scholarly journals Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce's disease

2021 ◽  
Author(s):  
Cassandra L Ettinger ◽  
Frank J Byrne ◽  
Matthew A Collin ◽  
Derreck Carter-House ◽  
Linda L Walling ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Assembly ◽  
Reference Genome ◽  
Whole Genome Sequence ◽  
Pierce's Disease ◽  
Future Research ◽  
Marker Genes ◽  
Trna Genes ◽  
Homalodisca Vitripennis ◽  
Pierce’S Disease

Abstract Homalodisca vitripennis (Hemiptera: Cicadellidae), known as the glassy-winged sharpshooter, is a xylem feeding leafhopper and an important agricultural pest as a vector of Xylella fastidiosa, which causes Pierce’s disease in grapes and a variety of other scorch diseases. The current H. vitripennis reference genome from the Baylor College of Medicine's i5k pilot project is a 1.4-Gb assembly with 110,000 scaffolds, which still has significant gaps making identification of genes difficult. To improve on this effort, we used a combination of Oxford Nanopore long-read sequencing technology combined with Illumina sequencing reads to generate a better assembly and first-pass annotation of the whole genome sequence of a wild-caught Californian (Tulare County) individual of H. vitripennis. The improved reference genome assembly for H. vitripennis is 1.93-Gb in length (21,254 scaffolds, N50 = 650 Mb, BUSCO completeness = 94.3%), with 33.06% of the genome masked as repetitive. In total, 108,762 gene models were predicted including 98,296 protein-coding genes and 10,466 tRNA genes. As an additional community resource, we identified 27 orthologous candidate genes of interest for future experimental work including phenotypic marker genes like white. Further, as part of the assembly process, we generated four endosymbiont metagenome-assembled genomes (MAGs), including a high-quality near complete 1.7-Mb Wolbachia sp. genome (1 scaffold, CheckM completeness = 99.4%). The improved genome assembly and annotation for H. vitripennis, curated set of candidate genes, and endosymbiont MAGs will be invaluable resources for future research of H. vitripennis.

scholarly journals Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce's disease

2021 ◽  
Author(s):  
Cassandra L Ettinger ◽  
Frank J Byrne ◽  
Matthew A Collin ◽  
Derreck Carter-House ◽  
Linda L Walling ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Assembly ◽  
Reference Genome ◽  
Whole Genome Sequence ◽  
Pierce's Disease ◽  
Future Research ◽  
Marker Genes ◽  
Trna Genes ◽  
Homalodisca Vitripennis ◽  
Pierce’S Disease

Homalodisca vitripennis (Hemiptera: Cicadellidae), known as the glassy-winged sharpshooter, is a xylem feeding leafhopper and an important agricultural pest as a vector of Xylella fastidiosa, which causes Pierce's disease in grapes and a variety of other scorch diseases. The current H. vitripennis reference genome from the Baylor College of Medicine's i5k pilot project is a 1.4-Gb assembly with 110,000 scaffolds, which still has significant gaps making identification of genes difficult. To improve on this effort, we used a combination of Oxford Nanopore long-read sequencing technology combined with Illumina sequencing reads to generate a better assembly and first-pass annotation of the whole genome sequence of a wild-caught Californian (Tulare County) individual of H. vitripennis. The improved reference genome assembly for H. vitripennis is 1.93 Gb in length (21,254 scaffolds, N50 = 650 Mb, BUSCO completeness = 94.3%), with 33.06% of the genome masked as repetitive. In total, 108,762 gene models were predicted including 98,296 protein-coding genes and 10,466 tRNA genes. As an additional community resource, we identified 27 orthologous candidate genes of interest for future experimental work including phenotypic marker genes like white. Further, as part of the assembly process, we generated four endosymbiont metagenome-assembled genomes (MAGs), including a high-quality near complete 1.7-Mb Wolbachia sp. genome (1 scaffold, CheckM completeness = 99.4%). The improved genome assembly and annotation for H. vitripennis, curated set of candidate genes, and endosymbiont MAGs will be invaluable resources for future research of H. vitripennis.

