scholarly journals Genome sequencing and transcriptome analysis of Geotrichum citri-aurantii on citrus reveal the potential pathogenic- and guazatine resistance-related genes

2019 ◽  
Author(s):  
Juan Zhao ◽  
DeYao Zhang ◽  
Zhe Wang ◽  
Zhonghuan Tian ◽  
Fan Yang ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Genome Sequence ◽  
Genomic Sequence ◽  
Resistance Mechanism ◽  
Effective Control ◽  
Postharvest Disease ◽  
Economic Losses ◽  
Sequencing Analysis ◽  
Transporter Family ◽  
High Quality Genome

Abstract Background: Citrus grow in more than 100 countries and is one of the most produced fruit genus. Sour rot, caused by Geotrichum citri-aurantii , is a major postharvest disease of citrus，and it causes economic losses. In recent years, the disease had a rising trend year by year. In this study, the genome sequence of G. citri-aurantii and transcriptome sequence of pathogenic- and guazatine resistance were sequenced with a view to explore the potential pathogenic mechanism and drug resistance mechanism of G. citri-aurantii on citrus. Results: We sequenced a high-quality genome sequence of G. citri-aurantii by SMRT. This sequence encodes 6,783 predicted genes of the 28.1-Mb G. citri-aurantii genome. Approximately 5.43 Gb of clean data were obtained after Hi-C sequencing, and a 27.94-Mb genomic sequence was positioned to the 10 chromosome groups after Hi-C assembly , accounting for 99.43% of the previously measured G. citri-aurantii genome. In the process of studying pathogenic mechanisms, the content of polygalacturonase (PG) and polymethylgalacturonase (PMG) was considerably increased in the Newhall navel orange infected by G. citri-aurantii. Then, three polygalacturonase (PG) genes (EVM0005942, EVM0004416, EVM0002276) related to pathogenicity were identified and the expression level was significantly increased during the infection by quantitative RT-PCR. Additionally, G. citri-aurantii is only sensitive to the chemical fungicide guazatine. Massive guazatine use has led to evolution of the wild G. citri-aurantii in citrus-producing areas. Owing to its uniqueness, RNA sequencing analysis of guazatine-resistance showed that the guazatine-resistance of G. citri-aurantii is may related to two ABC transporter family genes, six MFS transporter family genes and two MATE transporter family genes. Conclusions: We found three polygalacturonase (PG) genes related to pathogenicity and ten genes related to guazatine-resistance from molecular level. Our research may provide novel insights into the effective control of this pathogen. Keywords: Geotrichum citri-aurantii , citrus, genome, pathogenicity, guazatine, drug resistance

scholarly journals Draft Genome Sequence and Transcriptional Analysis of Rosellinia necatrix Infected with a Virulent Mycovirus

2018 ◽  
Vol 108 (10) ◽  
pp. 1206-1211 ◽  
Author(s):  
Takeo Shimizu ◽  
Satoko Kanematsu ◽  
Hajime Yaegashi
Keyword(s):  
Genome Sequence ◽  
Molecular Mechanisms ◽  
Plant Cell Wall ◽  
Draft Genome ◽  
Transcriptional Analysis ◽  
Draft Genome Sequence ◽  
Effective Control ◽  
Economic Losses ◽  
Rosellinia Necatrix ◽  
Cell Wall Degrading Enzymes

Understanding the molecular mechanisms of pathogenesis is useful in developing effective control methods for fungal diseases. The white root rot fungus Rosellinia necatrix is a soilborne pathogen that causes serious economic losses in various crops, including fruit trees, worldwide. Here, using next-generation sequencing techniques, we first produced a 44-Mb draft genome sequence of R. necatrix strain W97, an isolate from Japan, in which 12,444 protein-coding genes were predicted. To survey differentially expressed genes (DEGs) associated with the pathogenesis of the fungus, the hypovirulent W97 strain infected with Rosellinia necatrix megabirnavirus 1 (RnMBV1) was used for a comprehensive transcriptome analysis. In total, 545 and 615 genes are up- and down-regulated, respectively, in R. necatrix infected with RnMBV1. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of the DEGs suggested that primary and secondary metabolism would be greatly disturbed in R. necatrix infected with RnMBV1. The genes encoding transcriptional regulators, plant cell wall-degrading enzymes, and toxin production, such as cytochalasin E, were also found in the DEGs. The genetic resources provided in this study will accelerate the discovery of genes associated with pathogenesis and other biological characteristics of R. necatrix, thus contributing to disease control.

