Xiaogai Zhao ◽  
Xiaoqiao Zhai ◽  
Zhe Wang ◽  
Yabing Cao ◽  
Zhenli Zhao ◽  
...  
Keyword(s):  
Single Molecule ◽  
High Performance ◽  
Molecular Mechanisms ◽  
Economic Losses ◽  
Integrated Analysis ◽  
Liquid Chromatography Mass Spectrometry ◽  
Smrt Sequencing ◽  
Gene Annotations ◽  
Annotation Information ◽  
Paulownia Fortunei

Abstract Background: Paulownia witches' broom (PaWB) is a devastating disease caused by phytoplasma, which can lead to considerable economic losses. Previous studies have shown that 60 mg•L-1 methyl methane sulfonate (MMS) can restore infected Paulownia seedlings to healthy one. To improve the understanding of PaWB, we used single molecule real time (SMRT) sequencing, which can provide long sequences that can be effectively used to identify gene alternative splicing, obtain novel genes, improve gene annotations and comprehensive analysis of the metabolome. Results: Here, the first integrated analysis SMRT sequencing, the Illumina platforms, and high-performance liquid chromatography-mass spectrometry (HPLC-MS) to analyze changes in transcripts and metabolites in Paulownia fortunei. A total of 140,528 non redundant transcripts were identified, which supported 6,209 of novel gene loci that can enrich 70,223 annotation information of Paulownia fortunei （P. fortunei）genome. A total of 5,606 transcripts, 46 lncRNAs, 83 fusion transcripts, 597 transcription factors, and 57 metabolites were related indirectly or directly to PaWB. Subsequent analysis of the transcriptome and metabolome found trans-cinnamate 4-monooxygenase, caffeoyl-CoA-O methyltransferase, ferulic acid and peroxidase were up-regulated in Paulownia fortunei infected with phytoplasma. They were involved in flavonoid, phenylpropane and salicylic acid metabolism, which might be related to Paulownia-phytoplasma interaction. Conclusions: Our results will enrich the understanding of molecular mechanisms of PaWB. This study provides a foundation for better understanding the changes in gene expression, metabolites, and morphology of Paulownia fortunei with PaWB.

scholarly journals Identification of Antimicrobial Peptide Genes in Black Rockfish Sebastes schlegelii and Their Responsive Mechanisms to Edwardsiella tarda Infection

Biology ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1015
Author(s):  
Min Zhang ◽  
Min Cao ◽  
Yunji Xiu ◽  
Qiang Fu ◽  
Ning Yang ◽  
...  
Keyword(s):  
Antimicrobial Peptide ◽  
Single Molecule ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Amino Acid Sequences ◽  
Edwardsiella Tarda ◽  
Economic Losses ◽  
Dominant Type ◽  
Black Rockfish ◽  
Sebastes Schlegelii

The black rockfish, Sebastes schlegelii, is a typical viviparous teleost, which belongs to the family Scorpaenidae. Due to its high economic and ecological values, S. schlegelii has been widely cultured in East Asian countries. With the enlargement of cultivation scale, bacterial and viral diseases have become the main threats to the farming industry of S. schlegelii, which have resulted in significant economic losses. In this study, Illumina shotgun sequencing, single-molecule real-time (SMRT) sequencing, 10x genomics and high-throughput chromosome conformation capture (Hi-C) technologies were collectively applied to assemble the genome of S. schlegelii. Then, we identified the antimicrobial peptide genes (AMPs) in the S. schlegelii genome. In total, 214 AMPs were identified in the S. schlegelii genome, which can be divided into 33 classes according to the annotation and cataloging of the Antimicrobial Peptides Database (APD3). Among these AMPs, thrombin-derived C-terminal peptide (TCP) was the dominant type, followed by RegIIIgamma and chemokine. The amino acid sequences of the TCP, cgUbiquitin, RegIIIalpha, RegIIIgamma, chemokine shared 32.55%, 42.63%, 29.87%, 28.09%, and 32.15% similarities among the same type in S. schlegelii. Meanwhile, the expression patterns of these AMPs in nine healthy tissues and at different infection time points in intestine were investigated. The results showed that the numbers and types of AMPs that responded to Edwardsiella tarda infection gradually increased as the infection progressed. In addition, we analyzed the phylogenetic relationships of hepcidins in teleost. The identification of AMPs based on the whole genome could provide a comprehensive database of potential AMPs, and benefit for the understanding of the molecular mechanisms of immune responses to E. tarda infection in S. schlegelii. This would further offer insights into an accurate and effective design and development of AMP for aquaculture therapy in the future.

