Draft Genome Sequences for Three
            <i>Ophiostoma</i>
            Species Acquired during Revisions of Australian Plant Pathogen Reference Collections

Trollip, Conrad; Carnegie, Angus J.; Rodoni, Brendan; Edwards, Jacqueline

doi:10.1128/mra.00175-22

Cited by 3 publications

(3 citation statements)

References 16 publications

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“…The remaining six species were included to represent species of Ophiostomatales known from alternative hosts. Genomic DNA was readily available for thirty‐four of the chosen isolates (Trollip et al, 2021, 2022), with gDNA of Ophiostoma novo‐ulmi (NZFS2967), a phytopathogen exotic to Australia, and Sporothrix pallida (NZFS280), an environmental fungus already established in Australia (New 2017), shared by New Zealand's National Forestry Mycological Herbarium Culture Collection (NZFS). DNA of the Sporothrix variecibatus VPRI43724 isolate was extracted as described in Trollip et al (2021).…”

Section: Methodsmentioning

confidence: 99%

Modular, multi‐barcode amplicon sequencing for improved species‐level detection of fungal phytopathogens: A case study of pipeline establishment targeting the Ophiostomatales

et al. 2022

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Recent advances in the field of environmental DNA (eDNA) metabarcoding have produced a promising platform for early detection and broad‐spectrum monitoring of plant pests and pathogens. To date, the majority of fungal metabarcoding assays have relied upon universal primers amplifying segments of the ribosomal DNA, to ensure broad taxonomic coverage while studying changes in community composition, or more recently, to screen for presence/absence of target species. In a diagnostics framework however, single, universal molecular barcodes do not discriminate accurately enough for many groups of important fungal phytopathogens at the required species level. Here, a modular, multi‐barcode amplicon sequencing pipeline was established to provide rapid and reliable diagnostics targeting the Ophiostomatales, an order containing economically important phytopathogens vectored by bark and ambrosia beetles (Curculionidae). Using compositionally varied mock communities, we evaluated five barcoding loci: ITS1, ITS2, the large ribosomal sub‐unit (LSU), translation elongation factor 1‐alpha (TEF1α) and calmodulin (CAL), for their ability to provide species‐level resolution. The sensitivity and detection limit of the assay was established by spiking genomic DNA of the exotic Dutch elm disease pathogen, Ophiostoma novo‐ulmi Brasier, into both the controlled mock communities and eDNA sampled from Ips grandicollis (Eichhoff) beetles collected in New South Wales, Australia. The TEF1α barcode successfully detected the Dutch elm pathogen DNA with 100% accuracy down to approx. 5 pg/μl, while the ITS1 barcode had a 100% accuracy down to approx. 0.4 pg/μl within a given sample. Our results demonstrate that a dual‐barcode approach targeting the ITS1 and TEF1α regions simultaneously is sufficient for accurate species level detection and characterisation of the Ophiostomatales and offers confident detection of low‐abundance taxa (relative read abundances of 0.1%–0.01%). Multi‐barcode metabarcoding provides a framework which can quickly and efficiently be adapted to new targets when establishing high throughput diagnostics for post‐border biosecurity surveillance of fungal phytopathogens.

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Section: Methodsmentioning

confidence: 99%

Modular, multi‐barcode amplicon sequencing for improved species‐level detection of fungal phytopathogens: A case study of pipeline establishment targeting the Ophiostomatales

et al. 2022

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“…As more mitogenome sequences and multi-loci sequence data for reference specimens become available for members of the Ophiostomatales, these can serve as a resource for DNA-based markers that can be utilized for large-scale phylogenetic genomicbased diagnostics and species delimitation. This could eventually lead to the development of a platform that can be used to recognize and explore the taxonomic diversity within the Ophiostomatales and assist in developing high-throughput strategies in biosecurity services to detect pathogens and invasive fungi (Trollip et al, 2021(Trollip et al, , 2022.…”

Section: Conclusion and Applicationsmentioning

confidence: 99%

“…Biosecurity of forestry resources requires the development of accurate identification strategies. There is considerable interest to generate molecular data that can be used to identify potential plant pathogens or fungi of economic concerns using genomic approaches (Aylward et al, 2017;Trollip et al, 2021Trollip et al, , 2022. Kulik et al (2020Kulik et al ( , 2021 argued that fungal mitogenomes contain variable regions that could provide a source for molecular markers suitable for fungal identification.…”

Section: Introductionmentioning

confidence: 99%

The mitogenomes of Leptographium aureum, Leptographium sp., and Grosmannia fruticeta: expansion by introns

2023

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IntroductionMany members of the Ophiostomatales are of economic importance as they are bark-beetle associates and causative agents for blue stain on timber and in some instances contribute towards tree mortality. The taxonomy of these fungi has been challenging due to the convergent evolution of many traits associated with insect dispersal and a limited number of morphological characters that happen to be highly pleomorphic. This study examines the mitochondrial genomes for three members of Leptographium sensu lato [Leptographium aureum (also known as Grosmannia aurea), Grosmannia fruticeta (also known as Leptographium fruticetum), and Leptographium sp. WIN(M)1376)].MethodsIllumina sequencing combined with gene and intron annotations and phylogenetic analysis were performed.ResultsSequence analysis showed that gene content and gene synteny are conserved but mitochondrial genome sizes were variable: G. fruticeta at 63,821 bp, Leptographium sp. WIN(M)1376 at 81,823 bp and L. aureum at 104,547 bp. The variation in size is due to the number of introns and intron-associated open reading frames. Phylogenetic analysis of currently available mitochondrial genomes for members of the Ophiostomatales supports currently accepted generic arrangements within this order and specifically supports the separation of members with Leptographium-like conidiophores into two genera, with L. aureum grouping with Leptographium and G. fruticeta aligning with Grosmannia.DiscussionMitochondrial genomes are promising sequences for resolving evolutionary relationships within the Ophiostomatales.

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RNAi-biofungicides: a quantum leap for tree fungal pathogen management

Sellamuthu,

Chakraborty,

Vetukuri

et al. 2024

Critical Reviews in Biotechnology

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Draft Genome Sequences for Three Ophiostoma Species Acquired during Revisions of Australian Plant Pathogen Reference Collections

Cited by 3 publications

References 16 publications

Modular, multi‐barcode amplicon sequencing for improved species‐level detection of fungal phytopathogens: A case study of pipeline establishment targeting the Ophiostomatales

Modular, multi‐barcode amplicon sequencing for improved species‐level detection of fungal phytopathogens: A case study of pipeline establishment targeting the Ophiostomatales

The mitogenomes of Leptographium aureum, Leptographium sp., and Grosmannia fruticeta: expansion by introns

RNAi-biofungicides: a quantum leap for tree fungal pathogen management

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