scholarly journals Genome Data of Fusarium oxysporum f. sp. cubense Race 1 and Tropical Race 4 Isolates Using Long-Read Sequencing

2019 ◽  
Vol 32 (10) ◽  
pp. 1270-1272 ◽  
Author(s):  
Yingzi Yun ◽  
Aixia Song ◽  
JianDong Bao ◽  
Shasha Chen ◽  
Songmao Lu ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Single Molecule ◽  
Fungal Pathogen ◽  
High Quality ◽  
Genome Data ◽  
Long Read ◽  
Race 1 ◽  
Fusarium Wilt Of Banana ◽  
Race 4 ◽  
Chromosome Level

Fusarium wilt of banana is caused by the soilborne fungal pathogen Fusarium oxysporum f. sp. cubense. We generated two chromosome-level assemblies of F. oxysporum f. sp. cubense race 1 and tropical race 4 strains using single-molecule real-time sequencing. The F. oxysporum f. sp. cubense race 1 and tropical race 4 assemblies had 35 and 29 contigs with contig N50 lengths of 2.08 and 4.28 Mb, respectively. These two new references genomes represent a greater than 100-fold improvement over the contig N50 statistics of the previous short-read-based F. oxysporum f. sp. cubense assemblies. The two high-quality assemblies reported here will be a valuable resource for the comparative analysis of F. oxysporum f. sp. cubense races at the pathogenic level.

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 Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads

2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Jean-Marc Aury ◽  
Benjamin Istace
Keyword(s):  
Single Molecule ◽  
Direct Consequence ◽  
High Quality ◽  
Sequencing Errors ◽  
Coding Regions ◽  
Sequencing Technologies ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Long Read ◽  
Genome Assemblies

Abstract Single-molecule sequencing technologies have recently been commercialized by Pacific Biosciences and Oxford Nanopore with the promise of sequencing long DNA fragments (kilobases to megabases order) and then, using efficient algorithms, provide high quality assemblies in terms of contiguity and completeness of repetitive regions. However, the error rate of long-read technologies is higher than that of short-read technologies. This has a direct consequence on the base quality of genome assemblies, particularly in coding regions where sequencing errors can disrupt the coding frame of genes. In the case of diploid genomes, the consensus of a given gene can be a mixture between the two haplotypes and can lead to premature stop codons. Several methods have been developed to polish genome assemblies using short reads and generally, they inspect the nucleotide one by one, and provide a correction for each nucleotide of the input assembly. As a result, these algorithms are not able to properly process diploid genomes and they typically switch from one haplotype to another. Herein we proposed Hapo-G (Haplotype-Aware Polishing Of Genomes), a new algorithm capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.

scholarly journals Evaluation of the Efficacy of Commercial Disinfectants Against Fusarium oxysporum f. sp. cubense Race 1 and Tropical Race 4 Propagules

Plant Disease ◽  
2019 ◽  
Vol 103 (4) ◽  
pp. 721-728 ◽  
Author(s):  
T. V. Nguyen ◽  
L. T. T. Tran-Nguyen ◽  
C. L. Wright ◽  
P. Trevorrow ◽  
K. Grice
Keyword(s):  
Fusarium Oxysporum ◽  
Sodium Hypochlorite ◽  
Active Ingredient ◽  
Panama Disease ◽  
Banana Production ◽  
Race 1 ◽  
Race 4 ◽  
On Farm ◽  
Farm Biosecurity ◽  
Ammonium Compounds

Panama disease caused by Fusarium oxysporum f. sp. cubense has devastated banana production worldwide. This work aimed to determine effective disinfectants against two races of F. oxysporum f. sp. cubense, race 1 and tropical race 4 (TR4), for implementation with on-farm biosecurity procedures against this disease following the outbreak of TR4 in North Queensland in 2015. A total of 32 commercial disinfectants were screened and their activity was assessed after ≤30 s, 5 min, 30 min, and 24 h of contact with an F. oxysporum f. sp. cubense suspension containing 105 chlamydospores/ml without and with soil added (0.05 g/ml). Of the disinfectants tested, the quaternary ammonium compounds containing ≥10% active ingredient were found to be the most effective against both F. oxysporum f. sp. cubense races. These products, when used at a 1:100 dilution, completely inhibited the survival of all F. oxysporum f. sp. cubense propagules across all the contact times regardless of the absence or presence of soil. The bioflavonoid product EvoTech 213 and bleach (10% sodium hypochlorite) used at a 1:10 dilution also eliminated all F. oxysporum f. sp. cubense propagules across all the contact times. None of the detergent-based or miscellaneous products tested were completely effective against both F. oxysporum f. sp. cubense races even used at a 1:10 dilution. Soil decreases the efficacy of disinfectants and therefore must be removed from contaminated items before treatments are applied.

scholarly journals Comparative Transcriptomic Analysis of Race 1 and Race 4 of Fusarium oxysporum f. sp. cubense Induced with Different Carbon Sources

2017 ◽  
Vol 7 (7) ◽  
pp. 2125-2138 ◽  
Author(s):  
Shiwen Qin ◽  
Chunyan Ji ◽  
Yunfeng Li ◽  
Zhenzhong Wang
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Fusarium Oxysporum ◽  
Host Cell ◽  
Expression Profiles ◽  
Cell Wall Polysaccharide ◽  
Host Cell Wall ◽  
Race 1 ◽  
Race 4 ◽  
Banana Cultivar

