scholarly journals Whole Genome Sequences of the Tea Leaf Spot Pathogen Didymella segeticola

2019 ◽  
Vol 109 (10) ◽  
pp. 1676-1678 ◽  
Author(s):  
Yafeng Ren ◽  
Dongxue Li ◽  
Xiaozhen Zhao ◽  
Yong Wang ◽  
Xingtao Bao ◽  
...  
Keyword(s):  
Leaf Spot ◽  
Guizhou Province ◽  
Whole Genome Sequence ◽  
Future Research ◽  
Whole Genome ◽  
Plant Host ◽  
Illumina Hiseq ◽  
Leaf Production ◽  
Clusters Of Orthologous Groups ◽  
Tea Leaf

The fungal pathogen Didymella segeticola (basionym Phoma segeticola) causes leaf spot on tea (Camellia sinensis), which leads to a loss in tea leaf production in Guizhou Province, China. D. segeticola isolate GZSQ-4 was sequenced using Illumina HiSeq and Pacific Biosciences (PacBio) RS technologies, and then assembled to approximately 33.4 Mbp with a scaffold N50 value of approximately 2.3 Mbp. In total, 10,893 genes were predicted using the Nonredundant, Gene Ontology, Clusters of Orthologous Groups, Kyoto Encyclopedia of Genes and Genomes, and SWISS-PROT databases. The whole-genome sequence of D. segeticola will provide a resource for future research on host−pathogen interactions, determination of trait-specific genes, pathogen evolution, and plant−host adaptation mechanisms.

scholarly journals Whole genome sequence and gene annotation resource for Didymella bellidis, associated with tea leaf spot

Plant Disease ◽  
2020 ◽  
Author(s):  
Xue Wang ◽  
Xian Wu ◽  
Shilong Jiang ◽  
Qiaoxiu Yin ◽  
Dongxue Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Leaf Spot ◽  
Sequence Data ◽  
Gene Annotation ◽  
Gene Prediction ◽  
Guizhou Province ◽  
Whole Genome Sequence ◽  
Phytopathogenic Fungus ◽  
Future Research ◽  
Whole Genome

Didymella bellidis is a phytopathogenic fungus that causes leaf spot on tea plants (Camellia sinensis), which negatively affects the productivity and quality of tea leaves in Guizhou Province, China. D. bellidis isolate GZYQYQX2B was sequenced using Pacific Biosciences and Illumina technologies, and assembled into a whole genome of 35.5 Mbp. Transcripts of D. bellidis isolate GZYQYQX2B were predicted from the assembled genome and were further validated by RNA sequence data. In total, 10,731 genes were predicted by integrating three approaches, namely ab initio and homology-based gene prediction, as well as transcriptomics data. The whole-genome sequence of D. bellidis will provide a resource for future research on trait-specific genes of the pathogen and host-pathogen interactions.

scholarly journals Integrated mRNA and small RNA sequencing for analyzing tea leaf spot pathogen Lasiodiplodia theobromae, under in vitro conditions and the course of infection

2020 ◽  
Author(s):  
Shilong Jiang ◽  
Qiaoxiu Yin ◽  
Dongxue Li ◽  
Xian Wu ◽  
Yong Wang ◽  
...  
Keyword(s):  
Small Rna ◽  
Leaf Spot ◽  
Guizhou Province ◽  
Phytopathogenic Fungus ◽  
Future Research ◽  
Small Rna Sequencing ◽  
Rna Sequences ◽  
Lasiodiplodia Theobromae ◽  
Tea Leaf

Lasiodiplodia theobromae (Pat.) Griffon & Maubl. is a phytopathogenic fungus, which can cause many different diseases on different crops. The pathogen can cause leaf spot on tea plants (Camellia sinensis), which negatively affects the productivity and quality of tea leaves in tea plantations in Guizhou Province, China. Although the genome sequence of L. theobromae has been published, no data on the transcriptome or small RNA sequences of L. theobromae under in vitro conditions and the course of infection of tea leaf are available. Here, we report the high-quality transcriptome and small RNA sequences of L. theobromae under in vitro conditions and the course of infection of tea leaf using the platform of Illumina HiSeq. This comprehensive expression profiling of the fungal pathogen will provide a valuable resource for future research on trait-specific genes of the pathogen, host-pathogen interactions and on disease resistance in the host.

