scholarly journals De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease

2016 ◽  
Author(s):  
Taruna Aggarwal ◽  
Anthony Westbrook ◽  
Kirk Broders ◽  
Keith Woeste ◽  
Matthew D MacManes
Keyword(s):  
Genome Assembly ◽  
Fungal Pathogens ◽  
De Novo ◽  
Draft Genome ◽  
Black Walnut ◽  
De Novo Genome Assembly ◽  
Evolutionary Mechanisms ◽  
Geosmithia Morbida ◽  
Thousand Cankers Disease ◽  
Walnut Twig Beetle

Geosmithia morbida is a filamentous ascomycete that causes Thousand Cankers Disease in the eastern black walnut tree. This pathogen is commonly found in the western U.S.; however, recently the disease was also detected in several eastern states where the black walnut lumber industry is concentrated. G. morbida is one of two known phytopathogens within the genus Geosmithia, and it is vectored into the host tree via the walnut twig beetle. We present the first de novo draft genome of G. morbida. It is 26.5 Mbp in length and contains less than 1% repetitive elements. The genome possesses an estimated 6,273 genes, 277 of which are predicted to encode proteins with unknown functions. Approximately 31.5% of the proteins in G. morbida are homologous to proteins involved in pathogenicity, and 5.6% of the proteins contain signal peptides that indicate these proteins are secreted. Several studies have investigated the evolution of pathogenicity in pathogens of agricultural crops; forest fungal pathogens are often neglected because research efforts are focused on food crops. G. morbida is one of the few tree phytopathogens to be sequenced, assembled and annotated. The first draft genome of G. morbida serves as a valuable tool for comprehending the underlying molecular and evolutionary mechanisms behind pathogenesis within the Geosmithia genus. Keywords: de novo genome assembly, pathogenesis, forest pathogen, black walnut, walnut twig beetle.

scholarly journals De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease

2016 ◽  
Author(s):  
Taruna Aggarwal ◽  
Anthony Westbrook ◽  
Kirk Broders ◽  
Keith Woeste ◽  
Matthew D MacManes
Keyword(s):  
Genome Assembly ◽  
Fungal Pathogens ◽  
De Novo ◽  
Draft Genome ◽  
Black Walnut ◽  
De Novo Genome Assembly ◽  
Evolutionary Mechanisms ◽  
Geosmithia Morbida ◽  
Thousand Cankers Disease ◽  
Walnut Twig Beetle

Geosmithia morbida is a filamentous ascomycete that causes Thousand Cankers Disease in the eastern black walnut tree. This pathogen is commonly found in the western U.S.; however, recently the disease was also detected in several eastern states where the black walnut lumber industry is concentrated. G. morbida is one of two known phytopathogens within the genus Geosmithia, and it is vectored into the host tree via the walnut twig beetle. We present the first de novo draft genome of G. morbida. It is 26.5 Mbp in length and contains less than 1% repetitive elements. The genome possesses an estimated 6,273 genes, 277 of which are predicted to encode proteins with unknown functions. Approximately 31.5% of the proteins in G. morbida are homologous to proteins involved in pathogenicity, and 5.6% of the proteins contain signal peptides that indicate these proteins are secreted. Several studies have investigated the evolution of pathogenicity in pathogens of agricultural crops; forest fungal pathogens are often neglected because research efforts are focused on food crops. G. morbida is one of the few tree phytopathogens to be sequenced, assembled and annotated. The first draft genome of G. morbida serves as a valuable tool for comprehending the underlying molecular and evolutionary mechanisms behind pathogenesis within the Geosmithia genus. Keywords: de novo genome assembly, pathogenesis, forest pathogen, black walnut, walnut twig beetle.

scholarly journals De novo Genome Assembly of Geosmithia morbida, the Causal Agent of Thousand Cankers Disease

2016 ◽  
Author(s):  
Taruna Aggarwal ◽  
Anthony Westbrook ◽  
Kirk Broders ◽  
Keith Woeste ◽  
Matthew D MacManes
Keyword(s):  
Genome Assembly ◽  
Fungal Pathogens ◽  
De Novo ◽  
Draft Genome ◽  
Black Walnut ◽  
De Novo Genome Assembly ◽  
Evolutionary Mechanisms ◽  
Geosmithia Morbida ◽  
Thousand Cankers Disease ◽  
Walnut Twig Beetle

