scholarly journals Functional Analysis of a Novel ABL (Abnormal Browning Related to Light) Gene in Mycelial Brown Film Formation of Lentinula edodes

2020 ◽  
Vol 6 (4) ◽  
pp. 272
Author(s):  
Chang Pyo Hong ◽  
Suyun Moon ◽  
Seung-il Yoo ◽  
Jong-Hyun Noh ◽  
Han-Gyu Ko ◽  
...  
Keyword(s):  
Lentinula Edodes ◽  
Developmental Process ◽  
Film Formation ◽  
Edible Mushroom ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Mushroom Species ◽  
Commercial Cultivation ◽  
Mushroom Yield

Lentinula edodes is a globally important edible mushroom species that is appreciated for its medicinal properties as well as its nutritional value. During commercial cultivation, a mycelial brown film forms on the surface of the sawdust growth medium at the late vegetative stage. Mycelial film formation is a critical developmental process that contributes to the quantity and quality of the mushroom yield. However, little is known regarding the genetic underpinnings of brown film formation on the surface of mycelial tissue. A novel causal gene associated with the formation of the mycelial brown film, named ABL (Abnormal browning related to light), was identified in this study. The comparative genetic analysis by dihybrid crosses between normal and abnormal browning film cultivars demonstrated that a single dominant allele was responsible for the abnormal mycelium browning phenotype. Whole-genome sequencing analysis of hybrid isolates revealed five missense single-nucleotide polymorphisms (SNPs) in the ABL locus of individuals forming abnormal partial brown films. Additional whole-genome resequencing of a further 16 cultivars showed that three of the five missense SNPs were strongly associated with the abnormal browning phenotype. Overexpression of the dominant abl-D allele in a wild-type background conferred the abnormal mycelial browning phenotype upon transformants, with slender hyphae observed as a general defective mycelial growth phenotype. Our methodology will aid the future discovery of candidate genes associated with favorable traits in edible mushrooms. The discovery of a novel gene, ABL, associated with mycelial film formation will facilitate marker-associated breeding in L. edodes.

scholarly journals A Retrospective Whole-Genome Sequencing Analysis of Carbapenem and Colistin-Resistant Klebsiella pneumoniae Nosocomial Strains Isolated during an MDR Surveillance Program

Antibiotics ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 246 ◽  
Author(s):  
Bernardina Gentile ◽  
Antonella Grottola ◽  
Gabriella Orlando ◽  
Giulia Fregni Serpini ◽  
Claudia Venturelli ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Capsular Polysaccharide ◽  
University Hospital ◽  
Surveillance Program ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Colistin Resistance

Multidrug-resistant Klebsiella pneumoniae (MDR Kp), in particular carbapenem-resistant Kp (CR-Kp), has become endemic in Italy, where alarming data have been reported on the spread of colistin-resistant CR-Kp (CRCR-Kp). During the period 2013–2014, 27 CRCR-Kp nosocomial strains were isolated within the Modena University Hospital Policlinico (MUHP) multidrug resistance surveillance program. We retrospectively investigated these isolates by whole-genome sequencing (WGS) analysis of the resistome, virulome, plasmid content, and core single nucleotide polymorphisms (cSNPs) in order to gain insights into their molecular epidemiology. The in silico WGS analysis of the resistome revealed the presence of genes, such as blaKPC, related to the phenotypically detected resistances to carbapenems. Concerning colistin resistance, the plasmidic genes mcr 1–9 were not detected, while known and new genetic variations in mgrB, phoQ, and pmrB were found. The virulome profile revealed the presence of type-3 fimbriae, capsular polysaccharide, and iron acquisition system genes. The detected plasmid replicons were classified as IncFIB(pQil), IncFIB(K), ColRNAI, IncX3, and IncFII(K) types. The cSNPs genotyping was consistent with the multi locus sequence typing (MLST) and with the distribution of mutations related to colistin resistance genes. In a nosocomial drug resistance surveillance program, WGS proved to be a useful tool for elucidating the spread dynamics of CRCR-Kp nosocomial strains and could help to limit their diffusion.

