Draft Genome Sequence of the Phytopathogenic Fungus<i>Fusarium euwallaceae</i>, the Causal Agent of<i>Fusarium</i>Dieback

A key factor to take actions against phytosanitary problems is the accurate and rapid detection of the causal agent. Here, we develop a molecular diagnostics system based on comparative genomics to easily identify fusariosis and specific pathogenic species as the Fusarium kuroshium, the symbiont of the ambrosia beetle Euwallaceae kuroshio Gomez and Hulcr which is responsible for Fusarium dieback disease in San Diego CA, USA. We performed a pan-genome analysis using sixty-three ascomycetes fungi species including phytopathogens and fungi associated with the ambrosia beetles. Pan-genome analysis revealed that 2,631 orthologue genes are only shared by Fusarium spp., and on average 3,941 (SD ± 1,418.6) are species-specific genes. These genes were used for PCR primer design and tested on DNA isolated from i) different strains of ascomycete species, ii) artificially infected avocado stems and iii) plant tissue of field-collected samples presumably infected. Our results let us propose a useful set of primers to either identify any species from Fusarium genus or, in a specific manner, species such as F. kuroshium, F. oxysporum, and F. graminearum. The results suggest that the molecular strategy employed in this study can be expanded to design primers against different types of pathogens responsible for provoking critical plant diseases.

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“…Consistently with previously reported, 13,777 CDS were predicted into the F . kuroshium genome [ 42 ]. The predicted number of genes for F .…”

Section: Resultsmentioning

confidence: 99%

Design of a diagnostic system based on molecular markers derived from the ascomycetes pan-genome analysis: The case of Fusarium dieback disease

et al. 2021

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“…associated with KSBH some of these PKS are represented by partial OFRs, we looked for their complete coding sequences in the genome of Fusarium sp. associated with KSBH which has been recently announced [ 70 ] and was generated from the same strain used in this study.…”

Section: Resultsmentioning

confidence: 99%

“…associated with KSBH that were collected in the locations of El Cajon, Fallbrook, Bonsall and Escondido, CA. It is important to mention that in a previous work [ 70 ] we named this strain as F. euwallaceae because until that time there were not enough genomic data available that allow us to infer the differences between the Fusarium strains associated with KSBH or PSHB [ 21 ].…”

Section: Discussionmentioning

confidence: 99%

Environmental pH modulates transcriptomic responses in the fungus Fusarium sp. associated with KSHB Euwallacea sp. near fornicatus

et al. 2018

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BackgroundThe Ambrosia Fusarium Clade phytopathogenic Fusarium fungi species have a symbiotic relationship with ambrosia beetles in the genus Euwallacea (Coleoptera: Curculionidae). Related beetle species referred to as Euwallacea sp. near fornicatus have been spread in California, USA and are recognized as the causal agents of Fusarium dieback, a disease that causes mortality of many plant species. Despite the importance of this fungi, no transcriptomic resources have been generated. The datasets described here represent the first ever transcripts available for these species. We focused our study on the isolated species of Fusarium that is associated with one of the cryptic species referred to as Kuroshio Shot Hole Borer (KSHB) Euwallacea sp. near fornicatus.ResultsHydrogen concentration is a critical signal in fungi for growth and host colonization, the aim of this study was to evaluate the effect of different pH conditions on growth and gene expression of the fungus Fusarium sp. associated with KSHB. An RNA-seq approach was used to compare the gene expression of the fungus grown for 2 weeks in liquid medium at three different pH levels (5.0, 6.0, and 7.0). An unbuffered treatment was included to evaluate the capability of the fungus to change the pH of its environment and the impact in gene expression. The results showed that the fungus can grow and modulate its genetic expression at different pH conditions; however, growth was stunted in acidic pH in comparison with neutral pH. The results showed a differential expression pattern in each pH condition even when acidic conditions prevailed at the end of the experiment. After comparing transcriptomics data from the three treatments, we found a total of 4,943 unique transcripts that were differentially expressed.ConclusionsWe identified transcripts related to pH signaling such as the conserved PAL/RIM pathway, some transcripts related to secondary metabolism and other transcripts that were differentially expressed. Our analysis suggests possible mechanisms involved in pathogenicity in this novel Fusarium species. This is the first report that shows transcriptomic data of this pathogen as well as the first report of genes and proteins involved in their metabolism identifying potential virulence factors.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5083-1) contains supplementary material, which is available to authorized users.

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“…Reference sequences used consisted on whole genome sequences and/or unique-transcript collections resulting from transcriptomic studies, available in public databases such as JGI ( [46,47]) and GeneBank (). Only available sequences from fungi associated with ambrosia beetles were included [48,49,50] (see Table S2 for more details, [48,49,50,51,52,53])…”

Section: Methodsmentioning

confidence: 99%

“…Moreover, we used Raffaelea lauricola and Fusarium euwallaceae proteomes in the fungus-like sequence, searching (BLASTp) and Gene Ontology (GO) terms enrichment analysis. These proteomes were obtained through the gene model prediction in previously sequenced genomes ([48,49]; Table S2), which are available through the NCBI database. Ab initio and evidence-direct predictor AUGUSTUS [81,82] was used to generate these first versions of the gene models, which were corrected and improved by MAKER pipeline [83,84], entering the whole genome sequences with masked transposable elements, the available transcriptional dataset [49,85], and a reference protein database containing complete proteomes from some ascomycetes available from the JGI database.…”

Section: Methodsmentioning

confidence: 99%

Genomic Signals of Adaptation towards Mutualism and Sociality in Two Ambrosia Beetle Complexes

Blaz

Barrera‐Redondo

Vázquez-Rosas-Landa

et al. 2018

Life

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Mutualistic symbiosis and eusociality have developed through gradual evolutionary processes at different times in specific lineages. Like some species of termites and ants, ambrosia beetles have independently evolved a mutualistic nutritional symbiosis with fungi, which has been associated with the evolution of complex social behaviors in some members of this group. We sequenced the transcriptomes of two ambrosia complexes (Euwallacea sp. near fornicatus–Fusarium euwallaceae and Xyleborus glabratus–Raffaelea lauricola) to find evolutionary signatures associated with mutualism and behavior evolution. We identified signatures of positive selection in genes related to nutrient homeostasis; regulation of gene expression; development and function of the nervous system, which may be involved in diet specialization; behavioral changes; and social evolution in this lineage. Finally, we found convergent changes in evolutionary rates of proteins across lineages with phylogenetically independent origins of sociality and mutualism, suggesting a constrained evolution of conserved genes in social species, and an evolutionary rate acceleration related to changes in selective pressures in mutualistic lineages.

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Draft Genome Sequence of the Phytopathogenic FungusFusarium euwallaceae, the Causal Agent ofFusariumDieback

Cited by 11 publications

References 17 publications

Design of a diagnostic system based on molecular markers derived from the ascomycetes pan-genome analysis: The case of Fusarium dieback disease

Design of a diagnostic system based on molecular markers derived from the ascomycetes pan-genome analysis: The case of Fusarium dieback disease

Environmental pH modulates transcriptomic responses in the fungus Fusarium sp. associated with KSHB Euwallacea sp. near fornicatus

Genomic Signals of Adaptation towards Mutualism and Sociality in Two Ambrosia Beetle Complexes

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