Chromosome-level assemblies for the pine pitch canker pathogen Fusarium circinatum

dc.contributor.authorDe Vos, Lieschen
dc.contributor.authorVan der Nest, Magrieta Aletta
dc.contributor.authorSantana, Quentin C.
dc.contributor.authorVan Wyk, Stephanie
dc.contributor.authorLeeuwendaal, Kyle
dc.contributor.authorWingfield, Brenda D.
dc.contributor.authorSteenkamp, Emma Theodora
dc.contributor.emailemma.steenkamp@fabi.up.ac.zaen_US
dc.date.accessioned2025-04-09T04:58:10Z
dc.date.available2025-04-09T04:58:10Z
dc.date.issued2024-01
dc.descriptionDATA AVAILABILITY STATEMENT: The Whole Genome Shotgun project for Fusarium circinatum has been deposited at DDBJ/ENA/GenBank under the accession AYJV00000000 and LQBB00000000 for F. circinatum FSP34 and KS17, respectivelyen_US
dc.description.abstractThe pine pitch canker pathogen, Fusarium circinatum, is globally regarded as one of the most important threats to commercial pine-based forestry. Although genome sequences of this fungus are available, these remain highly fragmented or structurally ill-defined. Our overall goal was to provide high-quality assemblies for two notable strains of F. circinatum, and to characterize these in terms of coding content, repetitiveness and the position of telomeres and centromeres. For this purpose, we used Oxford Nanopore Technologies MinION long-read sequences, as well as Illumina short sequence reads. By leveraging the genomic synteny inherent to F. circinatum and its close relatives, these sequence reads were assembled to chromosome level, where contiguous sequences mostly spanned from telomere to telomere. Comparative analyses unveiled remarkable variability in the twelfth and smallest chromosome, which is known to be dispensable. It presented a striking length polymorphism, with one strain lacking substantial portions from the chromosome’s distal and proximal regions. These regions, characterized by a lower gene density, G+C content and an increased prevalence of repetitive elements, contrast starkly with the syntenic segments of the chromosome, as well as with the core chromosomes. We propose that these unusual regions might have arisen or expanded due to the presence of transposable elements. A comparison of the overall chromosome structure revealed that centromeric elements often underpin intrachromosomal differences between F. circinatum strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of F. circinatum and its relatives. The publicly available genome data generated here, together with the detailed metadata provided, represent essential resources for future studies of this important plant pathogen.en_US
dc.description.departmentBiochemistry, Genetics and Microbiology (BGM)en_US
dc.description.departmentForestry and Agricultural Biotechnology Institute (FABI)en_US
dc.description.sdgSDG-09: Industry, innovation and infrastructureen_US
dc.description.sdgSDG-15:Life on landen_US
dc.description.sponsorshipThe Department of Science and Innovation (DSI)—National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology and SARChI Chair in Fungal Genomics for their financial support.en_US
dc.description.urihttps://www.mdpi.com/journal/pathogensen_US
dc.identifier.citationDe Vos, L.; van der Nest, M.A.; Santana, Q.C.; van Wyk, S.; Leeuwendaal, K.S.; Wingfield, B.D.; Steenkamp, E.T. Chromosome-Level Assemblies for the Pine Pitch Canker Pathogen Fusarium circinatum. Pathogens 2024, 13, 70. https://doi.org/10.3390/pathogens13010070.en_US
dc.identifier.issn2076-0817 (online)
dc.identifier.other10.3390/pathogens13010070
dc.identifier.urihttp://hdl.handle.net/2263/101934
dc.language.isoenen_US
dc.publisherMDPIen_US
dc.rights© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an Open Access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).en_US
dc.subjectDispensable chromosomeen_US
dc.subjectCentromereen_US
dc.subjectTelomereen_US
dc.subjectIntrachromosomal translocationen_US
dc.subjectSDG-09: Industry, innovation and infrastructureen_US
dc.subjectSDG-15: Life on landen_US
dc.titleChromosome-level assemblies for the pine pitch canker pathogen Fusarium circinatumen_US
dc.typeArticleen_US

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