scholarly journals Integrated mRNA and Small RNA Sequencing for Analyzing Leaf Spot Pathogen Didymella segeticola and Its Host, Tea (Camellia sinensis), During Infection

2020 ◽  
pp. MPMI-07-20-0207
Author(s):  
Rui Yang ◽  
Silong Jiang ◽  
Dongxue Li ◽  
Qiaoxiu Yin ◽  
Xian Wu ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Leaf Spot ◽  
Resistance Mechanisms ◽  
Guizhou Province ◽  
Future Research ◽  
Small Rna Sequencing ◽  
Illumina Hiseq ◽  
Tea Plants ◽  
Open Access Article

Leaf spot on tea plants (Camellia sinensis [L.] Kuntze), caused by the fungus Didymella segeticola (Q. Chen) Q. Chen, Crous & L. Cai (syn. Phoma segeticola), negatively affects the productivity and quality of tea leaves in Guizhou Province, China. Although the genome sequence of D. segeticola has been published, no data on the transcriptome or microRNAs (miRNAs) of the pathogen or host during infection are available. Here, we report on the high-quality transcriptome and miRNA sequences of both D. segeticola and tea during infection, using the Illumina HiSeq 4000 or HiSeq 2500 platforms. Comprehensive expression profiling of the fungal pathogen and its host will provide a resource for future research into trait-specific genes of the pathogen and the host as well as on host-pathogen interactions and on disease resistance mechanisms. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

scholarly journals Functional Annotation of circRNAs of Tea Leaves during the Infection by the Tea Leaf Spot Pathogen, Didymella segeticola

2021 ◽  
Author(s):  
Shilong Jiang ◽  
Yuanyou Yang ◽  
Di Guo ◽  
Yu Wang ◽  
Honglin Huang ◽  
...  
Keyword(s):  
Leaf Spot ◽  
Functional Annotation ◽  
Differentially Expressed ◽  
Future Research ◽  
Circular Rnas ◽  
Tea Leaves ◽  
Illumina Hiseq ◽  
Host Pathogen ◽  
Plant Pathogen Interaction ◽  
Tea Leaf

Didymella segeticola (Q. Chen) Q. Chen, Crous & L. Cai (syn. Phoma segeticola) is an important phytopathogen that causes leaf spot on tea, Camellia sinensis [L.] O. Kuntze, which results in huge tea production losses. The functional annotation and analysis of circular RNAs (circRNAs) of tea leaves during D. segeticola infection may reveal the host–pathogen interaction mechanisms. In this study, a model of tea (C. sinensis ‘Fuding-dabaicha’) leaves infected by D. segeticola was constructed, and then circRNAs of tea leaves were sequenced on the Illumina HiSeq 4000 platform. In total, 231 and 118 differentially expressed circRNAs from tea leaves were significantly up- and down-regulated, respectively, by the D. segeticola infection. A Kyoto Encyclopedia of Genes and Genomes analysis indicated that the differentially expressed circRNA-hosting-genes were significantly enriched in the plant–pathogen interaction pathway. As the differentially expressed circRNA-hosting-gene of circRNA in the pathway, the U-box domain-containing protein 35 gene was enriched in response to stress according to a Gene Ontology analysis. The expression profiling of circRNAs and the annotation of circRNA-hosting-genes of tea leaves during D. segeticola infection will provide a resource for future research on host–pathogen interactions.

scholarly journals The antifungal mechanism of the biogenic antimicrobial Ningnanmycin on Didymella segeticola involves binding to tryptophanyl-tRNA synthetase, inhibiting translation

