scholarly journals Complete Genomic Characterization and Identification of Saccharomycopsisphalluae sp. nov., a Novel Pathogen Causes Yellow Rot Disease on Phallus rubrovolvatus

2021 ◽  
Vol 7 (9) ◽  
pp. 707
Author(s):  
Xiaoxiao Yuan ◽  
Keqin Peng ◽  
Changtian Li ◽  
Zhibo Zhao ◽  
Xiangyu Zeng ◽  
...  
Keyword(s):  
Single Molecule ◽  
De Novo ◽  
Severe Disease ◽  
Management Strategies ◽  
Control Measures ◽  
Guizhou Province ◽  
Effective Control ◽  
Economic Losses ◽  
Protein Coding ◽  
Rot Disease

“Hongtuozhusun” (Phallus rubrovolvatus) is an important edible and medicinal mushroom endemic to Southwest China. However, yellow rot disease is a severe disease of P. rubrovolvatus that occurs extensively in Guizhou Province. It has caused major economic losses and hinders the development of the P. rubrovolvatus industry. In this study, 28 microorganism strains were isolated from diseased fruiting bodies of P. rubrovolvatus at various stages, two of which were confirmed to be pathogenic based on Koch’s postulates. These two strains are introduced herein as Saccharomycopsisphalluae sp. nov. based on morphological, physiological, and molecular analysis. We reported a high-quality de novo sequencing and assembly of the S. phalluae genome using single-molecule real-time sequencing technology. The whole genome was approximately 14.148 Mb with a G+C content of 43.55%. Genome assembly generated 8 contigs with an N50 length of 1,822,654 bp. The genome comprised 5966 annotated protein-coding genes. This is the first report of mushroom disease caused by Saccharomycopsis species. We expect that the information on genome properties, particularly in pathogenicity-related genes, assist in developing effective control measures in order to prevent severe losses and make amendments in management strategies.

scholarly journals Genome sequence, transcriptome, and annotation of rodent malaria parasite Plasmodium yoelii nigeriensis N67

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cui Zhang ◽  
Cihan Oguz ◽  
Sue Huse ◽  
Lu Xia ◽  
Jian Wu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Malaria Parasite ◽  
Vaccine Development ◽  
De Novo ◽  
Gene Families ◽  
Plasmodium Yoelii ◽  
Control Measures ◽  
Effective Control ◽  
Malaria Parasites ◽  
Rodent Malaria

Abstract Background Rodent malaria parasites are important models for studying host-malaria parasite interactions such as host immune response, mechanisms of parasite evasion of host killing, and vaccine development. One of the rodent malaria parasites is Plasmodium yoelii, and multiple P. yoelii strains or subspecies that cause different disease phenotypes have been widely employed in various studies. The genomes and transcriptomes of several P. yoelii strains have been analyzed and annotated, including the lethal strains of P. y. yoelii YM (or 17XL) and non-lethal strains of P. y. yoelii 17XNL/17X. Genomic DNA sequences and cDNA reads from another subspecies P. y. nigeriensis N67 have been reported for studies of genetic polymorphisms and parasite response to drugs, but its genome has not been assembled and annotated. Results We performed genome sequencing of the N67 parasite using the PacBio long-read sequencing technology, de novo assembled its genome and transcriptome, and predicted 5383 genes with high overall annotation quality. Comparison of the annotated genome of the N67 parasite with those of YM and 17X parasites revealed a set of genes with N67-specific orthology, expansion of gene families, particularly the homologs of the Plasmodium chabaudi erythrocyte membrane antigen, large numbers of SNPs and indels, and proteins predicted to interact with host immune responses based on their functional domains. Conclusions The genomes of N67 and 17X parasites are highly diverse, having approximately one polymorphic site per 50 base pairs of DNA. The annotated N67 genome and transcriptome provide searchable databases for fast retrieval of genes and proteins, which will greatly facilitate our efforts in studying the parasite biology and gene function and in developing effective control measures against malaria.

scholarly journals Genomic Analysis of Sarcomyxa edulis Reveals the Basis of Its Medicinal Properties and Evolutionary Relationships

2021 ◽  
Vol 12 ◽  
Author(s):  
Fenghua Tian ◽  
Changtian Li ◽  
Yu Li
Keyword(s):  
Single Molecule ◽  
De Novo ◽  
Genomic Analysis ◽  
Single Copy ◽  
Whole Genome Sequence ◽  
Type I ◽  
Whole Genome ◽  
Uridine Diphosphate ◽  
Protein Coding ◽  
Medicinal Value