Whole genome de novo sequencing and genome annotation of the world popular cultivated edible mushroom, Lentinula edodes

2016 ◽  
Vol 223 ◽  
pp. 24-25 ◽  
Author(s):  
Donghwan Shim ◽  
Sin-Gi Park ◽  
Kangmin Kim ◽  
Wonsil Bae ◽  
Gir Won Lee ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Lentinula Edodes ◽  
De Novo ◽  
Edible Mushroom ◽  
De Novo Sequencing ◽  
Whole Genome ◽  
The World

scholarly journals Comparative Proteomic Analysis of Light-Induced Mycelial Brown Film Formation in Lentinula edodes

2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Li Hua Tang ◽  
Qi Tan ◽  
Da Peng Bao ◽  
Xue Hong Zhang ◽  
Hua Hua Jian ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Lentinula Edodes ◽  
Light Exposure ◽  
Film Formation ◽  
Edible Mushroom ◽  
Metabolic Processes ◽  
Comparative Proteomic Analysis ◽  
Flight Mass Spectrometry ◽  
Oxidation Reduction ◽  
Single Organism

Light-induced brown film (BF) formation by the vegetative mycelium of Lentinula edodes is important for ensuring the quantity and quality of this edible mushroom. Nevertheless, the molecular mechanism underlying this phenotype is still unclear. In this study, a comparative proteomic analysis of mycelial BF formation in L. edodes was performed. Seventy-three protein spots with at least a twofold difference in abundance on two-dimensional electrophoresis (2DE) maps were observed, and 52 of them were successfully identified by matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF/MS). These proteins were classified into the following functional categories: small molecule metabolic processes (39%), response to oxidative stress (5%), and organic substance catabolic processes (5%), followed by oxidation-reduction processes (3%), single-organism catabolic processes (3%), positive regulation of protein complex assembly (3%), and protein metabolic processes (3%). Interestingly, four of the proteins that were upregulated in response to light exposure were nucleoside diphosphate kinases. To our knowledge, this is the first proteomic analysis of the mechanism of BF formation in L. edodes. Our data will provide a foundation for future detailed investigations of the proteins linked to BF formation.

scholarly journals The Effect of Mushroom Extracts on Human Platelet and Blood Coagulation: In vitro Screening of Eight Edible Species

Nutrients ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 3040 ◽  
Author(s):  
Barbara Poniedziałek ◽  
Marek Siwulski ◽  
Adrian Wiater ◽  
Iwona Komaniecka ◽  
Anna Komosa ◽  
...  
Keyword(s):  
Lentinula Edodes ◽  
Edible Mushroom ◽  
International Normalized Ratio ◽  
Hot Water ◽  
Human Consumption ◽  
Mushroom Species ◽  
The One ◽  
Induced Aggregation ◽  
Mushroom Extracts

Cardiovascular diseases remain the leading global cause of mortality indicating the need to identify all possible factors reducing primary and secondary risk. This study screened the in vitro antiplatelet and anticoagulant activities of hot water extracts of eight edible mushroom species (Agaricus bisporus, Auricularia auricularia-judae, Coprinus comatus, Ganoderma lucidum, Hericium erinaceus, Lentinula edodes, Pleurotus eryngii, and Pleurotus ostreatus) increasingly cultivated for human consumption, and compared them to those evoked by acetylsalicylic acid (ASA). The antioxidant capacity and concentration of polysaccharides, phenolic compounds, organic acids, ergosterol, macro elements, and trace elements were also characterized. The most promising antiplatelet effect was exhibited by A. auricularia-judae and P. eryngii extracts as demonstrated by the highest rate of inhibition of adenosine-5′-diphosphate (ADP)-induced and arachidonic acid (AA)-induced aggregation. The response to both extracts exceeded the one evoked by 140 µmol/L of ASA in the ADP test and was comparable to it in the case of the AA test. Such a dual effect was also observed for G. lucidum extract, even though it was proven to be cytotoxic in platelets and leukocytes. The extract of P. ostreatus revealed an additive effect on AA-induced platelet aggregation. None of the mushroom extracts altered the monitored coagulation parameters (prothrombin time, prothrombin ratio, and International Normalized Ratio). The effect of mushroom extracts on platelet function was positively related to their antioxidative properties and concentration of polysaccharides and ergosterol, and inversely related to zinc concentration. The study suggests that selected mushrooms may exert favorable antiplatelet effects, highlighting the need for further experimental and clinical research in this regard.

scholarly journals Single-Nucleotide Polymorphisms Sequencing Identifies Candidate Functional Variants at Prostate Cancer Risk Loci

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 547 ◽  
Author(s):  
Peng Zhang ◽  
Lori S. Tillmans ◽  
Stephen N. Thibodeau ◽  
Liang Wang
Keyword(s):  
Prostate Cancer ◽  
Cancer Risk ◽  
Single Nucleotide Polymorphisms ◽  
Protein Binding ◽  
Prostate Cancer Risk ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Functional Variants ◽  
Dependent Protein