scholarly journals The Effect of Gut Bacteria on the Physiology of Red Palm Weevil, Rhynchophorus ferrugineus Olivier and Their Potential for the Control of This Pest

Insects ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 594
Author(s):  
Qian-Xia Liu ◽  
Zhi-Ping Su ◽  
Hui-Hui Liu ◽  
Sheng-Ping Lu ◽  
Bing Ma ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Management Strategies ◽  
Gut Bacteria ◽  
Economic Losses ◽  
Rhynchophorus Ferrugineus ◽  
Intestinal Immunity ◽  
Red Palm Weevil ◽  
Nutrient Metabolism ◽  
Palm Weevil

Red Palm Weevil (RPW), Rhynchophorus ferrugineus Olivier, is a notorious pest, which infests palm trees and has caused great economic losses worldwide. At present, insecticide applications are still the main way to control this pest. However, pesticide resistance has been detected in the field populations of RPW. Thus, future management strategies based on the novel association biological control need be developed. Recent studies have shown that the intestinal tract of RPW is often colonized by multiple microbial species as mammals and model insects, and gut bacteria have been found to promote the growth, development and immune activity of RPW larvae by modulating nutrient metabolism. Furthermore, two peptidoglycan recognition proteins (PGRPs), PGRP-LB and PGRP-S1, can act as the negative regulators to modulate the intestinal immunity to maintain the homeostasis of gut bacteria in RPW larvae. Here, we summarized the current knowledge on the gut bacterial composition of RPW and their impact on the physiological traits of RPW larvae. In contrast with metazoans, it is much easier to make genetic engineered microbes to produce some active molecules against pests. From this perspective, because of the profound effects of gut bacteria on host phenotypes, it is promising to dissect the molecular mechanisms behind their effect on host physiology and facilitate the development of microbial resource-based management methods for pest control.

scholarly journals RNAseq Reveals Differential Gene Expression Contributing to Phytophthora nicotianae Adaptation to Partial Resistance in Tobacco

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 656
Author(s):  
Jing Jin ◽  
Rui Shi ◽  
Ramsey Steven Lewis ◽  
Howard David Shew
Keyword(s):  
Partial Resistance ◽  
Molecular Mechanisms ◽  
Biological Activities ◽  
Effective Means ◽  
Phytophthora Nicotianae ◽  
Economic Losses ◽  
Black Shank ◽  
Differential Gene ◽  
Go Terms

Phytophthora nicotianae is a devastating oomycete plant pathogen with a wide host range. On tobacco, it causes black shank, a disease that can result in severe economic losses. Deployment of host resistance is one of the most effective means of controlling tobacco black shank, but adaptation to complete and partial resistance by P. nicotianae can limit the long-term effectiveness of the resistance. The molecular basis of adaptation to partial resistance is largely unknown. RNAseq was performed on two isolates of P. nicotianae (adapted to either the susceptible tobacco genotype Hicks or the partially resistant genotype K 326 Wz/Wz) to identify differentially expressed genes (DEGs) during their pathogenic interactions with K 326 Wz/Wz and Hicks. Approximately 69% of the up-regulated DEGs were associated with pathogenicity in the K 326 Wz/Wz-adapted isolate when sampled following infection of its adapted host K 326 Wz/Wz. Thirty-one percent of the up-regulated DEGs were associated with pathogenicity in the Hicks-adapted isolate on K 326 Wz/Wz. A broad spectrum of over-represented gene ontology (GO) terms were assigned to down-regulated genes in the Hicks-adapted isolate. In the host, a series of GO terms involved in nuclear biosynthesis processes were assigned to the down-regulated genes in K 326 Wz/Wz inoculated with K 326 Wz/Wz-adapted isolate. This study enhances our understanding of the molecular mechanisms of P. nicotianae adaptation to partial resistance in tobacco by elucidating how the pathogen recruits pathogenicity-associated genes that impact host biological activities.

scholarly journals Analysis of the Role of Bradysiaimpatiens (Diptera: Sciaridae) as a Vector Transmitting Peanut Stunt Virus on the Model Plant Nicotiana benthamiana

Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1546
Author(s):  
Marta Budziszewska ◽  
Patryk Frąckowiak ◽  
Aleksandra Obrępalska-Stęplowska
Keyword(s):  
Nicotiana Benthamiana ◽  
Molecular Mechanisms ◽  
Virus Transmission ◽  
Pathogenic Fungi ◽  
Economic Losses ◽  
Fungus Gnats ◽  
Droplet Pcr ◽  
Viral Coat ◽  
Peanut Stunt Virus