Abstract The fungal pathogen Fusarium oxysporum f. sp. cubense causes Fusarium wilt, one of the most destructive diseases in banana and plantain cultivars. Pathogenic race 1 attacks the “Gros Michel” banana cultivar, and race 4 is pathogenic to the Cavendish banana cultivar and those cultivars that are susceptible to Foc1. To understand the divergence in gene expression modules between the two races during degradation of the host cell wall, we performed RNA sequencing to compare the genome-wide transcriptional profiles of the two races grown in media containing banana cell wall, pectin, or glucose as the sole carbon source. Overall, the gene expression profiles of Foc1 and Foc4 in response to host cell wall or pectin appeared remarkably different. When grown with host cell wall, a much larger number of genes showed altered levels of expression in Foc4 in comparison with Foc1, including genes encoding carbohydrate-active enzymes (CAZymes) and other virulence-related genes. Additionally, the levels of gene expression were higher in Foc4 than in Foc1 when grown with host cell wall or pectin. Furthermore, a great majority of genes were differentially expressed in a variety-specific manner when induced by host cell wall or pectin. More specific CAZymes and other pathogenesis-related genes were expressed in Foc4 than in Foc1 when grown with host cell wall. The first transcriptome profiles obtained for Foc during degradation of the host cell wall may provide new insights into the mechanism of banana cell wall polysaccharide decomposition and the genetic basis of Foc host specificity.

scholarly journals Improving the Chromosome-Level Genome Assembly of the Siamese Fighting Fish (Betta splendens) in a University Master’s Course

2020 ◽  
Vol 10 (7) ◽  
pp. 2179-2183 ◽  
Author(s):  
Stefan Prost ◽  
Malte Petersen ◽  
Martin Grethlein ◽  
Sarah Joy Hahn ◽  
Nina Kuschik-Maczollek ◽  
...  
Keyword(s):  
Genome Assembly ◽  
High Throughput Sequencing ◽  
Siamese Fighting Fish ◽  
Betta Splendens ◽  
High Quality ◽  
Sequencing Platform ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Long Read ◽  
Chromosome Level

Ever decreasing costs along with advances in sequencing and library preparation technologies enable even small research groups to generate chromosome-level assemblies today. Here we report the generation of an improved chromosome-level assembly for the Siamese fighting fish (Betta splendens) that was carried out during a practical university master’s course. The Siamese fighting fish is a popular aquarium fish and an emerging model species for research on aggressive behavior. We updated the current genome assembly by generating a new long-read nanopore-based assembly with subsequent scaffolding to chromosome-level using previously published Hi-C data. The use of ∼35x nanopore-based long-read data sequenced on a MinION platform (Oxford Nanopore Technologies) allowed us to generate a baseline assembly of only 1,276 contigs with a contig N50 of 2.1 Mbp, and a total length of 441 Mbp. Scaffolding using the Hi-C data resulted in 109 scaffolds with a scaffold N50 of 20.7 Mbp. More than 99% of the assembly is comprised in 21 scaffolds. The assembly showed the presence of 96.1% complete BUSCO genes from the Actinopterygii dataset indicating a high quality of the assembly. We present an improved full chromosome-level assembly of the Siamese fighting fish generated during a university master’s course. The use of ∼35× long-read nanopore data drastically improved the baseline assembly in terms of continuity. We show that relatively in-expensive high-throughput sequencing technologies such as the long-read MinION sequencing platform can be used in educational settings allowing the students to gain practical skills in modern genomics and generate high quality results that benefit downstream research projects.

Characterisation of Strains of Fusarium oxysporum f.sp. cubense by Production of Volatiles

1991 ◽  
Vol 39 (2) ◽  
pp. 161 ◽  
Author(s):  
NY Moore ◽  
PA Hargreaves ◽  
KG Pegg ◽  
JAG Irwin
Keyword(s):  
Fusarium Oxysporum ◽  
Vegetative Compatibility ◽  
Vegetative Compatibility Group ◽  
Compatibility Group ◽  
Race 1 ◽  
Race 2 ◽  
Race 4

The production of volatiles on steamed rice by Australian isolates of Fusarium oxysporum f. sp. cubense correlated well with race and vegetative compatibility group (VCG). All race 4 isolates (VCGs 0120, 0129) produced distinctive volatile odours which gave characteristic gas chromatograms where the num- ber of peaks equated to VCG. Race 1 (VCGs 0124, 0125) and race 2 (VCG 0128) isolates, as well as non-pathogenic isolates of F. oxysporum from the banana rhizosphere, did not produce detectable volatiles and gave chromatograms without significant peaks.

scholarly journals LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Patrick Driguez ◽  
Salim Bougouffa ◽  
Karen Carty ◽  
Alexander Putra ◽  
Kamel Jabbari ◽  
...  
Keyword(s):  
De Novo ◽  
Plant Genome ◽  
Time Cost ◽  
Sequencing Technology ◽  
High Quality ◽  
Plant Genomes ◽  
Long Read ◽  
Generate Plant ◽  
Sequencing Platforms ◽  
Chromosome Level

AbstractCurrently, different sequencing platforms are used to generate plant genomes and no workflow has been properly developed to optimize time, cost, and assembly quality. We present LeafGo, a complete de novo plant genome workflow, that starts from tissue and produces genomes with modest laboratory and bioinformatic resources in approximately 7 days and using one long-read sequencing technology. LeafGo is optimized with ten different plant species, three of which are used to generate high-quality chromosome-level assemblies without any scaffolding technologies. Finally, we report the diploid genomes of Eucalyptus rudis and E. camaldulensis and the allotetraploid genome of Arachis hypogaea.

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