scholarly journals RLIP76 Gene Variants are not Associated with Drug Response in Turkish Epilepsy Patients

2011 ◽  
Vol 14 (1) ◽  
pp. 25-30 ◽  
Author(s):  
E Manguoğlu ◽  
S Akdeniz ◽  
N Dündar ◽  
Ö Duman ◽  
B Aktekin ◽  
...  
Keyword(s):  
Drug Resistance ◽  
High Performance ◽  
Drug Response ◽  
Resistance Mechanism ◽  
Sequence Variants ◽  
Gene Variants ◽  
Sequencing Analysis ◽  
Transporter Protein ◽  
Epileptic Patients ◽  
Response Status

RLIP76Gene Variants are not Associated with Drug Response in Turkish Epilepsy PatientsApproximately 30% of epileptic patients remain untreated, in spite of trials with maximum tolerable doses of more than one drug. The RalA binding protein 1 (RALBP1/RLIP76), a multifunctional, anti-apoptotic, multidrug transporter protein, has been proposed as being responsible for the drug resistance mechanism in epilepsy. We have investigated polymorphic differences in the coding regions and exon-intron boundaries of theRLIP76gene, between 146 refractory and 155 non refractory epileptic patients in Turkey, using denaturing high performance liquid chromatography (HPLC) and sequencing analysis techniques. We have detected the following sequence variants: c.160-4G>A, c.187C>G, c.1562-38G>A, c.1670+107G>A, c.1670+93G>A, c.1670+96G>A, c.1670+100C>T, c.1670+130C>T, c.1670+131G>C, c.1670+140 G>C, and found no statistically significant correlation between allele frequencies and drug response status. We conclude that sequence variants of this gene are not involved in drug resistance in epilepsy.

scholarly journals Genome Sequence of Acinetobacter baumannii Strain 10441_14 Belonging to ST451, Isolated from India

2015 ◽  
Vol 3 (6) ◽  
Author(s):  
Sunil Kumar ◽  
Prashant P. Patil ◽  
Samriti Midha ◽  
Pallab Ray ◽  
Prabhu B. Patil ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Cerebrospinal Fluid ◽  
Acinetobacter Baumannii ◽  
Genome Sequence ◽  
Draft Genome ◽  
Resistance Mechanism ◽  
Carbapenem Resistant ◽  
Global Concern

Acinetobacter baumannii resistance to carbapenems is of global concern. Here, we report the 3.9 Mb draft genome of a cerebrospinal fluid isolate of A. baumannii strain 10441_14 which is carbapenem resistant and belongs to ST451. This genome will further help in the understanding of the drug resistance mechanism, epidemiology, and pathology of this bacterium.

scholarly journals High-Quality Genome Sequence of Xanthomonas axonopodis pv. glycines Strain 12609 Isolated in Taiwan

2017 ◽  
Vol 5 (8) ◽  
Author(s):  
Shu-Fen Weng ◽  
An-Chi Luo ◽  
Che-Jui Lin ◽  
Tsai-Tien Tseng
Keyword(s):  
Gene Cluster ◽  
Genome Sequence ◽  
Cyclic Gmp ◽  
Genomic Sequence ◽  
Secretion Systems ◽  
High Quality ◽  
Content Type ◽  
Xanthomonas Axonopodis ◽  
Plasmid Sequence ◽  
High Quality Genome

ABSTRACT The genomic sequence was determined for Xanthomonas axonopodis pv. glycines strain 12609, isolated in Taiwan. Based on the genome sequence, we predicted the encoded genes, rRNA, tRNA, a plasmid sequence, secretion systems, cyclic GMP- and cyclic di-GMP-mediated pathways, and the gene cluster rpfABCHGDE (regulation of pathogenicity factor).

scholarly journals Uncovering transcriptional dark matter via gene annotation independent single-cell RNA sequencing analysis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Michael F. Z. Wang ◽  
Madhav Mantri ◽  
Shao-Pei Chou ◽  
Gaetano J. Scuderi ◽  
David W. McKellar ◽  
...  
Keyword(s):  
Single Cell ◽  
Genome Annotation ◽  
Gene Annotation ◽  
Active Regions ◽  
Sequencing Analysis ◽  
Biologically Relevant ◽  
Mole Rat ◽  
Genome Annotations ◽  
Cell Expression ◽  
High Quality Genome

