Genome-Based Selection and Characterization of<i>Fusarium circinatum</i>-Specific Sequences

Maphosa, Mkhululi; Steenkamp, Emma Theodora; Wingfield, Brenda D.

doi:10.1534/g3.115.025817

Cited by 16 publications

(14 citation statements)

References 61 publications

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“…Whole-genome sequences of closely related fungal species has provided new insight into many other economically important fungal pathogens (Jones et al 2014;Schmidt et al 2016), including other fusaria (Maphosa et al 2016). This diagnostic tool can easily be expanded in the event that other AFC-Euwallacea mutualists are introduced into the United States.…”

Section: Discussionmentioning

confidence: 99%

PCR Multiplexes DiscriminateFusariumSymbionts of InvasiveEuwallaceaAmbrosia Beetles that Inflict Damage on Numerous Tree Species Throughout the United States

et al. 2017

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Asian Euwallacea ambrosia beetles vector Fusarium mutualists. The ambrosial fusaria are all members of the ambrosia Fusarium clade (AFC) within the Fusarium solani species complex (FSSC). Several EuwallaceaFusarium mutualists have been introduced into nonnative regions and have caused varying degrees of damage to orchard, landscape, and forest trees. Knowledge of symbiont fidelity is limited by current identification methods, which typically requires analysis of DNA sequence data from beetles and the symbionts cultured from their oral mycangia. Here, polymerase chain reaction (PCR)-based diagnostic tools were developed to identify the six Fusarium symbionts of exotic Euwallacea spp. currently known within the United States. Whole-genome sequences were generated for representatives of six AFC species plus F. ambrosium and aligned to the annotated genome of F. euwallaceae. Taxon-specific primer-annealing sites were identified that rapidly distinguish the AFC species currently within the United States. PCR specificity, reliability, and sensitivity were validated using a panel of 72 Fusarium isolates, including 47 reference cultures. Culture-independent multiplex assays accurately identified two AFC fusaria using DNA isolated from heads of their respective beetle partners. The PCR assays were used to show that Euwallacea validus is exclusively associated with AF-4 throughout its sampled range within eastern North America. The rapid assay supports federal and state agency efforts to monitor spread of these invasive pests and mitigate further introductions.Several destructive fungal plant pathogens vectored by exotic bark and ambrosia beetles (Coleoptera: Curculionidae: Scolytinae) have invaded American landscapes and forests within the past century. For example, the redbay ambrosia beetle Xyleborus glabratus (Eichhoff) and its fungal symbiont Raffaelea lauricola T. C. Harr., Fraedrich & Aghayeva are responsible for the death of hundreds of millions of native Lauraceous plants, including avocado (Persea americana), redbay (P. borbonia), and sassafras (Sassafras albidum) (Fraedrich et al. 2008;Ploetz et al. 2013) throughout the coastal southeastern United States. Another group of scolytine beetles, the exotic Euwallacea ambrosia beetles, pose a threat to landscape trees as well as avocado Kasson et al. 2013;Mendel et al. 2012).At least six Euwallacea spp. from Asia have become established within the United States (Cognato et al. 2015;O'Donnell et al. 2015): Euwallacea interjectus (Blandford), E. validus (Eichhoff), E. denticulus (Motschulsky), and three morphologically cryptic species within the E. fornicatus species complex (Eichhoff) (Atkinson 2016;O'Donnell et al. 2015;Storer et al. 2015). Euwallacea spp. are fungus-farming ambrosia beetles that cultivate mutualistic fungi in the genus Fusarium, although this is presently unconfirmed for E. denticulus. Most of these insect species do not cause noticeable economic or ecological damage and, instead, attack and colonize declining and recently killed trees. Howe...

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Section: Discussionmentioning

confidence: 99%

PCR Multiplexes DiscriminateFusariumSymbionts of InvasiveEuwallaceaAmbrosia Beetles that Inflict Damage on Numerous Tree Species Throughout the United States

et al. 2017

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“…As a result, such taxonomic features need to be supplemented with other characters like molecular markers that differentiate biological entities at the genetic level. Currently there is a growing interest to assess the genetic diversity of fungi including Fusaria based on sequence analysis (McDonald et al, 2012;Leavitt et al, 2013;Maphosa et al, 2016;Laraba et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity among Fusarium species associated with sorghum stalk rot in Southern Ethiopia

Chala¹

2019

Afr. J. Biotechnol.