scholarly journals Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveals expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions

2021 ◽  
pp. gr.275325.121
Author(s):  
Rodrigo P. Baptista ◽  
Yiran Li ◽  
Adam Sateriale ◽  
Karen L. Brooks ◽  
Alan Tracey ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
Diarrheal Disease ◽  
Gene Copy ◽  
Future Research ◽  
Single Nucleotide Variants ◽  
Cryptosporidium Hominis ◽  
Entire Chromosome ◽  
Long Read ◽  
Subtelomeric Regions

Cryptosporidiosis is a leading cause of waterborne diarrheal disease globally and an important contributor to mortality in infants and the immunosuppressed. Despite its importance, the Cryptosporidium community has only had access to a good, but incomplete, Cryptosporidium parvum IOWA reference genome sequence. Incomplete reference sequences hamper annotation, experimental design and interpretation. We have generated a new C. parvum IOWA genome assembly supported by PacBio and Oxford Nanopore long-read technologies and a new comparative and consistent genome annotation for three closely related species C. parvum, Cryptosporidium hominis and Cryptosporidium tyzzeri. We made 1,926 C. parvum annotation updates based on experimental evidence. They include new transporters, ncRNAs, introns and altered gene structures. The new assembly and annotation revealed a complete Dnmt2 methylase ortholog. Comparative annotation between C. parvum, C. hominis and C. tyzzeri revealed that most "missing" orthologs are found suggesting that the biological differences between the species must result from gene copy number variation, differences in gene regulation and single nucleotide variants (SNVs). Using the new assembly and annotation as reference, 190 genes are identified as evolving under positive selection, including many not detected previously. The new C. parvum IOWA reference genome assembly is larger, gap free and lacks ambiguous bases. This chromosomal assembly recovers all 16 chromosome ends, 13 of which are contiguously assembled. The three remaining chromosome ends are provisionally placed. These ends represent duplication of entire chromosome ends including subtelomeric regions revealing a new level of genome plasticity that will both inform and impact future research.

scholarly journals Draft Genome Resources of Two Strains of Xylella fastidiosa XYL1732/17 and XYL2055/17 Isolated from Mallorca Vineyards

2019 ◽  
Vol 109 (2) ◽  
pp. 222-224 ◽  
Author(s):  
Margarita Gomila ◽  
Eduardo Moralejo ◽  
Antonio Busquets ◽  
Guillem Segui ◽  
Diego Olmo ◽  
...  
Keyword(s):  
De Novo ◽  
Xylella Fastidiosa ◽  
Draft Genome ◽  
Open Reading Frames ◽  
Pierce's Disease ◽  
Trna Genes ◽  
The European Union ◽  
Disease Symptoms ◽  
Pierce’S Disease ◽  
Reading Frames

Xylella fastidiosa is a plant-pathogenic bacterium that causes serious diseases in many crops of economic importance and is a quarantine organism in the European Union. This study reports a de novo-assembled draft genome sequence of the first isolates causing Pierce’s disease in Europe: X. fastidiosa subsp. fastidiosa strains XYL1732/17 and XYL2055/17. Both strains were isolated from grapevines (Vitis vinifera) showing Pierce’s disease symptoms at two different locations in Mallorca, Spain. The XYL1732/17 genome is 2,444,109 bp long, with a G+C content of 51.5%; it contains 2,359 open reading frames and 48 tRNA genes. The XYL2055/17 genome is 2,456,780 bp long, with a G+C content of 51.5%; it contains 2,384 open reading frames and 48 tRNA genes.

scholarly journals Infection of Blueberry Cultivar ‘Emerald’ with a California Pierce’s Disease Strain of Xylella fastidiosa and Acquisition by Glassy-Winged Sharpshooter