Yuanmo [Sarcomyxa edulis (Y.C. Dai, Niemelä & G.F. Qin) T. Saito, Tonouchi & T. Harada] is an important edible and medicinal mushroom endemic to Northeastern China. Here we report the de novo sequencing and assembly of the S. edulis genome using single-molecule real-time sequencing technology. The whole genome was approximately 35.65 Mb, with a G + C content of 48.31%. Genome assembly generated 41 contigs with an N50 length of 1,772,559 bp. The genome comprised 9,364 annotated protein-coding genes, many of which encoded enzymes involved in the modification, biosynthesis, and degradation of glycoconjugates and carbohydrates or enzymes predicted to be involved in the biosynthesis of secondary metabolites such as terpene, type I polyketide, siderophore, and fatty acids, which are responsible for the pharmacodynamic activities of S. edulis. We also identified genes encoding 1,3-β-glucan synthase and endo-1,3(4)-β-glucanase, which are involved in polysaccharide and uridine diphosphate glucose biosynthesis. Phylogenetic and comparative analyses of Basidiomycota fungi based on a single-copy orthologous protein indicated that the Sarcomyxa genus is an independent group that evolved from the Pleurotaceae family. The annotated whole-genome sequence of S. edulis can serve as a reference for investigations of bioactive compounds with medicinal value and the development and commercial production of superior S. edulis varieties.

scholarly journals The sequencing and de novo assembly of the Larimichthys crocea genome using PacBio and Hi-C technologies

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Baohua Chen ◽  
Zhixiong Zhou ◽  
Qiaozhen Ke ◽  
Yidi Wu ◽  
Huaqiang Bai ◽  
...  
Keyword(s):  
Marine Fish ◽  
Single Molecule ◽  
Large Scale ◽  
Reference Genome ◽  
De Novo ◽  
Larimichthys Crocea ◽  
Chromosome Conformation ◽  
Protein Coding ◽  
Total Length ◽  
Chromosome Level

Abstract Larimichthys crocea is an endemic marine fish in East Asia that belongs to Sciaenidae in Perciformes. L. crocea has now been recognized as an “iconic” marine fish species in China because not only is it a popular food fish in China, it is a representative victim of overfishing and still provides high value fish products supported by the modern large-scale mariculture industry. Here, we report a chromosome-level reference genome of L. crocea generated by employing the PacBio single molecule sequencing technique (SMRT) and high-throughput chromosome conformation capture (Hi-C) technologies. The genome sequences were assembled into 1,591 contigs with a total length of 723.86 Mb and a contig N50 length of 2.83 Mb. After chromosome-level scaffolding, 24 scaffolds were constructed with a total length of 668.67 Mb (92.48% of the total length). Genome annotation identified 23,657 protein-coding genes and 7262 ncRNAs. This highly accurate, chromosome-level reference genome of L. crocea provides an essential genome resource to support the development of genome-scale selective breeding and restocking strategies of L. crocea.

scholarly journals De novo assembly of the cattle reference genome with single-molecule sequencing

GigaScience ◽  
2020 ◽  
Vol 9 (3) ◽  
Author(s):  
Benjamin D Rosen ◽  
Derek M Bickhart ◽  
Robert D Schnabel ◽  
Sergey Koren ◽  
Christine G Elsik ◽  
...  
Keyword(s):  
Single Molecule ◽  
De Novo Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Bos Taurus ◽  
Future Research ◽  
Protein Coding ◽  
Single Molecule Sequencing ◽  
Assembly Accuracy ◽  
Genomic Tools

Abstract Background Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10–12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. Results We present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use. Conclusions We demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species.

scholarly journals Verticillium Wilt of Olive and Its Control: What Did We Learn during the Last Decade?

Plants ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 735 ◽  
Author(s):  
Nuria Montes-Osuna ◽  
Jesús Mercado-Blanco
Keyword(s):  
Integrated Management ◽  
Management Strategies ◽  
Control Measures ◽  
Effective Control ◽  
Soil Biology ◽  
Pests And Diseases ◽  
Sensing Technology ◽  
Olive Cultivation ◽  
Underlying Mechanisms ◽  
The Impact

