scholarly journals Genome Sequence Resource for Colletotrichum viniferum, the cause of grapevine ripe rot in China.

2021 ◽  
Author(s):  
Mengru Dou ◽  
Yu Hao ◽  
Jing Yang ◽  
Xiaojian Yuan ◽  
Xiao Yin ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gene Clusters ◽  
Cytochrome P450 Enzymes ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Yield And Quality ◽  
Genome Analyses ◽  
High Quality Genome ◽  
Important Disease

Grape ripe rot is an important disease that has seriously damaged the yield and quality of grape worldwide. The disease is caused by Colletotrichum viniferum, a hemibiotrophic fungus that belongs to the Glomerellaceae family of Sordariomycetes class. Here, this work presents the genome of C. viniferum stain CvYL2a from grape based on Illumina HiSeq 2500 and PacBio RS II. The high-quality genome consists of 70 contigs with a 73.41 Mb genome size and encodes 14,668 protein-coding genes. These genes were annotated using Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, EuKaryotic Orthologous Groups, Non-redundant Protein, and Swiss-Prot database. In addition, we identified a series of genes involved in pathogenicity including 909 carbohydrate-active enzymes, 67 secondary metabolite gene clusters, and 307 Cytochrome P450 enzymes. This genome sequence provides a valuable reference for the research on grape-C. viniferum interactions, the pathogenesis of C. viniferum, and comparative genome analyses. Keywords: Colletotrichum viniferum, grape, genome, pathogenesis

scholarly journals Genomic analysis of Elsinoë arachidis reveals its potential pathogenic mechanism and the biosynthesis pathway of elsinochrome toxin

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0261487
Author(s):  
Wenli Jiao ◽  
Mengxue Xu ◽  
Rujun Zhou ◽  
Yiwei Fu ◽  
Zibo Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Core Gene ◽  
Pathogenic Mechanism ◽  
Biosynthesis Pathway ◽  
Cytochrome P450 Enzymes ◽  
Cell Wall Degrading Enzymes ◽  
High Quality Genome ◽  
Metabolism Gene

Elsinochromes (ESCs) are virulence factors produced by Elsinoë arachidis which is the cause of peanut scab. However, the biosynthesis pathway of ESCs in E. arachidis has not been elucidated and the potential pathogenic mechanism of E. arachidis is poorly understood. In this study, we report a high-quality genome sequence of E. arachidis. The size of the E. arachidis genome is 33.18Mb, which is comparable to the Ascomycota genome (average 36.91 Mb), encoding 9174 predicted genes. The self-detoxification family including transporters and cytochrome P450 enzymes were analysis, candidate effectors and cell wall degrading enzymes were investigated as the pathogenicity genes by using PHI and CAZy databases. Additionally, the E. arachidis genome contains 24 secondary metabolism gene clusters, in which ESCB1 was identified as the core gene of ESC biosynthesis. Taken together, the genome sequence of E. arachidis provides a new route to explore its potential pathogenic mechanism and the biosynthesis pathway of ESCs.

scholarly journals First draft genome sequence resource of Colletotrichum liriopes causing leaf anthracnose on Ophiopogon japonicus

Plant Disease ◽  
2020 ◽  
Author(s):  
Mingshuang Wang ◽  
Xiujun Luo ◽  
Huizhong Wang
Keyword(s):  
Genome Sequence ◽  
Economic Value ◽  
Draft Genome ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Future Research ◽  
Ophiopogon Japonicus ◽  
Genome Analyses ◽  
Important Disease ◽  
Chinese Medicinal Plant

The leaf anthracnose of Ophiopogon japonicus is an important disease that can significantly reduce the quality and economic value of this traditional Chinese medicinal plant. The disease is caused by Colletotrichum liriopes, a necrotrophic fungus that belongs to the Glomerellaceae family of the Sordariomycetes class. Here, we present the draft whole-genome sequence of the C. liriopes strain A2 that caused leaf anthracnose on O. japonicus. The assembly consists of 407 contigs with an estimated genome size of 53.1 Mb. Furthermore, we identified 670 carbohydrate-active enzymes, 1377 secreted proteins, and 60 secondary metabolite gene clusters, which may be associated with the pathogenicity of this pathogen. This genome resource will provide a valuable resource for future research on the pathogenesis of C. liriopes and comparative genome analyses within Colletotrichum.

scholarly journals High-quality genome assembly and annotation resource of Botryosphaeria dothidea strain BDLA16-7, causing trunk canker disease on Chinese hickory

Plant Disease ◽  
2021 ◽  
Author(s):  
Jiandong Bao ◽  
Q. Q. Wu ◽  
Jianqin Huang ◽  
Chuan-Qing Zhang
Keyword(s):  
Genome Assembly ◽  
Gene Clusters ◽  
Botryosphaeria Dothidea ◽  
Cytochrome P450 Enzymes ◽  
Protein Coding ◽  
Canker Disease ◽  
Host Interaction ◽  
Oxford Nanopore ◽  
Infection Mechanisms ◽  
High Quality Genome