Bradysia species, commonly known as fungus gnats, are ubiquitous in greenhouses, nurseries of horticultural plants, and commercial mushroom houses, causing significant economic losses. Moreover, the insects from the Bradysia genus have a well-documented role in plant pathogenic fungi transmission. Here, a study on the potential of Bradysia impatiens to acquire and transmit the peanut stunt virus (PSV) from plant to plant was undertaken. Four-day-old larvae of B. impatiens were exposed to PSV-P strain by feeding on virus-infected leaves of Nicotiana benthamiana and then transferred to healthy plants in laboratory conditions. Using the reverse transcription-polymerase chain reaction (RT-PCR), real-time PCR (RT-qPCR), and digital droplet PCR (RT-ddPCR), the PSV RNAs in the larva, pupa, and imago of B. impatiens were detected and quantified. The presence of PSV genomic RNA strands as well as viral coat protein in N. benthamiana, on which the viruliferous larvae were feeding, was also confirmed at the molecular level, even though the characteristic symptoms of PSV infection were not observed. The results have shown that larvae of B. impatiens could acquire the virus and transmit it to healthy plants. Moreover, it has been proven that PSV might persist in the insect body transstadially. Although the molecular mechanisms of virion acquisition and retention during insect development need further studies, this is the first report on B. impatiens playing a potential role in plant virus transmission.

scholarly journals Hopping and Flipping of RNA Polymerase on DNA during Recycling for Reinitiation after Intrinsic Termination in Bacterial Transcription

2021 ◽  
Vol 22 (5) ◽  
pp. 2398
Author(s):  
Wooyoung Kang ◽  
Seungha Hwang ◽  
Jin Young Kang ◽  
Changwon Kang ◽  
Sungchul Hohng
Keyword(s):  
Single Molecule ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Facilitated Diffusion ◽  
One Dimensional ◽  
Bacterial Transcription ◽  
Fluorescence Measurements ◽  
Dimensional Diffusion ◽  
Single Molecule Studies ◽  
Hopping Diffusion

Two different molecular mechanisms, sliding and hopping, are employed by DNA-binding proteins for their one-dimensional facilitated diffusion on nonspecific DNA regions until reaching their specific target sequences. While it has been controversial whether RNA polymerases (RNAPs) use one-dimensional diffusion in targeting their promoters for transcription initiation, two recent single-molecule studies discovered that post-terminational RNAPs use one-dimensional diffusion for their reinitiation on the same DNA molecules. Escherichia coli RNAP, after synthesizing and releasing product RNA at intrinsic termination, mostly remains bound on DNA and diffuses in both forward and backward directions for recycling, which facilitates reinitiation on nearby promoters. However, it has remained unsolved which mechanism of one-dimensional diffusion is employed by recycling RNAP between termination and reinitiation. Single-molecule fluorescence measurements in this study reveal that post-terminational RNAPs undergo hopping diffusion during recycling on DNA, as their one-dimensional diffusion coefficients increase with rising salt concentrations. We additionally find that reinitiation can occur on promoters positioned in sense and antisense orientations with comparable efficiencies, so reinitiation efficiency depends primarily on distance rather than direction of recycling diffusion. This additional finding confirms that orientation change or flipping of RNAP with respect to DNA efficiently occurs as expected from hopping diffusion.

scholarly journals Infrared nanospectroscopy reveals the molecular interaction fingerprint of an aggregation inhibitor with single Aβ42 oligomers

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Francesco Simone Ruggeri ◽  
Johnny Habchi ◽  
Sean Chia ◽  
Robert I. Horne ◽  
Michele Vendruscolo ◽  
...  
Keyword(s):  
Small Molecules ◽  
Single Molecule ◽  
Protein Misfolding ◽  
Molecular Mechanisms ◽  
Chemical Sensitivity ◽  
Incomplete Knowledge ◽  
Parkinson’S Diseases ◽  
Aggregation Inhibitor ◽  
Misfolding Diseases

