Intra-Species Genomic Variation in the Pine Pathogen Fusarium circinatum

Maphosa, Mkhululi; Steenkamp, Emma Theodora; Kanzi, Aquillah M.; Wyk, Stephanie van; Vos, Lieschen De; Santana, Quentin C.; Duong, Tuan A.; Wingfield, Brenda D.

doi:10.3390/jof8070657

Cited by 5 publications

(10 citation statements)

References 95 publications

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“…To find the recovered genes within each sample, we first aligned each of the 120-mer probes to the reference genomes of three fungal species. Using this probe set, we captured 116 out of 14,653 genes, 101 out of 11,130 genes, and 47 out of 8,879 genes that we annotated in the F. circinatum (GCA_024047395.1) [ 54 ], S. sclerotiorum (GCA_001857865.1) [ 55 ], and A. rolfsii (GCA_002940785) genomes, respectively (Tables S11 - S13 ). Annotation of recovered genes of three fungal species is presented in Table S11 - 13 .…”

Section: Resultsmentioning

confidence: 99%

Next-generation fungal identification using target enrichment and Nanopore sequencing

Yu,

Fulton,

Hudson

et al. 2023

BMC Genomics

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Background Rapid and accurate pathogen identification is required for disease management. Compared to sequencing entire genomes, targeted sequencing may be used to direct sequencing resources to genes of interest for microbe identification and mitigate the low resolution that single-locus molecular identification provides. This work describes a broad-spectrum fungal identification tool developed to focus high-throughput Nanopore sequencing on genes commonly employed for disease diagnostics and phylogenetic inference. Results Orthologs of targeted genes were extracted from 386 reference genomes of fungal species spanning six phyla to identify homologous regions that were used to design the baits used for enrichment. To reduce the cost of producing probes without diminishing the phylogenetic power, DNA sequences were first clustered, and then consensus sequences within each cluster were identified to produce 26,000 probes that targeted 114 genes. To test the efficacy of our probes, we applied the technique to three species representing Ascomycota and Basidiomycota fungi. The efficiency of enrichment, quantified as mean target coverage over the mean genome-wide coverage, ranged from 200 to 300. Furthermore, enrichment of long reads increased the depth of coverage across the targeted genes and into non-coding flanking sequence. The assemblies generated from enriched samples provided well-resolved phylogenetic trees for taxonomic assignment and molecular identification. Conclusions Our work provides data to support the utility of targeted Nanopore sequencing for fungal identification and provides a platform that may be extended for use with other phytopathogens.

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Section: Resultsmentioning

confidence: 99%

Next-generation fungal identification using target enrichment and Nanopore sequencing

Yu,

Fulton,

Hudson

et al. 2023

BMC Genomics

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“…Identified QTLs were localized to the genome of F. circinatum FSP34 [55] using the genomic locations of the AFLP markers [26], flanking them, and the methods described by De Vos et al [16]. Briefly, this involved estimating the position of a QTL relative to the AFLP markers flanking it based on the known distance (in bp and cM) between the markers.…”

Section: Qtl Identification and Genomic Localizationmentioning

confidence: 99%

“…Briefly, this involved estimating the position of a QTL relative to the AFLP markers flanking it based on the known distance (in bp and cM) between the markers. Once localized, QTL regions in the F. circinatum FSP34 genome [55] were compared to homologous regions in the genome of F. temperatum Netza9 [56] using MUMmer v. 3.22 [57]. The latter employs suffix trees for identifying matching regions in two DNAs that can serve as anchors during the alignment process.…”

Section: Qtl Identification and Genomic Localizationmentioning

confidence: 99%

“…This was conducted by mapping the raw sequence reads of F. circinatum FSP34 back to the genomes of both F. circinatum FSP34 and KS17, as well as F. temperatum, using CLC Genomics Workbench v21.0.2 (Aarhus, Denmark). The sequence reads consisted of long reads from a MinION sequencer (Oxford Nanopore Technologies, Oxford Science Park, Oxford, United Kingdom) and a 550-bp paired-end library using the Illumina HiSeq 2500 (Macrogen, Seoul, Korea) [55]. We also attempted to PCR amplify across any predicted indels in the QTL regions, using primers designed with PRIMER3 and as described above (Supplementary File S2).…”

Section: Genome Assembly Confirmationmentioning

confidence: 99%

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Identification and Characterization of a QTL for Growth of Fusarium circinatum on Pine-Based Medium