AbstractConventional scRNA-seq expression analyses rely on the availability of a high quality genome annotation. Yet, as we show here with scRNA-seq experiments and analyses spanning human, mouse, chicken, mole rat, lemur and sea urchin, genome annotations are often incomplete, in particular for organisms that are not routinely studied. To overcome this hurdle, we created a scRNA-seq analysis routine that recovers biologically relevant transcriptional activity beyond the scope of the best available genome annotation by performing scRNA-seq analysis on any region in the genome for which transcriptional products are detected. Our tool generates a single-cell expression matrix for all transcriptionally active regions (TARs), performs single-cell TAR expression analysis to identify biologically significant TARs, and then annotates TARs using gene homology analysis. This procedure uses single-cell expression analyses as a filter to direct annotation efforts to biologically significant transcripts and thereby uncovers biology to which scRNA-seq would otherwise be in the dark.

scholarly journals A Novel Multidrug-Resistant Cell Line from an Italian Intrahepatic Cholangiocarcinoma Patient

Cancers ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 2051
Author(s):  
Caterina Peraldo-Neia ◽  
Annamaria Massa ◽  
Francesca Vita ◽  
Marco Basiricò ◽  
Chiara Raggi ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Cell Line ◽  
Intrahepatic Cholangiocarcinoma ◽  
Biological Behavior ◽  
Population Doubling ◽  
Sequencing Analysis ◽  
Tumor Type ◽  
Clinical Issue ◽  
Mesenchymal Transition

Chemotherapy resistance is a relevant clinical issue in tumor treatment, in particular in biliary tract carcinoma (BTC), for which there are no effective therapies, neither in the first nor in the second line. The development of chemoresistant cell lines as experimental models to investigate the mechanisms of resistance and identify alternative druggable pathways is mandatory. In BTC, in which genetics and biological behavior depend on the etiology, ethnicity, and anatomical site of origin, the creation of models that better recapitulate these characteristics is even more crucial. Here we have established and characterized an intrahepatic cholangiocarcinoma (iCCA) cell line derived from an Italian patient, called 82.3. Cells were isolated from a patient-derived xenograft (PDX) and, after establishment, immunophenotypic, biological, genetic, molecular characteristics, and tumorigenicity in vivo in NOD/SCID mice were investigated. 82.3 cells exhibited epithelial morphology and cell markers (EPCAM, CK7, and CK19); they also expressed different cancer stem markers (CD44, CD133, CD49b, CD24, Stro1, PAX6, FOXA2, OCT3/4), α–fetoprotein and under anchorage-independent and serum-free conditions were capable of originating cholangiospheres. The population doubling time was approximately 53 h. In vitro, they demonstrated a poor ability to migrate; in vivo, 82.3 cells retained their tumorigenicity, with a long latency period (16 weeks). Genetic identity using DNA fingerprinting analysis revealed 16 different loci, and the cell line was characterized by a complex hyperdiploid karyotype. Furthermore, 82.3 cells showed cross-resistance to gemcitabine, 5-fluorouracil, carboplatin, and oxaliplatin; in fact, their genetic profile showed that 60% of genes (n = 168), specific for drug resistance and related to the epithelial-mesenchymal transition, were deregulated in 82.3 cells compared to a control iCCA cell line sensitive to chemotherapeutics. RNA sequencing analysis revealed the enrichment for genes associated with epithelial to mesenchymal transition (EMT), vasculature development, and extracellular matrix (ECM) remodeling, underlining an aggressive phenotype. In conclusion, we have created a new iCCA cell line of Caucasian origin: this could be exploited as a preclinical model to study drug resistance mechanisms and to identify alternative therapies to improve the prognosis of this tumor type.

scholarly journals Molecular modeling study on the drug resistance mechanism of NS5B polymerase to TMC647055

2016 ◽  
Vol 94 (2) ◽  
pp. 147-158 ◽  
Author(s):  
Huiqun Wang ◽  
Wei Cui ◽  
Chenchen Guo ◽  
Bo-Zhen Chen ◽  
Mingjuan Ji
Keyword(s):  
Drug Resistance ◽  
Free Energy ◽  
Rational Design ◽  
Binding Free Energy ◽  
Resistance Mechanism ◽  
Free Energy Calculations ◽  
Side Chain ◽  
Free Energy Decomposition ◽  
Hcv Ns5b ◽  
Ns5b Polymerase