Background: Geosmithia morbida is a filamentous ascomycete that causes Thousand Cankers Disease in the eastern black walnut tree. This pathogen is commonly found in the western U.S.; however, recently the disease was also detected in several eastern states where the black walnut lumber industry is concentrated. G. morbida is one of two known phytopathogens within the genus Geosmithia, and it is vectored into the host tree via the walnut twig beetle. Results: We present the first de novo draft genome of G. morbida. It is 26.5 Mbp in length and contains less than 1% repetitive elements. The genome possesses an estimated 6,273 genes, 277 of which are predicted to encode proteins with unknown functions. Approximately 31.5% of the proteins in G. morbida are homologous to proteins involved in pathogenicity, and 5.6% of the proteins contain signal peptides that indicate these proteins are secreted. Conclusions: Several studies have investigated the evolution of pathogenicity in pathogens of agricultural crops; forest fungal pathogens are often neglected because research efforts are focused on food crops. G. morbida is one of the few tree phytopathogens to be sequenced, assembled and annotated. The first draft genome of G. morbida serves as a valuable tool for comprehending the underlying molecular and evolutionary mechanisms behind pathogenesis within the Geosmithia genus. Keywords: de novo genome assembly, pathogenesis, forest pathogen, black walnut, walnut twig beetle.

scholarly journals De novogenome assembly ofGeosmithia morbida, the causal agent of thousand cankers disease

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1952 ◽  
Author(s):  
Taruna A. Schuelke ◽  
Anthony Westbrook ◽  
Kirk Broders ◽  
Keith Woeste ◽  
Matthew D. MacManes
Keyword(s):  
Fungal Pathogens ◽  
De Novo ◽  
Draft Genome ◽  
Black Walnut ◽  
Lumber Industry ◽  
Evolutionary Mechanisms ◽  
Geosmithia Morbida ◽  
Filamentous Ascomycete ◽  
Thousand Cankers Disease ◽  
Walnut Twig Beetle

Geosmithia morbidais a filamentous ascomycete that causes thousand cankers disease in the eastern black walnut tree. This pathogen is commonly found in the western U.S.; however, recently the disease was also detected in several eastern states where the black walnut lumber industry is concentrated.G. morbidais one of two known phytopathogens within the genusGeosmithia, and it is vectored into the host tree via the walnut twig beetle. We present the firstde novodraft genome ofG. morbida. It is 26.5 Mbp in length and contains less than 1% repetitive elements. The genome possesses an estimated 6,273 genes, 277 of which are predicted to encode proteins with unknown functions. Approximately 31.5% of the proteins inG. morbidaare homologous to proteins involved in pathogenicity, and 5.6% of the proteins contain signal peptides that indicate these proteins are secreted. Several studies have investigated the evolution of pathogenicity in pathogens of agricultural crops; forest fungal pathogens are often neglected because research efforts are focused on food crops.G. morbidais one of the few tree phytopathogens to be sequenced, assembled and annotated. The first draft genome ofG. morbidaserves as a valuable tool for comprehending the underlying molecular and evolutionary mechanisms behind pathogenesis within theGeosmithiagenus.

scholarly journals Methyl Bromide Fumigation to Eliminate Thousand Cankers Disease Causal Agents from Black Walnut

2019 ◽  
Vol 65 (4) ◽  
pp. 452-459
Author(s):  
Kendhl W Seabright ◽  
Scott W Myers ◽  
Stephen W Fraedrich ◽  
Albert E Mayfield ◽  
Melissa L Warden ◽  
...  
Keyword(s):  
Methyl Bromide ◽  
The United States ◽  
Black Walnut ◽  
Wood Products ◽  
Treatment Schedule ◽  
Geosmithia Morbida ◽  
Thousand Cankers Disease ◽  
Pathogen Recovery ◽  
Canker Development ◽  
Walnut Twig Beetle