Plant Disease ◽  
2020 ◽  
Vol 104 (1) ◽  
pp. 154-160
Author(s):  
Lindsey P. Burbank ◽  
Mark S. Sisterson ◽  
Michael L. O’Leary
Keyword(s):  
United States ◽  
Xylella Fastidiosa ◽  
Southeastern United States ◽  
San Joaquin Valley ◽  
Pierce's Disease ◽  
Highbush Blueberry ◽  
Homalodisca Vitripennis ◽  
Pierce’S Disease ◽  
Fastidiosa Strain ◽  
Southern Highbush

Bacterial leaf scorch disease caused by Xylella fastidiosa occurs in southern highbush blueberry varieties in the southeastern United States. Susceptibility to X. fastidiosa varies by blueberry cultivar, and these interactions are often strain-specific. Xylella fastidiosa subsp. fastidiosa is the causal agent of Pierce’s disease in grapevines, and it has been problematic in the San Joaquin Valley of California since the introduction of the glassy-winged sharpshooter (Homalodisca vitripennis). The glassy-winged sharpshooter is known to feed on blueberry, a crop that is expanding in the San Joaquin Valley. Currently, little is known about the potential for the spread of X. fastidiosa between grape and blueberry in this region. The ability of a Pierce’s disease strain of X. fastidiosa from the San Joaquin Valley to cause disease in southern highbush blueberry and the potential for the glassy-winged sharpshooter to transmit X. fastidiosa between blueberry and grapevine were investigated. Experimental inoculations showed that the X. fastidiosa subsp. fastidiosa strain Bakersfield-1 can cause disease in blueberry cv. Emerald, and that the glassy-winged sharpshooter can acquire X. fastidiosa from artificially inoculated blueberry plants under laboratory conditions. Understanding the possibility for X. fastidiosa strains from the San Joaquin Valley to infect multiple crops grown in proximity is important for area-wide pest and disease management.

scholarly journals Glassy-Winged Sharpshooter (suggested common name), Homalodisca coagulata (Say) (Insecta: Hemiptera: Cicadellidae: Cicadellinae)

EDIS ◽  
1969 ◽  
Vol 2004 (18) ◽  
Author(s):  
Tracy Conklin ◽  
Russell F. Mizell, III
Keyword(s):  
Xylella Fastidiosa ◽  
Southeastern United States ◽  
Cooperative Extension Service ◽  
Plant Diseases ◽  
Pierce's Disease ◽  
Extension Service ◽  
Homalodisca Vitripennis ◽  
University Of Florida ◽  
Pierce’S Disease ◽  
Homalodisca Coagulata

The glassy-winged sharpshooter, Homalodisca coagulata (Say), is a large leafhopper species native to the southeastern United States. It is one of the main vectors of the bacterium Xylella fastidiosa, a plant pathogen that causes a variety of plant diseases, including phony peach disease of peach and Pierce's disease of grape. Though usually not a serious pest in the area of its native distribution, the glassy-winged sharpshooter has recently been introduced into southern California, where it has become a serious threat to viticulture due to its ability to vector Pierce's disease.  This document is EENY-274, one of a series of Featured Creatures from the Entomology and Nematology Department, Florida Cooperative Extension Service, Institute of Food and Agricultural Sciences, University of Florida. Published: October 2002. Revised: July 2004. EENY-274/IN552: Glassy-Winged Sharpshooter, Homalodisca vitripennis (=coagulata) (Germar) (Insecta: Hemiptera: Cicadellidae: Cicadellinae) (ufl.edu)

scholarly journals Understanding How an Invasive Vector Drives Pierce’s Disease Epidemics: Seasonality and Vine-to-Vine Spread

