Draft Genome Sequence of
            <i>Dactylonectria macrodidyma</i>
            , a Plant-Pathogenic Fungus in the
            <i>Nectriaceae</i>

Malapi‐Wight, Martha; Salgado‐Salazar, Catalina; Demers, Jill E.; Veltri, Daniel; Crouch, Jo Anne

doi:10.1128/genomea.00278-15

Cited by 28 publications

(13 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Genomic DNA was extracted and purified as previously described ( Malapi-Wight et al 2015 ) from a natural isolate of Limonomyces culmigenus , CBS 661.85. An Illumina TruSeq PCR-Free DNA sequencing library (Illumina, San Diego, CA) was constructed and quantified using the Qubit 2.0 fluorometer (Life Technologies, Grand Island, NY) and LabChipXT DNA 750 (Caliper Life Sciences, Hopkinton, MA), then sequenced on an Illumina MiSeq instrument using a 600-cycle sequencing cartridge (Illumina, Inc).…”

Section: Methodsmentioning

confidence: 99%

Draft genome sequences of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygamai, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata

et al. 2015

Self Cite

View full text Add to dashboard Cite

The genomes of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygami, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata are presented in this genome announcement. These seven genomes are from endophytes, plant pathogens and economically important fungal species. The genome sizes range from 26.6 Mb in the case of Leptographium lundbergii to 44 Mb for Chrysoporthe austroafricana. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera, and may contribute to our understanding of the lifestyles through comparative studies with closely related organisms.

show abstract

Section: Methodsmentioning

confidence: 99%

Draft genome sequences of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygamai, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata

et al. 2015

Self Cite

View full text Add to dashboard Cite

show abstract

“…For all three strategies, markers were identified by the alignment of whole draft genomes of C. henricotiae CBS 138102, C. pseudonaviculata CBS 139707 and three related species from the Nectriaceae family that served as outgroup taxa. The outgroup genomes were selected to provide sequence data from different levels of divergence relative to the ingroup genomes, and consisted of C. naviculata CBS 101121, C. leucothoës CBS 109166 and Dactylonectria macrodidyma JAC15-08 23 ( Table 1 ). Properties of all candidate marker regions and primers tested are summarized in Tables 2 and 3 .…”

Section: Resultsmentioning

confidence: 99%

“…Fungal gDNA was extracted as previously reported 23 . Nucleic acids were quantified using a Qubit 2.0 fluorometer (Life Technologies, Grand Island, NY), and subsequently normalized for use in LAMP reactions.…”

Section: Methodsmentioning

confidence: 99%

“…Candidate marker regions for LAMP assay design were identified based on the alignment of whole draft genomes of C. pseudonaviculata CBS 139707 and C. henricotiae CBS 138102 (data not shown). Genome sequence assemblies of three related species at different levels of divergence from the boxwood blight pathogens were used for comparative analyses: C. naviculata CBS 101121 isolated from leaf litter; C. leucothoës CBS 109166 isolated from Theobroma cacao ; and the plant pathogen D. macrodidyma 23 . In order to increase the chance of finding species-specific diagnostic targets, three different approaches were used to mine the genome datasets.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

LAMP Detection Assays for Boxwood Blight Pathogens: A Comparative Genomics Approach

Malapi‐Wight

Demers

Veltri

et al. 2016

Sci Rep

Self Cite

View full text Add to dashboard Cite

Rapid and accurate molecular diagnostic tools are critical to efforts to minimize the impact and spread of emergent pathogens. The identification of diagnostic markers for novel pathogens presents several challenges, especially in the absence of information about population diversity and where genetic resources are limited. The objective of this study was to use comparative genomics datasets to find unique target regions suitable for the diagnosis of two fungal species causing a newly emergent blight disease of boxwood. Candidate marker regions for loop-mediated isothermal amplification (LAMP) assays were identified from draft genomes of Calonectria henricotiae and C. pseudonaviculata, as well as three related species not associated with this disease. To increase the probability of identifying unique targets, we used three approaches to mine genome datasets, based on (i) unique regions, (ii) polymorphisms, and (iii) presence/absence of regions across datasets. From a pool of candidate markers, we demonstrate LAMP assay specificity by testing related fungal species, common boxwood pathogens, and environmental samples containing 445 diverse fungal taxa. This comparative-genomics-based approach to the development of LAMP diagnostic assays is the first of its kind for fungi and could be easily applied to diagnostic marker development for other newly emergent plant pathogens.

show abstract

“…The analysis of different species of fungi revealed that Dactylonectria was signi cantly different between the two groups of samples. Researchers found that Dactylonectria fungi are primarily related to plant diseases [33][34][35]. The change of Dactylonectria fungi may be related to the occurrence of pests and diseases of A. lancea.…”

Section: Analysis and Discussionmentioning

confidence: 99%

Analysis of microbial changes in the rhizosphere of unplanted and planted Atractylodes lancea via high-throughput sequencing

Niu

Chen

et al. 2020

Preprint

View full text Add to dashboard Cite

Background Atractylodes lancea is a traditional Chinese medicine, which typically requires more than 3–4 years of continuous cropping to obtain the underground medicinal components. With continuous cropping years, the quality and yields of A. lancea medicinal materials decrease, while pests and diseases increase. These aspects are intimately correlated with rhizospheric microorganisms. Methods This research paper employed high-throughput sequencing for its detection in soil that was cultivated for three years and never cultivated to clarify the relationship between the microbial diversity of the rhizosphere and continuous A. lancea cropping. Results The rhizosphere microbial community was altered following the continuous cropping of A. lancea. The bacterial diversity and richness were observed to decrease, while the fungal community diversity increased, and richness decreased. The total OUTs of the soil bacteria and fungi of unplanted and planted A. lancea were 59.58% and 37.65%, respectively. At the phylum level, the relative abundance of Proteobacteria, Gemmatimonadetes, Acidobacteria and Chloroflexi decreased, whereas the relative abundance of Mortierellomycota increased. At the genus level, Bradyrhizobium, Striaticonidium, Dactylonectria, Sphingomonas, Burkholderiaceae, Rhodanobacter, Arthrobacter, Scleroderma, Mortierella and Penicillium were significantly different between the two sample groups. Conclusions Our results revealed that following the cultivation of A. lancea, the rhizospheric microbial community was altered. This study preliminarily determined the

show abstract

Draft Genome Sequence of Dactylonectria macrodidyma , a Plant-Pathogenic Fungus in the Nectriaceae

Cited by 28 publications

References 9 publications

Draft genome sequences of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygamai, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata

Draft genome sequences of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygamai, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata

LAMP Detection Assays for Boxwood Blight Pathogens: A Comparative Genomics Approach

Analysis of microbial changes in the rhizosphere of unplanted and planted Atractylodes lancea via high-throughput sequencing

Contact Info

Product

Resources

About