Botryosphaeria dothidea is a latent pathogen with global importance to woody plant health, which causes serious tree trunk cankers on Chinese hickory. To date, only one Illumina short-read-based genome assembly of strain CK16 is available for host Chinese hickory. To address this problem, we reported a near telomere-to-telomere genome assembly of strain BDLA16-7 (46.05 Mb, N50 3.87 Mb) using Oxford Nanopore Sequencing Technology. Our genome assembly was consisted of 15 contigs, of which, 3 were assembled into chromosomal level and the maximum contig length was 6.19 Mb. The assembly contained 7.96% repeats and 12,815 protein-coding genes (10,274 genes were functional annotated). We also identified 3,642 pathogen-host interaction (PHI) genes, 250 carbohydrateactive enzymes (CAZymes), 252 cytochrome P450 enzymes (CYPs), 752 putative secreted proteins and 63 secondary metabolite biosynthesis gene clusters (SMBGCs). The BUSCO completeness of genome assembly and predicted genes was 99.34% and 97.50%, respectively, at fungal level (n=758). The almost chromosomal-level and well-annotated genome assembly will provide a valuable genetic resource for understanding of the infection mechanisms of B. dothidea in future.

scholarly journals Characterization of Streptomyces scabies isolates from potato tubers its pathogenic variations in Rawalpindi District

2014 ◽  
Vol 4 (1) ◽  
pp. 1-6
Author(s):  
S. Shazia ◽  
F. Naz ◽  
A. Rauf ◽  
M. Inam-ul-Haq ◽  
S. Bushra
Keyword(s):  
Solanum Tuberosum L ◽  
Economic Loss ◽  
Streptomyces Scabies ◽  
Potato Tubers ◽  
Yield And Quality ◽  
Isolation And Characterization ◽  
Pathogenic Variation ◽  
Important Disease

Potato (Solanum tuberosum L.) has various biotic constraints in its production due to pest attack. Among these, common scab caused by streptomyces scabies is an important disease in potato which causes economic loss with respect to plant yield and quality of tubers. The present study was conducted to determine the pathogenicity, pathogenic variation, characterization of morphological, physiological and biochemical aspects of Streptomyces associated with potato tubers grown in Rawalpindi district. Severity data and pathogenic variation of disease was studied by using different isolation and characterization techniques.

scholarly journals Gene recruitments and dismissals in argonaut octopus genome provide insights to pelagic lifestyle adaptation and shell-like eggcase reacquisition

2021 ◽  
Author(s):  
Masa-aki Yoshida ◽  
Kazuki Hirota ◽  
Junichi Imoto ◽  
Miki Okuno ◽  
Hiroyuki Tanaka ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Average Length ◽  
Draft Genome ◽  
Gene Clusters ◽  
Draft Genome Sequence ◽  
Shell Formation ◽  
Protein Coding ◽  
Homologous Genes ◽  
Phenotypic Structure ◽  
Comparative Genomics Analysis

The paper nautilus, Argonauta argo, also known as the greater argonaut, is a species of octopods distinctly characterized by its pelagic lifestyle and by the presence of a spiral-shaped shell-like eggcase in females. The eggcase functions by protecting the eggs laid inside it, and by building and keeping air intakes for buoyancy. To reveal the genomic background of the species′ adaptation to pelagic lifestyle and the acquisition of its shell-like eggcase, we sequenced the draft genome sequence of the species. The genome size was 1.1 Gb, which is the smallest among the cephalopods known to date, with the top 215 scaffolds (average length 5,064,479 bp) covering 81% (1.09 Gb) of the total assembly. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified nearly intact HOX, Parahox, Wnt clusters and some gene clusters probably related to the pelagic lifestyle, such as reflectin, tyrosinase, and opsin. For example, opsin might have undergone an extensive duplication in order to adapt to the pelagic lifestyle, as opposed to other octopuses, which are mostly the benthic. Our gene models also discovered several genes homologous to those related to calcified shell formation in Conchiferan Mollusks, such as Pif-like, SOD, and TRX. Interestingly, comparative genomics analysis revealed that the homologous genes for such genes were also found in the genome of the octopus, which does not have a shell, as well as the basal cephalopods Nautilus. Therefore, the draft genome sequence of A. argo we presented here had not only helped us to gain further insights into the genetic background of the dynamic recruitment and dismissal of genes for the formation of an important, converging extended phenotypic structure such as the shell and the shell-like eggcase, but also the evolution of lifestyles in Cephalopods and the octopods, from benthic to pelagic.

scholarly journals Draft Genome Sequence of Streptomyces cavourensis YBQ59, an Endophytic Producer of Antibiotics Bafilomycin D, Nonactic Acid, Prelactone B, and 5,11-Epoxy-10-Cadinanol