Verticillium (Verticillium dahliae Kleb.) wilt is one of the most devastating diseases affecting olive (Olea europaea L. subsp. europaea var. europaea) cultivation. Its effective control strongly relies on integrated management strategies. Olive cultivation systems are experiencing important changes (e.g., high-density orchards, etc.) aiming at improving productivity. The impact of these changes on soil biology and the incidence/severity of olive pests and diseases has not yet been sufficiently evaluated. A comprehensive understanding of the biology of the pathogen and its populations, the epidemiological factors contributing to exacerbating the disease, the underlying mechanisms of tolerance/resistance, and the involvement of the olive-associated microbiota in the tree’s health is needed. This knowledge will be instrumental to developing more effective control measures to confront the disease in regions where the pathogen is present, or to exclude it from V. dahliae-free areas. This review compiles the most recent advances achieved to understand the olive–V. dahliae interaction as well as measures to control the disease. Aspects such as the molecular basis of the host–pathogen interaction, the identification of new biocontrol agents, the implementation of “-omics” approaches to unravel the basis of disease tolerance, and the utilization of remote sensing technology for the early detection of pathogen attacks are highlighted.

scholarly journals De Novo Whole-Genome Sequencing of the Wood Rot Fungus Polyporus brumalis, Which Exhibits Potential Terpenoid Metabolism

2017 ◽  
Vol 5 (28) ◽  
Author(s):  
Su-Yeon Lee ◽  
Ji-eun An ◽  
Sun-Hwa Ryu ◽  
Myungkil Kim
Keyword(s):  
Single Molecule ◽  
De Novo ◽  
Gene Annotation ◽  
Draft Genome ◽  
Fungal Growth ◽  
Protein Coding ◽  
Sequencing Platform ◽  
Protein Coding Genes ◽  
Polyporus Brumalis ◽  
Terpenoid Metabolism

ABSTRACT Polyporus brumalis is able to synthesize several sesquiterpenes during fungal growth. Using a single-molecule real-time sequencing platform, we present the 53-Mb draft genome of P. brumalis, which contains 6,231 protein-coding genes. Gene annotation and isolation support genetic information, which can increase the understanding of sesquiterpene metabolism in P. brumalis.

scholarly journals The presence of bacterial stalk rot disease on corn in Indonesia: A review

2021 ◽  
Vol 911 (1) ◽  
pp. 012058
Author(s):  
Suriani ◽  
Baharuddin Patandjengi ◽  
Muh. Junaid ◽  
Amran Muis
Keyword(s):  
Pathogenic Bacteria ◽  
Aloe Vera ◽  
Control Measures ◽  
Economic Losses ◽  
Maize Production ◽  
Stalk Rot ◽  
Efficient Control ◽  
Quarantine Station ◽  
Rot Disease ◽  
The Impact

Abstract Bacterial stalk rot disease in corn results in a significant reduction in yield due to the interruption of the flow of nutrients from the roots to other parts of the plant. Pathogenic bacteria infect the inner tissue of the stalk until it rots. This disease has been reported to attack corn crops in Asia and Europe such as India, Korea, Thailand, Philippines, Nepal, Mexico, Serbia, and China. In Indonesia, this disease was first reported to attack corn in the West Sulawesi region by the Mamuju Class II Quarantine Station. The results of molecular identification indicated that this disease is caused by the bacterium Dickeya zeae, previously known as Erwinia chrysanthemi pv. zeae that previously reported attacked pineapple and aloe vera in Indonesia. The potential for economic losses due to this disease is quite high, so appropriate and efficient control measures are needed. Based on those, this research study about the symptom, the characteristic of the bacteria agent caused the stalk rot disease, the distribution and the impact to the maize production in Indonesia.

scholarly journals MYCOPLASMA SYNOVIAE INFECTION IN LAYERS: DIAGNOSIS AND CONTROL MEASURES – A REVIEW

2019 ◽  
Vol 12 (2) ◽  
pp. 63-82
Author(s):  
Khaled Kaboudi ◽  
Adem Jbenyeni
Keyword(s):  
Immune System ◽  
Egg Quality ◽  
Severe Disease ◽  
Control Measures ◽  
Economic Losses ◽  
Mycoplasma Synoviae ◽  
Important Species ◽  
Emergent Pathogen ◽  
Breeding Farms ◽  
And Control

