scholarly journals Nematode Genome Announcement: Draft genome of Meloidogyne chitwoodi, an economically important pest of potato in the Pacific Northwest

2021 ◽  
Author(s):  
Sapinder Bali ◽  
Shengwei Hu ◽  
Kelly Vining ◽  
Charles R Brown ◽  
Hassan Majtahedi ◽  
...  
Keyword(s):  
Pacific Northwest ◽  
Draft Genome ◽  
Single Copy ◽  
Economic Losses ◽  
Meloidogyne Chitwoodi ◽  
The Pacific ◽  
Important Pest ◽  
Genome Assemblies ◽  
The U.S ◽  
Nematode Genome

Meloidogyne chitwoodi is one of the most devastating pests of potato in the U.S. Pacific Northwest (PNW). Nematode-infected tubers develop external as well as internal defects, making the potatoes unmarketable, and resulting in economic losses. Draft genome assemblies of three M. chitwoodi genotypes, Mc1, Mc2 and Mc1Roza, were generated using Illumina and PacBio Sequel RS II sequencing. The final assemblies consist of 30, 39 and 38 polished contigs for Mc1, Mc2 and Mc1Roza, respectively, with average N50 of 2.37 Mb and average assembled genome size of ~47.41 Mb. An average of 10,508 genes were annotated for each genome. BUSCO analysis indicated that 69.80% of the BUSCOs were complete whereas 68.80%, 0.93% and 12.67% were single copy, duplicated and fragmented, respectively. These highly contiguous genomes will enrich resources to study potato-nematode interactions and enhance breeding efforts to develop nematode resistant potato varieties for PNW.

Identification of Resistance to Powdery Mildew in Publicly Available Male Hop Germplasm

2018 ◽  
Vol 19 (3) ◽  
pp. 258-264
Author(s):  
David H. Gent ◽  
Briana J. Claassen ◽  
Megan C. Twomey ◽  
Sierra N. Wolfenbarger
Keyword(s):  
United States ◽  
Powdery Mildew ◽  
Pacific Northwest ◽  
Western United States ◽  
R Genes ◽  
Sources Of Resistance ◽  
Department Of Agriculture ◽  
Breeding Programs ◽  
The Pacific ◽  
The U.S

Powdery mildew (caused by Podosphaera macularis) is one of the most important diseases of hop in the western United States. Strains of the fungus virulent on cultivars possessing the resistance factor termed R6 and the cultivar Cascade have become widespread in the Pacific Northwestern United States, the primary hop producing region in the country, rendering most cultivars grown susceptible to the disease at some level. In an effort to identify potential sources of resistance in extant germplasm, 136 male accessions of hop contained in the U.S. Department of Agriculture collection were screened under controlled conditions. Iterative inoculations with three isolates of P. macularis with varying race identified 23 (16.9%) accessions with apparent resistance to all known races of the pathogen present in the Pacific Northwest. Of the 23 accessions, 12 were resistant when inoculated with three additional isolates obtained from Europe that possess novel virulences. The nature of resistance in these individuals is unclear but does not appear to be based on known R genes. Identification of possible novel sources of resistance to powdery mildew will be useful to hop breeding programs in the western United States and elsewhere.

scholarly journals Loop-Mediated Isothermal Amplification for the Diagnostic Detection of Meloidogyne chitwoodi and M. fallax

Plant Disease ◽  
2019 ◽  
Vol 103 (1) ◽  
pp. 12-18 ◽  
Author(s):  
Lei Zhang ◽  
Cynthia Gleason
Keyword(s):  
Pacific Northwest ◽  
Intergenic Spacer ◽  
Lamp Assay ◽  
The United States ◽  
Isothermal Amplification ◽  
Root Knot Nematode ◽  
Meloidogyne Chitwoodi ◽  
Loop Mediated Isothermal Amplification ◽  
The Pacific ◽  
Potato Nematodes

Meloidogyne chitwoodi is a root-knot nematode that parasitizes a broad range of plants. In the Pacific Northwest (PNW) of the United States, M. chitwoodi is a major potato pest. The nematodes infect roots and tubers; blemishes caused by the nematodes on the tubers significantly affect potato marketability. M. chitwoodi is a quarantine pathogen by many regulatory agencies, limiting potato trade opportunities when it is present. A loop-mediated isothermal amplification (LAMP) assay was developed to amplify the intergenic spacer (IGS2)-18S region of the ribosomal rDNA of M. chitwoodi. Using the LAMP assay, we could detect the presence of M. chitwoodi from infected Washington State soil samples. The LAMP primers showed specificity for DNA from M. chitwoodi and the closely related species M. fallax. There was no cross reaction of the LAMP primers with DNA from tropical nematodes M. incognita, M. arenaria, and M. javanica, or the Northern root-knot nematode M. hapla. The LAMP assays can be completed within 45 min, and they were 100 times more sensitive in nematode detection than conventional PCR. The LAMP assay will facilitate detection of potato nematodes M. chitwoodi and M. fallax. Knowledge of potato nematodes, particularly M. chitwoodi in PNW soils, will aid management decisions.