2018 ◽  
Vol 7 (11) ◽  
Author(s):  
Huy Quang Nguyen ◽  
Nguyen Thi-Hanh Vu ◽  
Ha Hoang Chu ◽  
Son Ky Chu ◽  
Ha Hoang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
Gene Clusters ◽  
Draft Genome Sequence ◽  
Biosynthetic Pathways ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes

This study reports the draft genome sequence of the endophytic Streptomyces cavourensis strain YBQ59, produces the antibiotics bafilomycin D, nonactic acid, prelactone B, and 5,11-epoxy-10-cadinanol. The draft genome sequence comprises ∼10.2 Mb, with a GC content of 64% and 8,958 predicted protein-coding genes, of which 14 gene clusters were found to associate with antibiotic biosynthetic pathways.

scholarly journals Genome Sequence Resource for Elsinoë ampelina, the Causal Organism of Grapevine Anthracnose

2020 ◽  
Vol 33 (4) ◽  
pp. 576-579 ◽  
Author(s):  
Zhi Li ◽  
Yanchun Fan ◽  
Pingping Chang ◽  
Linlin Gao ◽  
Xiping Wang
Keyword(s):  
Genome Sequence ◽  
Management Strategies ◽  
Comparative Genomic ◽  
Causal Organism ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Elsinoe Ampelina ◽  
Genomic Studies ◽  
High Quality Genome ◽  
Ascomycetous Fungus

Elsinoë ampelina is an ascomycetous fungus that causes grape anthracnose, a potentially devastating disease worldwide. Here, we report a 28.29 Mb high-quality genome sequence of E. ampelina YL-1 that encodes 8,057 predicted protein-coding genes and represents the first sequenced genome assembly of E. ampelina. This study adds to the current genomic resources for the genus Elsinoë and paves the way for research on comparative genomic studies, E. ampelina–grape interactions, and improvement of management strategies.

scholarly journals Genome Sequence of Fusarium oxysporum f. sp. conglutinans, the Etiological Agent of Cabbage Fusarium Wilt

2020 ◽  
pp. MPMI-08-20-0245
Author(s):  
Fangwei Yu ◽  
Wei Zhang ◽  
Shenyun Wang ◽  
Hong Wang ◽  
Li Yu ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Fusarium Wilt ◽  
Genome Sequence ◽  
High Quality ◽  
Total Size ◽  
Protein Coding ◽  
Long Read ◽  
Race 1 ◽  
High Quality Genome ◽  
Open Access Article

Fusarium oxysporum f. sp. conglutinans is the causal agent of Fusarium wilt of cabbage (Brassica oleracea var. capitata L.), which results in severe yield loss. Here, we report a high-quality genome sequence of a race 1 strain (IVC-1) of F. oxysporum f. sp. conglutinans, which was assembled using a combination of PacBio long-read and Illumina short-read sequences. The assembled IVC-1 genome has a total size of 71.18 Mb, with a contig N50 length of 4.59 Mb, and encodes 23,374 predicted protein-coding genes. The high-quality genome of IVC-1 provides a valuable resource for facilitating our understanding of F. oxysporum f. sp. conglutinans–cabbage interaction. [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 Draft Genome Sequence of Lactobacillus plantarum EBKLp545, Isolated from Piglet Feces

2019 ◽  
Vol 8 (16) ◽  
Author(s):  
Sukjung Choi ◽  
Eun Bae Kim
Keyword(s):  
South Korea ◽  
Lactobacillus Plantarum ◽  
Genome Sequence ◽  
Noncoding Rna ◽  
Draft Genome ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Rna Genes

Lactobacillus plantarum strain EBKLp545 was isolated from piglet feces in South Korea and sequenced using an Illumina HiSeq system. This draft genome of strain EBKLp545 consists of 3,306,513 bp with 3,049 protein-coding genes in 138 contigs (≥500 bp), 54 noncoding RNA genes, and a 44.3% G+C content.

scholarly journals Genome Sequence of Ustilaginoidea virens IPU010, a Rice Pathogenic Fungus Causing False Smut

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Toshitaka Kumagai ◽  
Tomoko Ishii ◽  
Goro Terai ◽  
Myco Umemura ◽  
Masayuki Machida ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Pathogenic Fungus ◽  
Effector Proteins ◽  
Ustilaginoidea Virens ◽  
Metabolic Genes ◽  
Yield And Quality ◽  
False Smut

Ustilaginoidea virens is a rice pathogenic fungus that causes false smut disease, a disease that seriously damages the yield and quality of the grain. Analysis of the U. virens IPU010 33.6-Mb genome sequence will aid in the understanding of the pathogenicity of the strain, particularly in regard to effector proteins and secondary metabolic genes.

Sign in / Sign up

Export Citation Format

Share Document