Mycoplasmas are widespread bacteria in domestic and wild birds. Among the important species in laying hen, Mycoplasma gallisepticum and Mycoplasma synoviae, are considered as an emergent pathogen in the last few years worldwide, causing considerable economic losses as a result of falling eggs and the decrease in egg quality. Transmission of M. synoviae occurs horizontally, more rapidly in multi-age sites, and vertically, leading to a decline in hatchability in breeding farms. The interaction between M. synoviae and the host’s immune system explains the immunosuppression induced by this pathogen. Inside the cell, M. synoviae can escape the immune system by implementing several mechanisms.Subclinical respiratory infection is oft en associated to M. synoviae. However, severe disease may be observed in the presence of other factors (respiratory viruses, stressors). The emergence of a new form of clinical manifestation of disease associated to M. synoviae infection has been described since the 2000s. Eggshell apex abnormalities of the produced eggs, associated to high risk of cracks and breakage, is described.The diagnosis of M. synoviae infection is based on various tests, including serology, culture and biomolecular methods. Control is based on theacquisition of free mycoplasma birds, biosecurity, regular monitoring and vaccination. Management of other risk factors is essential.

scholarly journals The chromosome-level draft genome of Dalbergia odorifera

GigaScience ◽  
2020 ◽  
Vol 9 (8) ◽  
Author(s):  
Zhou Hong ◽  
Jiang Li ◽  
Xiaojin Liu ◽  
Jinmin Lian ◽  
Ningnan Zhang ◽  
...  
Keyword(s):  
Single Molecule ◽  
De Novo ◽  
Populus Trichocarpa ◽  
Draft Genome ◽  
Heartwood Formation ◽  
Genetic Studies ◽  
Protein Coding ◽  
Dalbergia Odorifera ◽  
Paired End Sequencing ◽  
Chromosome Level

Abstract Background Dalbergia odorifera T. Chen (Fabaceae) is an International Union for Conservation of Nature red-listed tree. This tree is of high medicinal and commercial value owing to its officinal, insect-proof, durable heartwood. However, there is a lack of genome reference, which has hindered development of studies on the heartwood formation. Findings We presented the first chromosome-scale genome assembly of D. odorifera obtained on the basis of Illumina paired-end sequencing, Pacific Biosciences single-molecule real-time sequencing, 10x Genomics linked reads, and Hi-C technology. We assembled 97.68% of the 653.45 Mb D. odorifera genome with scaffold N50 and contig sizes of 56.16 and 5.92 Mb, respectively. Ten super-scaffolds corresponding to the 10 chromosomes were assembled, with the longest scaffold reaching 79.61 Mb. Repetitive elements account for 54.17% of the genome, and 30,310 protein-coding genes were predicted from the genome, of which ∼92.6% were functionally annotated. The phylogenetic tree showed that D. odorifera diverged from the ancestor of Arabidopsis thaliana and Populus trichocarpa and then separated from Glycine max and Cajanus cajan. Conclusions We sequence and reveal the first chromosome-level de novo genome of D. odorifera. These studies provide valuable genomic resources for the research of heartwood formation in D. odorifera and other timber trees. The high-quality assembled genome can also be used as reference for comparative genomics analysis and future population genetic studies of D. odorifera.

scholarly journals Impact of viral features, host jumps and phylogeography on the rapid evolution of Aleutian mink disease virus (AMDV)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Giovanni Franzo ◽  
Matteo Legnardi ◽  
Laura Grassi ◽  
Giorgia Dotto ◽  
Michele Drigo ◽  
...  
Keyword(s):  
Disease Virus ◽  
Rapid Evolution ◽  
Global Scale ◽  
Control Measures ◽  
Viral Population ◽  
Effective Control ◽  
Economic Losses ◽  
Aleutian Mink Disease Virus ◽  
Different Populations

AbstractAleutian mink disease virus (AMDV) is one the most relevant pathogens of domestic mink, where it can cause significant economic losses, and wild species, which are considered a threat to mink farms. Despite their relevance, many aspects of the origin, evolution, and geographic and host spreading patterns of AMDV have never been investigated on a global scale using a comprehensive biostatistical approach. The present study, benefitting from a large dataset of sequences collected worldwide and several phylodynamic-based approaches, demonstrates the ancient origin of AMDV and its broad, unconstrained circulation from the initial intercontinental spread to the massive among-country circulation, especially within Europe, combined with local persistence and evolution. Clear expansion of the viral population size occurred over time until more effective control measures started to be applied. The role of frequent changes in epidemiological niches, including different hosts, in driving the high nucleotide and amino acid evolutionary rates was also explored by comparing the strengths of selective pressures acting on different populations. The obtained results suggest that the viral passage among locations and between wild and domesticated animals poses a double threat to farm profitability and animal welfare and health, which is particularly relevant for endangered species. Therefore, further efforts must be made to limit viral circulation and to refine our knowledge of factors enhancing AMDV spread, particularly at the wild-domestic interface.

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