2019 ◽  
Vol 109 (2) ◽  
pp. 277-285 ◽  
Author(s):  
Matthew P. Daugherty ◽  
Rodrigo P. P. Almeida
Keyword(s):  
Plant Pathogens ◽  
Disease Incidence ◽  
Disease Model ◽  
Pierce's Disease ◽  
Homalodisca Vitripennis ◽  
Field Cage ◽  
Secondary Spread ◽  
Pierce’S Disease ◽  
Vector Borne ◽  
Disease Epidemics

For vector-borne plant pathogens, disease epidemics may be attributable to multiple mechanisms, including introduction of a novel vector whose epidemiological role differs from that of native vectors. In such cases, understanding an exotic vector’s ability to drive an epidemic is central to mitigating its impact. We studied how the invasive glassy-winged sharpshooter (Homalodisca vitripennis Germar) can drive Pierce’s disease outbreaks in vineyards, focusing on its potential to promote vine-to-vine (i.e., secondary) spread of Xylella fastidiosa relative to potential constraints stemming from seasonality in the pathosystem. First, we developed a general vector-borne disease model to understand the consequences for disease dynamics of (i) seasonal acquisition efficiency and (ii) seasonal host recovery from infection. Results of the modeling indicate that these two sources of seasonality could constrain disease incidence, particularly when working in concert. Next, we established a field cage experiment to determine whether H. vitripennis promotes vine-to-vine spread, and looked for evidence of seasonality in spread. Broadly, results from the experiment supported assumptions of the model; there was modest to significant increase in the frequency of pathogen spread over the first season, and those new infections that occurred later in the season were more likely to recover during winter. Ultimately, by the end of the second season, there was not evidence of significant secondary spread, likely due to a combination of seasonal constraints and low transmission efficiency by H. vitripennis. Collectively, these results suggest that, although H. vitripennis may be able to promote vine-to-vine spread in certain contexts, it may not be the key factor explaining its impact. Rather, the ability of H. vitripennis to drive epidemics is likely to be more directly related to its potential to reach higher population densities than native vectors.

scholarly journals Chromosomal-level assembly of Juglans sigillata genome using Nanopore, BioNano, and Hi-C analysis

GigaScience ◽  
2020 ◽  
Vol 9 (2) ◽  
Author(s):  
De-Lu Ning ◽  
Tao Wu ◽  
Liang-Jun Xiao ◽  
Ting Ma ◽  
Wen-Liang Fang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
Juglans Regia ◽  
Future Research ◽  
High Quality ◽  
Illumina Hiseq ◽  
A Genome ◽  
Contact Frequency ◽  
Juglans Sigillata ◽  
Chromosome Level

Abstract Background Juglans sigillata, or iron walnut, belonging to the order Juglandales, is an economically important tree species in Asia, especially in the Yunnan province of China. However, little research has been conducted on J. sigillata at the molecular level, which hinders understanding of its evolution, speciation, and synthesis of secondary metabolites, as well as its wide adaptability to its plateau environment. To address these issues, a high-quality reference genome of J. sigillata would be useful. Findings To construct a high-quality reference genome for J. sigillata, we first generated 38.0 Gb short reads and 66.31 Gb long reads using Illumina and Nanopore sequencing platforms, respectively. The sequencing data were assembled into a 536.50-Mb genome assembly with a contig N50 length of 4.31 Mb. Additionally, we applied BioNano technology to identify contacts among contigs, which were then used to assemble contigs into scaffolds, resulting in a genome assembly with scaffold N50 length of 16.43 Mb and contig N50 length of 4.34 Mb. To obtain a chromosome-level genome assembly, we constructed 1 Hi-C library and sequenced 79.97 Gb raw reads using the Illumina HiSeq platform. We anchored ∼93% of the scaffold sequences into 16 chromosomes and evaluated the quality of our assembly using the high contact frequency heat map. Repetitive elements account for 50.06% of the genome, and 30,387 protein-coding genes were predicted from the genome, of which 99.8% have been functionally annotated. The genome-wide phylogenetic tree indicated an estimated divergence time between J. sigillata and Juglans regia of 49 million years ago on the basis of single-copy orthologous genes. Conclusions We provide the first chromosome-level genome for J. sigillata. It will lay a valuable foundation for future research on the genetic improvement of J. sigillata.