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Fusaria are very diverse and destructive pathogens affecting different crops. However, their identity and diversity are unresolved in countries like Ethiopia, where various crop species are grown under differing environmental conditions. The objectives of this paper were to identify Fusarium spp. associated with sorghum stalk rot in Southern Ethiopia, and elucidate the genetic diversity within and between the species. For this purpose, Fusaria associated with sorghum from two locations in Southern Ethiopia were isolated. Sequencing of the elongation factor 1-alpha gene (EF-1α) was used for species identification. In addition, AFLP analysis was employed for further diversity studies within and between the Fusarium spp. Sequence analyses revealed the presence of two Fusarium spp. The first was identified as Fusarium andiyazi, while the identity of the second remains to be solved. AFLP analysis clustered the isolates into two major groups. The Dice similarity coefficients ranged from 0.39 to 0.91 for isolates of F. andiyazi while isolates within the new Fusarium spp. had a Dice similarity coefficient varying between 0.69 and 0.96. Cluster analysis and principal coordinate analysis clearly indicated a genetic separation between the two species. Both groups were pathogenic to mature sorghum plants following a toothpick inoculation test. More researches are required to identify the new species and elucidate the pathogenicity of the isolates.

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“…From the environmental perspective, the metabolic pathways of aromatic compounds, such as chloroalkane and styrene, are of importance (20). A variety of enzymes present in these pathways play a role in the degradation of xenobiotics by the Fusarium spp.…”

Section: Methodsmentioning

confidence: 99%

Genomic sequencing of the aquaticFusariumspp. QHM and BWC1 and their potential application in environmental protection

Zhu

Ding

2019

Preprint

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12Fusarium species are distributed widely in ecosystems of a wide pH range and play 13 a pivotal role in the aquatic community through the degradation of xenobiotic 14 compounds and secretion of secondary metabolites. The elucidation of their genome 15 would therefore be highly impactful with regard to the control of environmental 16 pollution. Therefore, in this study, two indigenous strains of aquatic Fusarium, QHM 17 and BWC1, were isolated from a coal mine pit and a subterranean river respectively, 18 cultured under acidic conditions, and sequenced. Phylogenetic analysis of these two 19isolates was conducted based on the sequences of internal transcript (ITS1 and ITS4) 20 and encoding β-microtubulin (TUB2), translation elongation factors (TEFs) and the 21 2 second large sub-unit of RNA polymerase (RPB2). Fusarium, QHM could potentially 22 represent a new species within the Fusarium fujikuroi species complex. Fusarium 23 BWC1 were found to form a clade with Fusarium subglutinans NRRL 22016, and 24 predicted to be Fusarium subglutinans. Shot-gun sequencing on the Illumina 25Hiseq×10 Platform was used to elucidate the draft genomes of the two species. Gene 26 annotation and functional analyses revealed that they had bio-degradation pathways 27 for aromatic compounds; further, their main pathogenic mechanism was found to be 28 the efflux pump. To date, the genomes of only a limited number of acidic species from 29the Fusarium fujikuroi species complex, especially from the aquatic species, have 30 been sequenced. Therefore, the present findings are novel and have important 31 potential for the future in terms of environmental control. 32 33 IMPORTANCE Fusarium genus has over 300 species and were distributed in a 34 variety of ecosystem. Increasing attention has been drawn to Fusarium due to the 35 importance in aquatic community, pathogenicity and environmental protection. The 36 genomes of the strains in this work isolated in acidic condition, were sequenced. The 37 analysis has indicated that the isolates were able to biodegrade xenobiotics, which 38 makes it potentially function as environmental bio-agent for aromatic pollution 39 control and remediation. Meanwhile, the virulence and pathogenicity were also 40 predicted for reference of infection control. The genome information may lay 41 foundation for the fungal identification, disease prevention resulting from these 42 3 isolates and other "-omics" research. The isolates were phylogenetically classified 43into Fusarium fujikuroi species complex by means of concatenated gene analysis, 44serving as new addition to the big complex. 45 46 47 48

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Genome-Based Selection and Characterization ofFusarium circinatum-Specific Sequences

Cited by 16 publications

References 61 publications

PCR Multiplexes DiscriminateFusariumSymbionts of InvasiveEuwallaceaAmbrosia Beetles that Inflict Damage on Numerous Tree Species Throughout the United States

PCR Multiplexes DiscriminateFusariumSymbionts of InvasiveEuwallaceaAmbrosia Beetles that Inflict Damage on Numerous Tree Species Throughout the United States

Genetic diversity among Fusarium species associated with sorghum stalk rot in Southern Ethiopia

Genomic sequencing of the aquaticFusariumspp. QHM and BWC1 and their potential application in environmental protection

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