scholarly journals Identification of individual root-knot nematodes using low coverage long-read sequencing

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0253248
Author(s):  
Graham S. Sellers ◽  
Daniel C. Jeffares ◽  
Bex Lawson ◽  
Tom Prior ◽  
David H. Lunt
Keyword(s):  
Plant Pathogens ◽  
Low Cost ◽  
Hybrid Origin ◽  
Taxonomic Identification ◽  
Taxonomic Assignment ◽  
Root Knot Nematodes ◽  
Marker Loci ◽  
Long Read ◽  
Low Coverage ◽  
Individual Root

Root-knot nematodes (RKN; genus Meloidogyne) are polyphagous plant pathogens of great economic importance to agriculturalists globally. These species are small, diverse, and can be challenging for accurate taxonomic identification. Many of the most important crop pests confound analysis with simple genetic marker loci as they are polyploids of likely hybrid origin. Here we take a low-coverage, long-read genome sequencing approach to characterisation of individual root-knot nematodes. We demonstrate library preparation for Oxford Nanopore Technologies Flongle sequencing of low input DNA from individual juveniles and immature females, multiplexing up to twelve samples per flow cell. Taxonomic identification with Kraken 2 (a k-mer-based taxonomic assignment tool) is shown to reliably identify individual nematodes to species level, even within the very closely related Meloidogyne incognita group. Our approach forms a robust, low-cost, and scalable method for accurate RKN species diagnostics.

scholarly journals Genomic taxonomic assignment of individual root-knot nematodes

2021 ◽  
Author(s):  
Graham S Sellers ◽  
Daniel C Jeffares ◽  
Bex Lawson ◽  
Tom Prior ◽  
David H Lunt
Keyword(s):  
Plant Pathogens ◽  
Low Cost ◽  
Hybrid Origin ◽  
Taxonomic Identification ◽  
Taxonomic Assignment ◽  
Root Knot Nematodes ◽  
Oxford Nanopore ◽  
Marker Loci ◽  
Long Read ◽  
Individual Root

Root-knot nematodes (RKN; genus Meloidogyne) are polyphagous plant pathogens of great economic importance to agriculturalists globally. These species are small, diverse, and can be challenging for accurate taxonomic identification. Many of the most important crop pests confound analysis with simple genetic marker loci as they are polyploids of likely hybrid origin. Here we take a low-coverage, long-read genome sequencing approach to characterisation of individual root-knot nematodes. We demonstrate library preparation for Oxford Nanopore Technologies Flongle sequencing of low input DNA from individual juveniles and immature females, multiplexing up to twelve samples per flow cell. Taxonomic identification with Kraken 2 (a k-mer-based taxonomic assignment tool) is shown to reliably identify individual nematodes to species level, even within the very closely related Meloidogyne incognita group. Our approach forms a robust, low-cost, and scalable method for accurate RKN species diagnostics.

scholarly journals Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing

2018 ◽  
Vol 8 (10) ◽  
pp. 3143-3154 ◽  
Author(s):  
Edwin A. Solares ◽  
Mahul Chakraborty ◽  
Danny E. Miller ◽  
Shannon Kalsow ◽  
Kate Hall ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Reference Genome ◽  
Low Cost ◽  
Long Read ◽  
Low Coverage

The effect of ultra high-diluted drugs on plant-nematode interaction

2021 ◽  
Vol 14 (2) ◽  
pp. 09-10
Author(s):  
Natalia Rodiuc
Keyword(s):  
Plant Pathogens ◽  
Low Cost ◽  
Genetically Modified Crops ◽  
Root Knot Nematodes ◽  
Physiological Variability ◽  
Resistant Varieties ◽  
Plant Nematode ◽  
High Dilutions ◽  
Model Plant Arabidopsis Thaliana ◽  
Alternative Routes

Among plant pathogens, sedentary endoparasitic nematodes are one of the most damaging pests in global agriculture. Within this group, root-knot nematodes (RKN) Meloidogyne spp. is one of the most specialized phytoparasitic nematodes according to the complexity of the induced feeding sites. These phytopathogenic worms are highly resistant due to the large physiological variability, therefore difficult to fight against. The traditional methods of control, such as the crop rotation and the use of resistant varieties by classical selection are not always effective, time consuming and costly. The modern methods including the application of genetically modified crops (GMO), synthetic pesticides and bionematicides could be dangerous for human health and ecologically hazardous (Thomason, 1987; Malatesta et al. 2002a,b, 2008a,b; Spiroux de Vendômois et al., 2010; Seralini et al., 2012). Therefore, alternative routes must be taken in order to obtain plants resistant to nematodes. The ultra high dilutions (HDs) approach is largely in charge to dissect the infective process. HDs method is eco-friendly, low cost and leaves no residue in the environment. The classical phytopathological methods combined with modern microscopy approaches allowed to characterize the effect of different HD drugs on compatible interaction between model plant Arabidopsis thaliana and root-knot nematodes Meloidogyne incognita.