2020 ◽  
Author(s):  
Li Dongxue ◽  
Qiaoxiu Yin ◽  
Xue Wang ◽  
Shilong Jiang ◽  
Dissanayake Saman Pradeep Dharmasena ◽  
...  
Keyword(s):  
Leaf Spot ◽  
Mycelial Growth ◽  
Morphological Changes ◽  
Binding Free Energy ◽  
Trna Synthetase ◽  
Guizhou Province ◽  
Leaf Spot Disease ◽  
Mrna Levels ◽  
Action Mechanism ◽  
Tea Leaf

Abstract BackgroundTea [Camellia sinensis (L.) Kuntze] has been recently cultivated in Guizhou Province, China, where the cultivated area has reached 350,000 hectares, making it the major tea-growing region in world. Tea leaf spot caused by Didymella segeticola can induce the decreases in quality and quantity of tea leaves, which is an important disease in tea plantations at higher altitude, where cold spells occur in late spring. As a promising biogenic antimicrobial agent against crop diseases, Ningnanmycin (NNM) was produced from Streptomyces noursei var. xichangensisn, represented higher field efficiency against fungal, bacterial and viral phytopathogens, lower toxicity and lower residue. However, the action mechanism of NNM against phytopathogens just stays on the stage of anti-viral mechanism, which limits the application of NNM in the management of plant fungal diseases. Here, we studied the action mechanism of NNM against D. segeticola using many methods of transcriptome, ultrastructure, molecular biology and molecular docking.ResultsNNM strongly inhibited the mycelial growth of D. segeticola with the half-maximal effective concentration of 1287.54 U/mL. Optical, fluorescence, scanning and transmission electron microscopy were applied to observe morphological changes of cellular, organelle for D. segeticola treated by NNM. A great number of morphological changes of D. segeticola indicated that NNM could affect the biosynthesis of the phytopathogen. For further, RNA-Seq results showed that NNM treated D. segeticola induced 1,363 significantly differentially expressed genes (DEGs) comparing with the control (P < 0.05). The DEGs were highly enriched in structural component of ribosome, ribosome and translation by Gene Ontology, as well as in ribosome pathway at Kyoto Encyclopedia of Genes and Genomes. NNM regulated the mRNA levels of RPS7, RPS9, RPS10b, RPL9, RPL11 and TrpRS, and represent the different regulation mode by the comparative analysis with a classical translation extension inhibitor, cycloheximide. The molecular docking indicated that NNM possessed a marked affinity with TrpRS, with the binding free energy is -101.55 kcal/mol.ConclusionsNNM could potentially affect translation by binding to tryptophanyl-tRNA synthetase, thus inhibiting mycelial growth. This study will provide insights for anti-fungal mechanism of NNM and contribute to the control and prevention of tea leaf spot disease.

PSXIV-24 Real-time, on-site whole genome sequencing with oxford nanopore technologies’ MinION

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 257-258
Author(s):  
Hanna Ostrovski ◽  
Rodrigo Pelicioni Savegnago ◽  
Wen Huang ◽  
Cedric Gondro
Keyword(s):  
Real Time ◽  
Ease Of Use ◽  
Whole Genome Sequence ◽  
Genomic Sequencing ◽  
Whole Genome ◽  
Illumina Hiseq ◽  
Base Calling ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies

Abstract Most quantitative geneticists are traditionally trained for data analysis in genetic evaluation and genomic prediction, but rarely have extensive knowledge of molecular genetics or experience in experimental labs. Recent products, such as those launched by Oxford Nanopore Technologies (ONT), give those quantitative geneticists a comprehensible and hands-on toolkit to explore DNA sequencing. The ‘MinION’, a small DNA sequencer, is of interest for quantitative geneticists due to both the minimal learning curve and the non-proprietary USB connectivity. This device is small enough to be portable, allowing for potential real-time, on-farm sequencing. The objective of this project is to compare the whole genome sequence (WGS) output of the MinION sequencer to that of the Illumina HiSeq 4000. Blood was collected from a 6-month-old Akaushi calf born on a Michigan State University farm. DNA was extracted from the sample using the QIAamp DNA Blood Kit from Qiagen, and library DNA ligation preparation (SQK-LSK109) from ONT was used. After base-calling with guppy software (provided by ONT), the data were preprocessed and experimental runs with the MinION were compared using quality control. Finally, the data were aligned with guppy software, and was compared to the aligned WGS obtained with Illumina HiSeq. Quality results from each MinION indicate that, despite the low amount of sequence collected in each run (~225,303 reads per run), the quality of bases sequenced was high (Q≥7). The aligned data from the Illumina sequencer provided 40x coverage of the genome, with a total of 739,339,742 reads. Although the amount of data obtained with MinION is much smaller than that of Illumina HiSeq, the high quality of MinION’s data combined with its ease of use give an opportunity of genomic sequencing for users who are either inexperienced or do not have access to large genomic sequencing devices.

scholarly journals Genome Sequence Data of the Soybean Pathogen Stagonosporopsis vannaccii: A Resource for Studies on Didymellaceae Evolution

2020 ◽  
Vol 33 (8) ◽  
pp. 1022-1024
Author(s):  
Giovanni Cafà ◽  
Thaís Regina Boufleur ◽  
Renata Rebellato Linhares de Castro ◽  
Nelson Sidnei Massola ◽  
Riccardo Baroncelli
Keyword(s):  
Comparative Genomics ◽  
Genome Sequence ◽  
Plant Pathogens ◽  
Sequence Data ◽  
Gene Prediction ◽  
Whole Genome Sequence ◽  
Future Research ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Associated Species

The genus Stagonosporopsis is classified within the Didymellaceae family and has around 40 associated species. Among them, several species are important plant pathogens responsible for significant losses in economically important crops worldwide. Stagonosporopsis vannaccii is a newly described species pathogenic to soybean. Here, we present the draft whole-genome sequence, gene prediction, and annotation of S. vannaccii isolate LFN0148 (also known as IMI 507030). To our knowledge, this is the first genome sequenced of this species and represents a new useful source for future research on fungal comparative genomics studies.

scholarly journals Determination and Structural Analysis of the Whole-Genome Sequence of Fusarium equiseti D25-1

2020 ◽  
Author(s):  
Xueping LI ◽  
Jianhong Li ◽  
Yonghong Qi ◽  
Yonggang Liu ◽  
Minquan Li
Keyword(s):  
Molecular Mechanisms ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Effective Control ◽  
Sequence Length ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Illumina Hiseq ◽  
Fusarium Equiseti ◽  
Wide Range

Abstract BackgroundFusarium equiseti is a plant pathogen with a wide range of hosts and diverse effects, including probiotic activity. However, the underlying molecular mechanisms remain unclear, hindering its effective control and utilization. In this study, the Illumina HiSeq 4000 and PacBio platforms were used to sequence and assemble the whole genome of Fusarium equiseti D25-1.ResultsThe assembly included 16 fragments with a GC content of 48.01%, gap number of zero, and size of 40,776,005 bp. There were 40,110 exons and 26,281 introns having a total size of 19,787,286 bp and 2,290,434 bp, respectively. The genome had an average copy number of 333, 71, 69, 31, and 108 for tRNAs, rRNAs, sRNAs, snRNAs, and miRNAs, respectively. The total repetitive sequence length was 1,713,918 bp, accounting for 4.2033% of the genome. In total, 13,134 functional genes were annotated, accounting for 94.97% of the total gene number. Toxin-related genes, including two related to zearalenone and 23 related to trichothecene, were identified. A comparative genomic analysis supported the high quality of the F. equiseti assembly, exhibiting good collinearity with the reference strains, 3,483 species-specific genes, and 1,805 core genes. A gene family analysis revealed more than 2,500 single-copy orthologs. F. equiseti was most closely related to Fusarium pseudograminearum based on a phylogenetic analysis at the whole-genome level.ConclusionsOur comprehensive analysis of the whole genome of F. equiseti provides basic data for studies of gene expression, regulatory and functional mechanisms, evolutionary processes, as well as disease prevention and control.