Abstract Phytosanitary treatments for logs and barked wood products are needed to mitigate the spread of thousand cankers disease through the movement of these commodities. The disease threatens eastern black walnut (Juglans nigra L.) populations in the United States. It is caused by repeated attacks by the walnut twig beetle (Pityophthorus juglandis Blackman) and subsequent canker development caused by the fungal pathogen Geosmithia morbida M. Kolařík et al. Methyl bromide (MB) fumigations were evaluated for efficacy against P. juglandis and G. morbida in J. nigra bolts. Fumigation with 82 mg/L MB for 24 h at 4.5° C eliminated P. juglandis in J. nigra, but was ineffective against G. morbida. Subsequent experiments focused on eliminating G. morbida, but results were inconclusive because of low rates of pathogen recovery from naturally infested control bolts. Final experiments used J. nigra bolts artificially inoculated with G. morbida. Fumigations with 240 and 320 mg/L MB for 72 h at 10° C were effective in eliminating G. morbida from J. nigra bolts. Results confirm that the USDA fumigation treatment schedule for logs with the oak wilt pathogen will also mitigate the risk of spreading the thousand cankers disease vector and pathogen by movement of walnut bolts and wood products.

scholarly journals LongStitch: High-quality genome assembly correction and scaffolding using long reads

2021 ◽  
Author(s):  
Lauren Coombe ◽  
Janet X Li ◽  
Theodora Lo ◽  
Johnathan Wong ◽  
Vladimir Nikolic ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Draft Genome ◽  
Model Organisms ◽  
High Quality ◽  
De Novo Genome Assembly ◽  
Long Reads ◽  
Long Read ◽  
Genomic Regions ◽  
Genome Assemblies

Background Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through the use of long-range information. Long reads are better able to span repetitive genomic regions compared to short reads, and thus have tremendous utility for resolving problematic regions and helping generate more complete draft assemblies. Here, we present LongStitch, a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads. Results LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tigmint-long and ARKS-long are misassembly correction and scaffolding utilities, respectively, previously developed for linked reads, that we adapted for long reads. Here, we describe the LongStitch pipeline and introduce our new long-read scaffolder, ntLink, which utilizes lightweight minimizer mappings to join contigs. LongStitch was tested on short and long-read assemblies of three different human individuals using corresponding nanopore long-read data, and improves the contiguity of each assembly from 2.0-fold up to 304.6-fold (as measured by NGA50 length). Furthermore, LongStitch generates more contiguous and correct assemblies compared to state-of-the-art long-read scaffolder LRScaf in most tests, and consistently runs in under five hours using less than 23GB of RAM. Conclusions Due to its effectiveness and efficiency in improving draft assemblies using long reads, we expect LongStitch to benefit a wide variety of de novo genome assembly projects. The LongStitch pipeline is freely available at https://github.com/bcgsc/longstitch.

scholarly journals First Record of Thousand Cankers Disease Fungal Pathogen Geosmithia morbida and Walnut Twig Beetle Pityophthorus juglandis on Juglans regia in Europe

Plant Disease ◽  
2014 ◽  
Vol 98 (10) ◽  
pp. 1445-1445 ◽  
Author(s):  
L. Montecchio ◽  
G. Fanchin ◽  
M. Simonato ◽  
M. Faccoli
Keyword(s):  
Bark Beetle ◽  
Juglans Regia ◽  
First Record ◽  
The United States ◽  
Black Walnut ◽  
Geosmithia Morbida ◽  
Pityophthorus Juglandis ◽  
Blast Analysis ◽  
Thousand Cankers Disease ◽  
Walnut Twig Beetle