Swalarsk-Parry

Steenkamp

Wyk

et al. 2022

JoF

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Fusarium circinatum is an economically important pathogen of pine and resides in the Fusarium fujikuroi species complex. Here we investigated the molecular processes underlying growth in F. circinatum by exploring the association between growth and the nutritional environment provided by the pine host. For this purpose, we subjected a mapping population consisting of F. circinatum X F. temperatum hybrid progeny to an analysis of growth rate on a pine-tissue derived medium. These data, together with the available genetic linkage map for F. circinatum, were then used to identify Quantitative Trait Loci (QTLs) associated with growth. The single significant QTL identified was then characterized using the available genome sequences for the hybrid progeny’s parental isolates. This revealed that the QTL localized to two non-homologous regions in the F. circinatum and F. temperatum genomes. For one of these, the F. circinatum parent contained a two-gene deletion relative to the F. temperatum parent. For the other region, the two parental isolates encoded different protein products. Analysis of repeats, G+C content, and repeat-induced point (RIP) mutations further suggested a retrotransposon origin for the two-gene deletion in F. circinatum. Nevertheless, subsequent genome and PCR-based analyses showed that both regions were similarly polymorphic within a collection of diverse F. circinatum. However, we observed no clear correlation between the respective polymorphism patterns and growth rate in culture. These findings support the notion that growth is a complex multilocus trait and raise the possibility that the identified QTL contains multiple small-effect QTLs, of which some might be dependent on the genetic backgrounds. This study improved our current knowledge of the genetic determinants of vegetative growth in F. circinatum and provided an important foundation for determining the genes and processes underpinning its ability to colonize its host environment.

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“…The completeness of each genome assembly was evaluated through the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool v. 3.0.2 [45] using the "Sordariomyceta" database. Using the significant synteny found within the FFSC [29,30], scaffolds from the genomes of F. pininemorale (isolated from diseased P. tecunumanii tissue [13,91]) and F. fracticaudum (isolated from diseased Pinus maximinoi tissue [13,92]) were compared against the genomes of F. circinatum [93] (isolated from diseased Pinus radiata tissue [11,111]), F. fujikuroi [29] and F. temperatum [90] (isolated from diseased teosinte tissue [10,90]), as these have been assembled into chromosomes. The scaffolds were ordered and orientated into 12 contiguous pseudochromosomes (representing the core chromosomes (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11) and the accessory chromosome ( 12)) [30].…”

Section: Genome Sequences Assembly Completeness and Gene Predictionmentioning

confidence: 99%

Characterization of Host-Specific Genes from Pine- and Grass-Associated Species of the Fusarium fujikuroi Species Complex

et al. 2022

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The Fusarium fujikuroi species complex (FFSC) includes socioeconomically important pathogens that cause disease for numerous crops and synthesize a variety of secondary metabolites that can contaminate feedstocks and food. Here, we used comparative genomics to elucidate processes underlying the ability of pine-associated and grass-associated FFSC species to colonize tissues of their respective plant hosts. We characterized the identity, possible functions, evolutionary origins, and chromosomal positions of the host-range-associated genes encoded by the two groups of fungi. The 72 and 47 genes identified as unique to the respective genome groups were potentially involved in diverse processes, ranging from transcription, regulation, and substrate transport through to virulence/pathogenicity. Most genes arose early during the evolution of Fusarium/FFSC and were only subsequently retained in some lineages, while some had origins outside Fusarium. Although differences in the densities of these genes were especially noticeable on the conditionally dispensable chromosome of F. temperatum (representing the grass-associates) and F. circinatum (representing the pine-associates), the host-range-associated genes tended to be located towards the subtelomeric regions of chromosomes. Taken together, these results demonstrate that multiple mechanisms drive the emergence of genes in the grass- and pine-associated FFSC taxa examined. It also highlighted the diversity of the molecular processes potentially underlying niche-specificity in these and other Fusarium species.

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Intra-Species Genomic Variation in the Pine Pathogen Fusarium circinatum

Cited by 5 publications

References 95 publications

Next-generation fungal identification using target enrichment and Nanopore sequencing

Next-generation fungal identification using target enrichment and Nanopore sequencing

Identification and Characterization of a QTL for Growth of Fusarium circinatum on Pine-Based Medium

Characterization of Host-Specific Genes from Pine- and Grass-Associated Species of the Fusarium fujikuroi Species Complex

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