NS5B polymerase plays an important role in viral replication machinery. TMC647055 (TMC) is a novel and potent non-nucleoside inhibitor of the HCV NS5B polymerase. However, mutations that result in drug resistance to TMC have been reported. In this study, we used molecular dynamics (MD) simulations, binding free energy calculations, and free energy decomposition to investigate the drug resistance mechanism of HCV to TMC resulting from L392I, P495T, P495S, and P495L mutations in NS5B polymerase. From the calculated results we determined that the decrease in the binding affinity between TMC and NS5BL392I polymerase is mainly caused by the extra methyl group at the CB atom of Ile. The polarity of the side-chain of residue 495 has no distinct influence on residue 495 binding with TMC, whereas the smaller size of the side-chain of residue 495 causes a substantial decrease in the van der Walls interaction between TMC and residue 495. Moreover, the longer length of the side-chain of residue 495 has a significant effect on the electrostatic interaction between TMC and Arg-503. Finally, we performed the same calculations and detailed analysis on other 3 mutations (L392V, P495V, and P495I). The results further confirmed our conclusions. The computational results not only reveal the drug resistance mechanism between TMC647055 and NS5B polymerase, but also provide valuable information for the rational design of more potent non-nucleoside inhibitors targeting HCV NS5B polymerase.

scholarly journals Complete Genome Sequence of a Vampire Bat Rabies Virus from French Guiana

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Anne Lavergne ◽  
Edith Darcissac ◽  
Hervé Bourhy ◽  
Sourakhata Tirera ◽  
Benoît de Thoisy ◽  
...  
Keyword(s):  
Rabies Virus ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
French Guiana ◽  
Genomic Sequence ◽  
Amazon Region ◽  
Desmodus Rotundus ◽  
Bat Rabies ◽  
Vampire Bat

A rabies virus was detected in a common vampire bat ( Desmodus rotundus ) in French Guiana. Its genomic sequence was obtained and found to be closely related to other hematophagous bat-related viruses that widely circulate in the northern Amazon region. This virus is named AT6.

Characterization, Pathogenicity, Phylogeny, and Comparative Genomic Analysis of Pseudomonas tolaasii Strains Isolated from Various Mushrooms in China

2021 ◽  
Author(s):  
Zhenghui Liu ◽  
Yitong Zhao ◽  
Frederick Leo Sossah ◽  
Benjamin Azu Okorley ◽  
Daniel G. Amoako ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Genomic Analysis ◽  
Gene Families ◽  
Effective Control ◽  
Economic Losses ◽  
Comparative Genomic ◽  
Bacterial Strains ◽  
Secretion Systems ◽  
Pseudomonas Tolaasii ◽  
Antimicrobial Resistance Genes

Since 2016, devastating bacterial blotch affecting the fruiting bodies of Agaricus bisporus, Cordyceps militaris, Flammulina filiformis, and Pleurotus ostreatus in China has caused severe economic losses. We isolated 102 bacterial strains and characterized them polyphasically. We identified the causal agent as Pseudomonas tolaasii and confirmed the pathogenicity of the strains. A host range test further confirmed the pathogen’s ability to infect multiple hosts. This is the first report in China of bacterial blotch in C. militaris caused by P. tolaasii. Whole-genome sequences were generated for three strains: Pt11 (6.48 Mb), Pt51 (6.63 Mb), and Pt53 (6.80 Mb), and pangenome analysis was performed with 13 other publicly accessible P. tolaasii genomes to determine their genetic diversity, virulence, antibiotic resistance, and mobile genetic elements. The pangenome of P. tolaasii is open, and many more gene families are likely to emerge with further genome sequencing. Multilocus sequence analysis using the sequences of four common housekeeping genes (glns, gyrB, rpoB, and rpoD) showed high genetic variability among the P. tolaasii strains, with 115 strains clustered into a monophyletic group. The P. tolaasii strains possess various genes for secretion systems, virulence factors, carbohydrate-active enzymes, toxins, secondary metabolites, and antimicrobial resistance genes that are associated with pathogenesis and adapted to different environments. The myriad of insertion sequences, integrons, prophages, and genome islands encoded in the strains may contribute to genome plasticity, virulence, and antibiotic resistance. These findings advance understanding of the determinants of virulence, which can be targeted for the effective control of bacterial blotch disease.

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