Nematode management through genome editing.

2021 ◽  
pp. 408-413
Author(s):  
Shahid Siddique ◽  
Sebastian Eves-van den Akker
Keyword(s):  
Rna Interference ◽  
Recent Progress ◽  
Plant Pathogens ◽  
Low Cost ◽  
Parasitic Nematodes ◽  
Plant Parasitic Nematodes ◽  
Cyst Nematodes ◽  
Root Knot Nematodes ◽  
Plant Parasitic

Abstract Plant parasitic nematodes are among the most destructive plant pathogens, causing an estimated US$78 billion yield losses globally. Although approximately 3000 species of plant parasitic nematodes have been described, most of the damage is caused by a small group of root-infecting sedentary endoparasitic nematodes that include root-knot nematodes (Meloidogyne spp.) and cyst nematodes (Heterodera spp.). Given that previous literature amply reviews the breadth of biotechnological methods for the control of plant parasitic nematodes, this chapter will briefly touch on long-standing biotechnological methods but focus on recent progress in, and long-term promise of, the use of CRISPR technology for introducing targeted modifications into host genomes with the goal of enhancing resistance against plant parasitic nematodes. It is predicted that expanding reverse genetic approaches beyond RNA interference, using low-cost, technically simple and efficient transformation (transient or stable) will be the single most important advance in the field in some years.

scholarly journals Pathogenicity and Volatile Nematicidal Metabolites from Duddingtonia flagrans against Meloidogyne incognita

2021 ◽  
Vol 9 (11) ◽  
pp. 2268
Author(s):  
Xiaoyu Mei ◽  
Xin Wang ◽  
Guohong Li
Keyword(s):  
Meloidogyne Incognita ◽  
Plant Pathogens ◽  
Plant Root ◽  
Nematicidal Activity ◽  
Mass Spectrometry Analysis ◽  
Gas Chromatography Mass Spectrometry ◽  
Egg Mass ◽  
Duddingtonia Flagrans ◽  
Egg Hatching ◽  
Root Knot Nematodes

Plant parasitic nematodes, especially parasitic root-knot nematodes, are one of the most destructive plant pathogens worldwide. The control of plant root-knot nematodes is extremely challenging. Duddingtonia flagrans is a type of nematode-trapping fungi (NTF), which produces three-dimensional adhesive networks to trap nematodes. In this study, the pathogenicity and volatile organic compounds (VOCs) of the NTF D. flagrans against the plant root-knot nematode, Meloidogyne incognita, were investigated. The predatory process of D. flagrans trapping M. incognita was observed using scanning electron microscopy. Gas chromatography-mass spectrometry analysis of the VOCs from D. flagrans led to the identification of 52 metabolites, of which 11 main compounds were tested individually for their activity against M. incognita. Three compounds, cyclohexanamine, cyclohexanone, and cyclohexanol, were toxic to M. incognita. Furthermore, these three VOCs inhibited egg hatching of M. incognita. Cyclohexanamine showed the highest nematicidal activity, which can cause 97.93% mortality of M. incognita at 8.71 µM within 12 h. The number of hatched juveniles per egg mass after 3 days was just 8.44 when treated with 26.14 µM cyclohexanamine. This study is the first to demonstrate the nematicidal activity of VOCs produced by D. flagrans against M. incognita, which indicates that D. flagrans has the potential to biocontrol plant root-knot nematodes.

scholarly journals DNA Preparation In Vitis Vinifera L. for Third Generation Sequencing

2021 ◽  
Author(s):  
Androniki C. Bibi ◽  
Anastasios Kollias ◽  
Maria Astrinaki ◽  
Despoina Vassou ◽  
Dimitris Kafetzopoulos ◽  
...  
Keyword(s):  
Vitis Vinifera ◽  
Low Cost ◽  
Ease Of Use ◽  
Vitis Vinifera L ◽  
Full Potential ◽  
Third Generation ◽  
High Quality ◽  
Fresh Tissue ◽  
Long Read ◽  
Young Leaves