AbstractSignificant efforts have been devoted in the last twenty years to developing compounds that can interfere with the aggregation pathways of proteins related to misfolding disorders, including Alzheimer’s and Parkinson’s diseases. However, no disease-modifying drug has become available for clinical use to date for these conditions. One of the main reasons for this failure is the incomplete knowledge of the molecular mechanisms underlying the process by which small molecules interact with protein aggregates and interfere with their aggregation pathways. Here, we leverage the single molecule morphological and chemical sensitivity of infrared nanospectroscopy to provide the first direct measurement of the structure and interaction between single Aβ42 oligomeric and fibrillar species and an aggregation inhibitor, bexarotene, which is able to prevent Aβ42 aggregation in vitro and reverses its neurotoxicity in cell and animal models of Alzheimer’s disease. Our results demonstrate that the carboxyl group of this compound interacts with Aβ42 aggregates through a single hydrogen bond. These results establish infrared nanospectroscopy as a powerful tool in structure-based drug discovery for protein misfolding diseases.

scholarly journals Comparative Transcriptomic Analysis of Riptortus pedestris (Hemiptera: Alydidae) to Characterize Wing Formation across All Developmental Stages

Insects ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 226
Author(s):  
Siying Fu ◽  
Yujie Duan ◽  
Siqi Wang ◽  
Yipeng Ren ◽  
Wenjun Bu
Keyword(s):  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Expression Profiles ◽  
Economic Losses ◽  
Future Research ◽  
Economic Damage ◽  
Wing Formation ◽  
Riptortus Pedestris

Riptortus pedestris (Hemiptera: Alydidae) is a major agricultural pest in East Asia that causes considerable economic losses to the soybean crop each year. However, the molecular mechanisms governing the growth and development of R. pedestris have not been fully elucidated. In this study, the Illumina HiSeq6000 platform was employed to perform de novo transcriptome assembly and determine the gene expression profiles of this species across all developmental stages, including eggs, first-, second-, third-, fourth-, and fifth-instar nymphs, and adults. In this study, a total of 60,058 unigenes were assembled from numerous raw reads, exhibiting an N50 length of 2126 bp and an average length of 1199 bp, and the unigenes were annotated and classified with various databases, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Gene Ontology (GO). Furthermore, various numbers of differentially expressed genes (DEGs) were calculated through pairwise comparisons of all life stages, and some of these DEGs were associated with immunity, metabolism, and development by GO and KEGG enrichment. In addition, 35,158 simple sequence repeats (SSRs) and 715,604 potential single nucleotide polymorphisms (SNPs) were identified from the seven transcriptome libraries of R. pedestris. Finally, we identified and summarized ten wing formation-related signaling pathways, and the molecular properties and expression levels of five wing development-related genes were analyzed using quantitative real-time PCR for all developmental stages of R. pedestris. Taken together, the results of this study may establish a foundation for future research investigating developmental processes and wing formation in hemimetabolous insects and may provide valuable data for pest control efforts attempting to reduce the economic damage caused by this pest.

scholarly journals Molecular mechanisms of growth depression in broiler chickens (Gallus Gallus domesticus) mediated by immune stress: a hepatic proteome study

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Aijuan Zheng ◽  
Anrong Zhang ◽  
Zhimin Chen ◽  
Shoaib Ahmed Pirzado ◽  
Wenhuan Chang ◽  
...  
Keyword(s):  
Broiler Chickens ◽  
Molecular Mechanisms ◽  
Gallus Gallus ◽  
Gallus Domesticus ◽  
Economic Losses ◽  
Poultry Production ◽  
Gallus Gallus Domesticus ◽  
Growth Depression ◽  
Stress Group ◽  
Immune Stress

Abstract Background Immunological stress decreases feed intake, suppresses growth and induces economic losses. However, the underlying molecular mechanism remains unclear. Label-free liquid chromatography and mass spectrometry (LC-MS) proteomics techniques were employed to investigate effects of immune stress on the hepatic proteome changes of Arbor Acres broilers (Gallus Gallus domesticus) challenged with Escherichia coli lipopolysaccharide (LPS). Results Proteomic analysis indicated that 111 proteins were differentially expressed in the liver of broiler chickens from the immune stress group. Of these, 28 proteins were down-regulated, and 83 proteins were up-regulated in the immune stress group. Enrichment analysis showed that immune stress upregulated the expression of hepatic proteins involved in defense function, amino acid catabolism, ion transport, wound healing, and hormone secretion. Furthermore, immune stress increased valine, leucine and isoleucine degradation pathways. Conclusion The data suggests that growth depression of broiler chickens induced by immune stress is triggered by hepatic proteome alterations, and provides a new insight into the mechanism by which immune challenge impairs poultry production.

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