scholarly journals Control of Pierce’s Disease Through Areawide Management of Glassy-Winged Sharpshooter (Hemiptera: Cicadellidae) and Roguing of Infected Grapevines

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
David R Haviland ◽  
Beth Stone-Smith ◽  
Minerva Gonzalez
Keyword(s):  
Disease Incidence ◽  
Public Funding ◽  
Pilot Project ◽  
Treatment Programs ◽  
Pierce's Disease ◽  
Homalodisca Vitripennis ◽  
California Department ◽  
Voluntary Programs ◽  
Pierce’S Disease ◽  
Food And Agriculture

Abstract The General Beale Pilot Project serves as a case study for the use of areawide monitoring and treatment programs for glassy-winged sharpshooter (GWSS), Homalodisca vitripennis (Germar), and monitoring and roguing programs for grapevines infected with Xylella fastidiosa, to achieve regional management of Pierce’s disease. The Project is located in southeast Kern County, CA, and contains ~2,800 ha of citrus and grapevines grown within approximately 50 km2. For nearly 20 yr, an average of 470 traps have been used to monitor GWSS populations regionally by the California Department of Food and Agriculture, and to inform coordinated, areawide treatments by the USDA-APHIS Areawide Treatment Program to overwintering GWSS in citrus. Grape growers were responsible for treating their own vineyards, and for the roguing of infected grapevines based on surveys provided by the University of California. Herein, we provide a history of the General Beale Pilot Project, broken down into six eras based on levels of Project success, which incorporate data on GWSS captures, pesticide use, and disease incidence. We describe patterns of success related to the regional coordination of effective treatment and roguing programs that can be used by grape and neighboring citrus growers for areawide management of Pierce’s disease. We conclude by describing current and future challenges for Pierce’s disease management, including pesticide availability and resistance, GWSS refuges, the inability to detect and rogue infected vines in the year they become infected, and the sustainability of voluntary programs that rely on public funding.

scholarly journals Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal new biological insights

2021 ◽  
Author(s):  
Rodrigo P. Baptista ◽  
Yiran Li ◽  
Adam Sateriale ◽  
Mandy J. Sanders ◽  
Karen L. Brooks ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
Diarrheal Disease ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Future Research ◽  
Gene Copy Number Variation ◽  
Long Read ◽  
Number Variation ◽  
Gene Structures

ABSTRACTCryptosporidiosis is a leading cause of waterborne diarrheal disease globally and an important contributor to mortality in infants and the immunosuppressed. Despite its importance, the Cryptosporidium community still relies on a fragmented reference genome sequence from 2004. Incomplete reference sequences hamper experimental design and interpretation. We have generated a new C. parvum IOWA genome assembly supported by PacBio and Oxford Nanopore long-read technologies and a new comparative and consistent genome annotation for three closely related species C. parvum, C. hominis and C. tyzzeri. The new C. parvum IOWA reference genome assembly is larger, gap free and lacks ambiguous bases. This chromosomal assembly recovers 13 of 16 possible telomeres and raises a new hypothesis for the remaining telomeres and associated subtelomeric regions. Comparative annotation revealed that most “missing” orthologs are found suggesting that species differences result primarily from structural rearrangements, gene copy number variation and SNVs in C. parvum, C. hominis and C. tyzzeri. We made >1,500 C. parvum annotation updates based on experimental evidence. They included new transporters, ncRNAs, introns and altered gene structures. The new assembly and annotation revealed a complete DNA methylase Dnmt2 ortholog. 190 genes under positive selection including many new candidates were identified using the new assembly and annotation as reference. Finally, possible subtelomeric amplification and variation events in C. parvum are detected that reveal a new level of genome plasticity that will both inform and impact future research.

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