Abstract Background: There have been several attempts to sequence the genome of Vitis vinifera L. (grapevine), utilizing low-resolution second-generation platforms. Nevertheless, the characterization of the grapevine genetic resources and its adaptation to vulnerable conditions could be better addressed through extensive and high-resolution genome sequencing.MinION is a third-generation sequencer preferred by many laboratories due to its relatively low cost, ease of use and small size. Even though this long-read technology has been rapidly improving, to reach its full potential requires high-quality DNA.Results: Here we establish a workflow for DNA extraction suitable for MinION sequencing long reads from grapevine. This protocol was tested with leaf samples from different positions on annual growing branches of grapevine, Purified nuclei from fresh young leaves that led to high quality, long DNA fragments, suitable for long-read sequencing were successfully generated. It is evident that longer reads in grapevine associate with both fresh tissue and adjusted conditions used for nuclei purification.Conclusions: We propose that this workflow presents a significant advancement for long-read quality DNA isolation for grapevine and likely other plant species.

scholarly journals Genome Resources for the Ex-type of Phytophthora citricola, and well-authenticated isolates of P. hibernalis, P. nicotianae and P. syringae

2021 ◽  
Author(s):  
Subodh K. Srivastava ◽  
Leandra M. Knight ◽  
Mark K. Nakhla ◽  
Z. Gloria Abad
Keyword(s):  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Economic Losses ◽  
Biological Research ◽  
Type Specimens ◽  
High Coverage ◽  
Oxford Nanopore ◽  
Long Read ◽  
Basic And Applied Research ◽  
Diagnostic Applications

Phytophthora is one of the most important genera of plant pathogens with many members causing high economic losses world-wide. To build robust molecular identification systems, it is very important to have information from well-authenticated specimens and in preference the ex-type specimens. The reference genomes of well-authenticated specimens form a critical foundation for genetics, biological research, and diagnostic applications. In this study, we describe four draft Phytophthora genomes resources for the Ex-type of P. citricola BL34 (P0716 WPC) (118 contigs for 50 Mb), and well-authenticated specimens of P. syringae BL57G (P10330 WPC) (591 contigs for 75 Mb), P. hibernalis BL41G (P3822 WPC) (404 contigs for 84 Mb), and P. nicotianae BL162 (P6303 WPC) (3984 contigs for 108 Mb) generated with MinION long-read High-Throughput Sequencing (HTS) technology (Oxford Nanopore Technologies, ONT). Using the quality reads we assembled high coverage genomes of P. citricola with 291X coverage and 16,662 annotated genes; P. nicotianae with 205X coverage and 29,271 annotated genes; P. syringae with 76X coverage and 23,331 annotated genes, and P. hibernalis with 42X coverage and 21,762 annotated genes. With the availability of genomes sequences and its annotations, we predict that these draft genomes will be accommodating for various basic and applied research including diagnostics to protect global agriculture.

scholarly journals Assessment of Imputation from Low-Pass Sequencing to Predict Merit of Beef Steers

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1312
Author(s):  
Warren M. Snelling ◽  
Jesse L. Hoff ◽  
Jeremiah H. Li ◽  
Larry A. Kuehn ◽  
Brittney N. Keel ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Genomic Sequence ◽  
Bos Taurus ◽  
Low Cost ◽  
Bos Indicus ◽  
Snp Array ◽  
Attractive Alternative ◽  
Functional Variant ◽  
Low Pass ◽  
Low Coverage

Decreasing costs are making low coverage sequencing with imputation to a comprehensive reference panel an attractive alternative to obtain functional variant genotypes that can increase the accuracy of genomic prediction. To assess the potential of low-pass sequencing, genomic sequence of 77 steers sequenced to >10X coverage was downsampled to 1X and imputed to a reference of 946 cattle representing multiple Bos taurus and Bos indicus-influenced breeds. Genotypes for nearly 60 million variants detected in the reference were imputed from the downsampled sequence. The imputed genotypes strongly agreed with the SNP array genotypes (r¯=0.99) and the genotypes called from the transcript sequence (r¯=0.97). Effects of BovineSNP50 and GGP-F250 variants on birth weight, postweaning gain, and marbling were solved without the steers’ phenotypes and genotypes, then applied to their genotypes, to predict the molecular breeding values (MBV). The steers’ MBV were similar when using imputed and array genotypes. Replacing array variants with functional sequence variants might allow more robust MBV. Imputation from low coverage sequence offers a viable, low-cost approach to obtain functional variant genotypes that could improve genomic prediction.