Thousand cankers disease (TCD) is a disease complex caused by the fungus Geosmithia morbida Kolařik (Ascomycota, Hypocreales) and its vector Pityophthorus juglandis Blackman 1928 (Coleoptera, Scolytinae; walnut twig beetle, WTB). Since the mid-1990s, the disease was responsible for widespread mortality of many walnut species in the United States (4). After the first detection of TCD on black walnut (Juglans nigra L.) in Italy (3), an extensive survey was activated in cooperation with the Regional Phytosanitary Service. In May 2014, early TCD symptoms (4) were observed on English walnuts (J. regia L.). Canopies showed yellowing, wilting, and dieback of the youngest twigs, and a number of small brown cankers. Longitudinal and radial sections sampled through the cankers revealed gray to brown discoloration of both phloem and bark, and the presence of bark beetle galleries. Xylem discoloration was never observed. From one ~20-year-old European walnut growing in a garden neighboring an infected black walnut plantation (Santorso, Vicenza, 45°72′ N, 11°40′ E), a number of 1- to 2.5-cm-diameter twigs showing cankers up to 2 cm long surrounding bark beetle holes were collected. Whitish mycelium producing verticillate conidiophores was detected inside the insect galleries. From the necrotic margin of eight cankers previously surface-sterilized with 3% sodium hypochlorite, two 4-mm-wide chips per canker were placed on potato dextrose agar and incubated at 28 ± 1°C in the dark. Slow growing lobate, plane, yellowish-ocher colonies with hyaline mycelium appeared in 5 days. After subculturing to the same medium, growth features, mycelium, conidiophores, and conidia with morphological characteristics matching Kolarik's description of G. morbida (2) were observed. The ITS region of rDNA from the fungus strain LM14GM001-JR was amplified by using ITS1F and ITS4 primers and sequenced obtaining a 387-bp gene fragment. BLAST analysis showed 99% identity to the G. morbida strain U19 (GenBank Accession No. KF808301.1) for 384 bp, and 99% identity to the G. morbida strain LM13GM001-JN previously isolated from J. nigra in Italy (3). From the same samples, two emerging beetles were collected and identified as P. juglandis both morphologically (5) and genetically by DNA extraction following a standard salting out protocol. The barcode region of the mitochondrial gene cytochrome oxidase I was then amplified by using universal primers (1) and sequenced to obtain a 614-bp fragment of the gene. BLAST analysis showed 100% identity to P. juglandis based on comparison with KJ451422. A few other English walnuts with both the fungus and WTB were also found close to other infected black walnut plantations. To our knowledge, this is the first record of G. morbida and P. juglandis on J. regia in Europe, where the tree is cultivated for both fruit and timber production, as well as a traditional landscape tree. Voucher specimens are stored in the TeSAF herbarium and in the DAFNAE insect collection. References: (1) O. Folmer et al. Mol. Marine Biol. Biotechnol. 3:294, 1994. (2) M. Kolarik et al. Mycologia 103:325, 2011. (3) L. Montecchio and M. Faccoli. Plant Dis. 98:696, 2014. (4) S. J. Seybold et al. USDA Forest Service, NA-PR-02-10, 2013. (5) S. L. Wood. Great Basin Naturalist Memoirs 6:1123, 1982.

scholarly journals De novo genome assembly of the land snail Candidula unifasciata (Mollusca: Gastropoda)

2021 ◽  
Author(s):  
Luis J Chueca ◽  
Tilman Schell ◽  
Markus Pfenninger
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Draft Genome ◽  
Land Snail ◽  
Land Snails ◽  
Agricultural Pests ◽  
De Novo Genome Assembly ◽  
Draft Genome Assembly ◽  
Western Palearctic ◽  
A Genome

Abstract Among all molluscs, land snails are a scientifically and economically interesting group comprising edible species, alien species and agricultural pests. Yet, despite their high diversity, the number of genome drafts publicly available is still scarce. Here, we present the draft genome assembly of the land snail Candidula unifasciata, a widely distributed species along central Europe, belonging to the Geomitridae family, a highly diversified taxon in the Western-Palearctic region. We performed whole genome sequencing, assembly and annotation of an adult specimen based on PacBio and Oxford Nanopore long read sequences as well as Illumina data. A genome draft of about 1.29 Gb was generated with a N50 length of 246 kb. More than 60% of the assembled genome was identified as repetitive elements. 22,464 protein-coding genes were identified in the genome, of which 62.27% were functionally annotated. This is the first assembled and annotated genome for a geometrid snail and will serve as reference for further evolutionary, genomic and population genetic studies of this important and interesting group.

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