Comparison of three species of Elizabethkingia genus by whole-genome sequence analysis

2021 ◽  
Vol 368 (5) ◽  
Author(s):  
Chen Yang ◽  
Zhe Liu ◽  
Shuai Yu ◽  
Kun Ye ◽  
Xin Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genomic Analysis ◽  
Information Storage ◽  
Whole Genome Sequence ◽  
Neonatal Meningitis ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Significant Finding ◽  
Beta Lactams ◽  
Clusters Of Orthologous Groups

Abstract Elizabethkingia are found to cause severe neonatal meningitis, nosocomial pneumonia, endocarditis and bacteremia. However, there are few studies on Elizabethkingia genus by comparative genomic analysis. In this study, three species of Elizabethkingia were found: E. meningoseptica, E. anophelis and E. miricola. Resistance genes and associated proteins of seven classes of antibiotics including beta-lactams, aminoglycosides, macrolides, tetracyclines, quinolones, sulfonamides and glycopeptides, as well as multidrug resistance efflux pumps were identified from 20 clinical isolates of Elizabethkingia by whole-genome sequence. Genotype and phenotype displayed a good consistency in beta-lactams, aminoglycosides and glycopeptides, while contradictions exhibited in tetracyclines, quinolones and sulfonamides. Virulence factors and associated genes such as hsp60 (htpB), exopolysaccharide (EPS) (galE/pgi), Mg2+ transport (mgtB/mgtE) and catalase (katA/katG) existed in all clinical and reference strains. The functional analysis of the clusters of orthologous groups indicated that ‘metabolism’ occupied the largest part in core genome, ‘information storage and processing’ was the largest group in both accessory genome and unique genome. Abundant mobile elements were identified in E. meningoseptica and E. anophelis. The most significant finding in our study was that a single clone of E. anophelis had been circulating within diversities of departments in a clinical setting for nearly 18 months.

scholarly journals Isolation, Identification, and Whole-Genome Sequence Analysis of Pantoea Agglomerans Causing Leaf Spot-Hole Disease in Wild Apricot in Xinjiang, China

2022 ◽  
Author(s):  
Fangyuan Xu ◽  
Liqiang Liu ◽  
Jun Liu ◽  
Wei He ◽  
Kang Liao
Keyword(s):  
Sequence Analysis ◽  
Leaf Spot ◽  
Pantoea Agglomerans ◽  
Whole Genome Sequence ◽  
Pathogenicity Test ◽  
Whole Genome ◽  
Bacterial Strains ◽  
Wild Fruit ◽  
Wild Apricot ◽  
In The Wild

Abstract Wild apricot in Yili wild fruit forest in Xinjiang have been seriously affected by leaf spot-hole disease, with the incidence reaching 100%. To identify the pathogen of apricot perforation in the Yili wild fruit forest, two bacterial strains with strong virulence were obtained by the dilution separation method. The bacterial strains were gram-negative bacteria with yellow colonies, smooth surfaces and neat edges. The results of the pathogenicity test showed that the bacteria could cause symptoms of leaf spot-hole disease in wild apricot, similar to the symptoms in the field, and could cause HR in tobacco. Based on the 16S rDNA gene sequence and multilocus sequence analysis of fusA, gyrB, leuS, pyrG, rpoB and rlpB, combined with the physiological and biochemical characteristics, the isolated strain was identified as Pantoea agglomerans. The pathogen causing bacterial leaf spot-hole disease in wild apricot was determined to be P. agglomerans in the wild fruit forest of Yili, Xinjiang. The whole genome of the pathogen strain GL9-2 was sequenced based on the Illumina HiSeq500 and PacBio RS platforms. The genome size was 4765392 bp, and the G+C value was 55.27%. There was one chromosome and two plasmids in the genome, and 4353 CDs were identified. The annotation results showed that 52 glycoside hydrolase-related genes, 38 bacterial secretory system-related genes and 600 toxin-related genes were predicted.

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