scholarly journals Spectral Grouping of Nominally Aspergillus versicolor Microbial-Collection Deposits by MALDI-TOF MS

2019 ◽  
Vol 7 (8) ◽  
pp. 235
Author(s):  
Reeve ◽  
Caine ◽  
Buddie
Keyword(s):  
Low Cost ◽  
Resolving Power ◽  
Indoor Environments ◽  
Aspergillus Versicolor ◽  
Taxonomic Assignment ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Resource Collection ◽  
Tof Ms

Historical microbial collections often contain samples that have been deposited over extended time periods, during which accepted taxonomic classification (and also available methods for taxonomic assignment) may have changed considerably. Deposited samples can, therefore, have historical taxonomic assignments (HTAs) that may now be in need of revision, and subdivisions of previously-accepted taxa may also be possible with the aid of current methodologies. One such methodology is matrix-assisted laser-desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS). Motivated by the high discriminating power of MALDI-TOF MS coupled with the speed and low cost of the method, we have investigated the use of MALDI-TOF MS for spectral grouping of past deposits made to the Centre for Agriculture and Bioscience International (CABI) Genetic Resource Collection under the HTA Aspergillus versicolor, a common ascomycete fungus frequently associated with soil and plant material, food spoilage, and damp indoor environments. Despite their common HTA, the 40 deposits analyzed in this study fall into six clear spectral-linkage groups (containing nine, four, four, four, four, and two members, respectively), along with a group of ten spectrally-unique samples. This study demonstrates the clear resolving power of MALDI-TOF MS when applied to samples deposited in historical microbial collections.

scholarly journals An Optimized Microsatellite Scheme for Assessing Populations of Xanthomonas phaseoli pv. manihotis

2019 ◽  
Vol 109 (5) ◽  
pp. 859-869
Author(s):  
Leidy Rache ◽  
Laurence Blondin ◽  
Carolina Flores ◽  
Cesar Trujillo ◽  
Boris Szurek ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Tandem Repeat ◽  
Plant Pathogens ◽  
Low Cost ◽  
Accurate Determination ◽  
Variable Number ◽  
Local Scale ◽  
Caribbean Region ◽  
Fast Method ◽  
Cassava Bacterial Blight

Diverse molecular markers have been used to analyze the genetic diversity of plant pathogens. Compared with traditional fingerprinting methods, multiple loci variable number of tandem repeat analyses (MLVAs) have gained importance recently due to their reproducibility, high discriminatory power, ease of performance, low cost, and throughput potential. These characteristics are desirable for continuous pathogen monitoring, especially for pathogens with relatively low genetic diversity, and for disease epidemiology studies. Genetic diversity studies of Xanthomonas phaseoli pv. manihotis, which is the causal agent of cassava bacterial blight, have shown variability and changes in the bacterial population over time. Thus, an easy and fast method needs to be developed to type populations of this pathogen in different countries of the world, especially on small scales. In this study, we developed an MLVA scheme to analyze X. phaseoli pv. manihotis variability on a local scale. The MLVA-15 scheme comprises 15 variable number of tandem repeat loci grouped into four multiplex polymerase chain reaction pools. We showed that the MLVA-15 scheme had slightly higher discriminatory ability at the locality level when compared with amplified fragment length polymorphisms. The MLVA-15 scheme allowed for an accurate determination of the number of genotypes in the sample and showed reproducibility and portability. Additionally, this scheme could be used to analyze numerous strains in a reasonable timeframe. The MLVA-15 scheme was highly specific to X. phaseoli but up to eight tandem repeat loci could be amplified from other Xanthomonas spp. Finally, we assessed the utility of the scheme for analyses of X. phaseoli pv. manihotis genetic variability in the Colombian Caribbean region. MLVA-15 distinguished 88.9% of the haplotypes in our sample. Strains originating from the same field and isolated at the same time could be discriminated. In this study, the advantages of the MLVA-15 scheme targeting 6- or 7-bp repeats were demonstrated. Moreover, this scheme was a fast method that was appropriate for routine monitoring of X. phaseoli pv. manihotis populations on a local scale and, thus, was useful for addressing epidemiological questions.

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