scholarly journals Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology

2020 ◽  
Author(s):  
Joseph R. Fauver ◽  
Mary E. Petrone ◽  
Emma B. Hodcroft ◽  
Kayoko Shioda ◽  
Hanna Y. Ehrlich ◽  
...  
Keyword(s):  
United States ◽  
Pacific Northwest ◽  
The United States ◽  
International Travel ◽  
Viral Genomes ◽  
Genomic Epidemiology ◽  
The Pacific ◽  
Travel Restrictions ◽  
Novel Coronavirus ◽  
The U.S

SummarySince its emergence and detection in Wuhan, China in late 2019, the novel coronavirus SARS-CoV-2 has spread to nearly every country around the world, resulting in hundreds of thousands of infections to date. The virus was first detected in the Pacific Northwest region of the United States in January, 2020, with subsequent COVID-19 outbreaks detected in all 50 states by early March. To uncover the sources of SARS-CoV-2 introductions and patterns of spread within the U.S., we sequenced nine viral genomes from early reported COVID-19 patients in Connecticut. Our phylogenetic analysis places the majority of these genomes with viruses sequenced from Washington state. By coupling our genomic data with domestic and international travel patterns, we show that early SARS-CoV-2 transmission in Connecticut was likely driven by domestic introductions. Moreover, the risk of domestic importation to Connecticut exceeded that of international importation by mid-March regardless of our estimated impacts of federal travel restrictions. This study provides evidence for widespread, sustained transmission of SARS-CoV-2 within the U.S. and highlights the critical need for local surveillance.

scholarly journals Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1839 ◽  
Author(s):  
Tom O. Delmont ◽  
A. Murat Eren
Keyword(s):  
High Throughput Sequencing ◽  
Draft Genome ◽  
Cost Effective ◽  
Single Copy ◽  
Eukaryotic Genome ◽  
Sequencing Data ◽  
Bacterial Genomes ◽  
Long Read ◽  
Domains Of Life ◽  
Genome Assemblies

High-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics approaches and practices. Here, we re-analyzed the sequencing data generated for the tardigradeHypsibius dujardini,and created a holistic display of the eukaryotic genome assembly using DNA data originating from two groups and eleven sequencing libraries. By using bacterial single-copy genes, k-mer frequencies, and coverage values of scaffolds we could identify and characterize multiple near-complete bacterial genomes from the raw assembly, and curate a 182 Mbp draft genome forH. dujardinisupported by RNA-Seq data. Our results indicate that most contaminant scaffolds were assembled from Moleculo long-read libraries, and most of these contaminants have differed between library preparations. Our re-analysis shows that visualization and curation of eukaryotic genome assemblies can benefit from tools designed to address the needs of today’s microbiologists, who are constantly challenged by the difficulties associated with the identification of distinct microbial genomes in complex environmental metagenomes.

Television for the Peace Arch Country: Transnational Broadcasting History in the Pacific Northwest

2019 ◽  
Vol 21 (5) ◽  
pp. 510-529
Author(s):  
Helen Morgan Parmett
Keyword(s):  
Pacific Northwest ◽  
Liberal Democracy ◽  
Television Station ◽  
Cross Border ◽  
International Broadcasting ◽  
The Pacific ◽  
Northwest Region ◽  
The U.S

This article contributes to international broadcasting history through a case study of a local, independent television station in the Pacific Northwest. KVOS-TV was one of a few stations on the U.S./Canadian border that sought out a cross-border audience, but it is unique in its efforts to produce programming to bridge these audiences into a unified viewing public that it termed the Peace Arch Country. The station’s international programming constituted its viewing public as translocal citizens in ways that supported the broader global ambitions of the Pacific Northwest region, as well as responded to and promoted the global ambitions of western liberal democracy and capitalism in the fight against Communism. KVOS-TV’s constitution of Peace Arch citizenship shows how television was a tool for creating translocal citizens, educating and governing them from a distance.

scholarly journals 1055 PRODUCTION AND MARKETING OF SPICES, TEA HERBS AND MEDICINAL PLANTS IN THE PACIFIC NORTHWEST

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 579f-579
Author(s):  
Lon Johnson
Keyword(s):  
Quality Assurance ◽  
Medicinal Plants ◽  
Pacific Northwest ◽  
Public Interest ◽  
Global Market ◽  
Specialty Crops ◽  
The Past ◽  
The Pacific ◽  
Organically Grown ◽  
The U.S

Concurrent with the development of the U.S. market for certified organically-grown produce, there has been a growth in the production and marketing of organically-grown botanicals. This activity has been centered in the Pacific Northwest for the past 20 years. The current global market for biologically-grown botanicals has been stimulated by public interest in alternative and traditional plant-based medicines. Trout Lake Farm has organized efforts to stimulate the production and marketing of medicinal plants and spices. The efforts include R&D, growing methodologies, quality assurance, drying, and processing. Research of many ornamentals has revealed potential uses for them other than strictly ornamental. Cultivation is necessary to avoid extirpation of fragile and threatened wild medicinals. The use of organic growing practices is necessary, particularly for specialty crops which have no EPA level inclusions for pesticides. Increasing domestic production of temperate and subtropical herbs and spices helps reduce U.S. imports.

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