Genome-wide association studies have identified over 150 risk loci that increase prostate cancer risk. However, few causal variants and their regulatory mechanisms have been characterized. In this study, we utilized our previously developed single-nucleotide polymorphisms sequencing (SNPs-seq) technology to test allele-dependent protein binding at 903 SNP sites covering 28 genomic regions. All selected SNPs have shown significant cis-association with at least one nearby gene. After preparing nuclear extract using LNCaP cell line, we first mixed the extract with dsDNA oligo pool for protein–DNA binding incubation. We then performed sequencing analysis on protein-bound oligos. SNPs-seq analysis showed protein-binding differences (>1.5-fold) between reference and variant alleles in 380 (42%) of 903 SNPs with androgen treatment and 403 (45%) of 903 SNPs without treatment. From these significant SNPs, we performed a database search and further narrowed down to 74 promising SNPs. To validate this initial finding, we performed electrophoretic mobility shift assay in two SNPs (rs12246440 and rs7077275) at CTBP2 locus and one SNP (rs113082846) at NCOA4 locus. This analysis showed that all three SNPs demonstrated allele-dependent protein-binding differences that were consistent with the SNPs-seq. Finally, clinical association analysis of the two candidate genes showed that CTBP2 was upregulated, while NCOA4 was downregulated in prostate cancer (p < 0.02). Lower expression of CTBP2 was associated with poor recurrence-free survival in prostate cancer. Utilizing our experimental data along with bioinformatic tools provides a strategy for identifying candidate functional elements at prostate cancer susceptibility loci to help guide subsequent laboratory studies.

scholarly journals Whole-genome sequencing reveals rare off-target mutations in CRISPR/Cas9-edited grapevine

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Xianhang Wang ◽  
Mingxing Tu ◽  
Ya Wang ◽  
Wuchen Yin ◽  
Yu Zhang ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Editing ◽  
Genome Sequencing ◽  
Plant Biotechnology ◽  
High Specificity ◽  
Fruit Trees ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Indel Mutation ◽  
Target Sites

AbstractThe CRISPR (clustered regularly interspaced short palindromic repeats)-associated protein 9 (Cas9) system is a powerful tool for targeted genome editing, with applications that include plant biotechnology and functional genomics research. However, the specificity of Cas9 targeting is poorly investigated in many plant species, including fruit trees. To assess the off-target mutation rate in grapevine (Vitis vinifera), we performed whole-genome sequencing (WGS) of seven Cas9-edited grapevine plants in which one of two genes was targeted by CRISPR/Cas9 and three wild-type (WT) plants. In total, we identified between 202,008 and 272,397 single nucleotide polymorphisms (SNPs) and between 26,391 and 55,414 insertions/deletions (indels) in the seven Cas9-edited grapevine plants compared with the three WT plants. Subsequently, 3272 potential off-target sites were selected for further analysis. Only one off-target indel mutation was identified from the WGS data and validated by Sanger sequencing. In addition, we found 243 newly generated off-target sites caused by genetic variants between the Thompson Seedless cultivar and the grape reference genome (PN40024) but no true off-target mutations. In conclusion, we observed high specificity of CRISPR/Cas9 for genome editing of grapevine.

scholarly journals Whole-Genome DNA Methylation Analysis in Hydrogen Peroxide Overproducing Transgenic Tobacco Resistant to Biotic and Abiotic Stresses

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 178
Author(s):  
Ana L. Villagómez-Aranda ◽  
Luis F. García-Ortega ◽  
Irineo Torres-Pacheco ◽  
Ramón G. Guevara-González
Keyword(s):  
Hydrogen Peroxide ◽  
Dna Methylation ◽  
Transgenic Tobacco ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Methylation Status ◽  
Physiological Adaptation ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Biotic And Abiotic Stresses

Epigenetic regulation is a key component of stress responses, acclimatization and adaptation processes in plants. DNA methylation is a stable mark plausible for the inheritance of epigenetic traits, such that it is a potential scheme for plant breeding. However, the effect of modulators of stress responses, as hydrogen peroxide (H2O2), in the methylome status has not been elucidated. A transgenic tobacco model to the CchGLP gene displayed high H2O2 endogen levels correlated with biotic and abiotic stresses resistance. The present study aimed to determine the DNA methylation status changes in the transgenic model to obtain more information about the molecular mechanism involved in resistance phenotypes. The Whole-genome bisulfite sequencing analysis revealed a minimal impact of overall levels and distribution of methylation. A total of 9432 differential methylated sites were identified in distinct genome regions, most of them in CHG context, with a trend to hypomethylation. Of these, 1117 sites corresponded to genes, from which 83 were also differentially expressed in the plants. Several genes were associated with respiration, energy, and calcium signaling. The data obtained highlighted the relevance of the H2O2 in the homeostasis of the system in stress conditions, affecting at methylation level and suggesting an association of the H2O2 in the physiological adaptation to stress functional linkages may be regulated in part by DNA methylation.

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