Chromosome-Level Assemblies for the Pine Pitch Canker Pathogen <i<Fusarium circinatum</i<
The pine pitch canker pathogen, <i<Fusarium circinatum</i<, 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 wa...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Lieschen De Vos [verfasserIn] Magriet A. van der Nest [verfasserIn] Quentin C. Santana [verfasserIn] Stephanie van Wyk [verfasserIn] Kyle S. Leeuwendaal [verfasserIn] Brenda D. Wingfield [verfasserIn] Emma T. Steenkamp [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2024 |
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| Schlagwörter: |
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| Übergeordnetes Werk: |
In: Pathogens - MDPI AG, 2012, 13(2024), 1, p 70 |
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| Übergeordnetes Werk: |
volume:13 ; year:2024 ; number:1, p 70 |
| Links: |
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| DOI / URN: |
10.3390/pathogens13010070 |
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| Katalog-ID: |
DOAJ096311584 |
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| 520 | |a The pine pitch canker pathogen, <i<Fusarium circinatum</i<, 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 <i<F. circinatum</i<, 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 <i<F. circinatum</i< 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 <i<F. circinatum</i< strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of <i<F. circinatum</i< 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. | ||
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10.3390/pathogens13010070 doi (DE-627)DOAJ096311584 (DE-599)DOAJcd1f09946a1c47e2a68604f3567716c6 DE-627 ger DE-627 rakwb eng Lieschen De Vos verfasserin aut Chromosome-Level Assemblies for the Pine Pitch Canker Pathogen <i<Fusarium circinatum</i< 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The pine pitch canker pathogen, <i<Fusarium circinatum</i<, 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 <i<F. circinatum</i<, 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 <i<F. circinatum</i< 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 <i<F. circinatum</i< strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of <i<F. circinatum</i< 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. dispensable chromosome centromere telomere intrachromosomal translocation Medicine R Magriet A. van der Nest verfasserin aut Quentin C. Santana verfasserin aut Stephanie van Wyk verfasserin aut Kyle S. Leeuwendaal verfasserin aut Brenda D. Wingfield verfasserin aut Emma T. Steenkamp verfasserin aut In Pathogens MDPI AG, 2012 13(2024), 1, p 70 (DE-627)732627885 (DE-600)2695572-6 20760817 nnns volume:13 year:2024 number:1, p 70 https://doi.org/10.3390/pathogens13010070 kostenfrei https://doaj.org/article/cd1f09946a1c47e2a68604f3567716c6 kostenfrei https://www.mdpi.com/2076-0817/13/1/70 kostenfrei https://doaj.org/toc/2076-0817 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2024 1, p 70 |
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10.3390/pathogens13010070 doi (DE-627)DOAJ096311584 (DE-599)DOAJcd1f09946a1c47e2a68604f3567716c6 DE-627 ger DE-627 rakwb eng Lieschen De Vos verfasserin aut Chromosome-Level Assemblies for the Pine Pitch Canker Pathogen <i<Fusarium circinatum</i< 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The pine pitch canker pathogen, <i<Fusarium circinatum</i<, 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 <i<F. circinatum</i<, 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 <i<F. circinatum</i< 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 <i<F. circinatum</i< strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of <i<F. circinatum</i< 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. dispensable chromosome centromere telomere intrachromosomal translocation Medicine R Magriet A. van der Nest verfasserin aut Quentin C. Santana verfasserin aut Stephanie van Wyk verfasserin aut Kyle S. Leeuwendaal verfasserin aut Brenda D. Wingfield verfasserin aut Emma T. Steenkamp verfasserin aut In Pathogens MDPI AG, 2012 13(2024), 1, p 70 (DE-627)732627885 (DE-600)2695572-6 20760817 nnns volume:13 year:2024 number:1, p 70 https://doi.org/10.3390/pathogens13010070 kostenfrei https://doaj.org/article/cd1f09946a1c47e2a68604f3567716c6 kostenfrei https://www.mdpi.com/2076-0817/13/1/70 kostenfrei https://doaj.org/toc/2076-0817 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2024 1, p 70 |
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10.3390/pathogens13010070 doi (DE-627)DOAJ096311584 (DE-599)DOAJcd1f09946a1c47e2a68604f3567716c6 DE-627 ger DE-627 rakwb eng Lieschen De Vos verfasserin aut Chromosome-Level Assemblies for the Pine Pitch Canker Pathogen <i<Fusarium circinatum</i< 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The pine pitch canker pathogen, <i<Fusarium circinatum</i<, 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 <i<F. circinatum</i<, 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 <i<F. circinatum</i< 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 <i<F. circinatum</i< strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of <i<F. circinatum</i< 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. dispensable chromosome centromere telomere intrachromosomal translocation Medicine R Magriet A. van der Nest verfasserin aut Quentin C. Santana verfasserin aut Stephanie van Wyk verfasserin aut Kyle S. Leeuwendaal verfasserin aut Brenda D. Wingfield verfasserin aut Emma T. Steenkamp verfasserin aut In Pathogens MDPI AG, 2012 13(2024), 1, p 70 (DE-627)732627885 (DE-600)2695572-6 20760817 nnns volume:13 year:2024 number:1, p 70 https://doi.org/10.3390/pathogens13010070 kostenfrei https://doaj.org/article/cd1f09946a1c47e2a68604f3567716c6 kostenfrei https://www.mdpi.com/2076-0817/13/1/70 kostenfrei https://doaj.org/toc/2076-0817 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2024 1, p 70 |
| allfieldsGer |
10.3390/pathogens13010070 doi (DE-627)DOAJ096311584 (DE-599)DOAJcd1f09946a1c47e2a68604f3567716c6 DE-627 ger DE-627 rakwb eng Lieschen De Vos verfasserin aut Chromosome-Level Assemblies for the Pine Pitch Canker Pathogen <i<Fusarium circinatum</i< 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The pine pitch canker pathogen, <i<Fusarium circinatum</i<, 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 <i<F. circinatum</i<, 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 <i<F. circinatum</i< 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 <i<F. circinatum</i< strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of <i<F. circinatum</i< 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. dispensable chromosome centromere telomere intrachromosomal translocation Medicine R Magriet A. van der Nest verfasserin aut Quentin C. Santana verfasserin aut Stephanie van Wyk verfasserin aut Kyle S. Leeuwendaal verfasserin aut Brenda D. Wingfield verfasserin aut Emma T. Steenkamp verfasserin aut In Pathogens MDPI AG, 2012 13(2024), 1, p 70 (DE-627)732627885 (DE-600)2695572-6 20760817 nnns volume:13 year:2024 number:1, p 70 https://doi.org/10.3390/pathogens13010070 kostenfrei https://doaj.org/article/cd1f09946a1c47e2a68604f3567716c6 kostenfrei https://www.mdpi.com/2076-0817/13/1/70 kostenfrei https://doaj.org/toc/2076-0817 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2024 1, p 70 |
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10.3390/pathogens13010070 doi (DE-627)DOAJ096311584 (DE-599)DOAJcd1f09946a1c47e2a68604f3567716c6 DE-627 ger DE-627 rakwb eng Lieschen De Vos verfasserin aut Chromosome-Level Assemblies for the Pine Pitch Canker Pathogen <i<Fusarium circinatum</i< 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The pine pitch canker pathogen, <i<Fusarium circinatum</i<, 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 <i<F. circinatum</i<, 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 <i<F. circinatum</i< 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 <i<F. circinatum</i< strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of <i<F. circinatum</i< 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. dispensable chromosome centromere telomere intrachromosomal translocation Medicine R Magriet A. van der Nest verfasserin aut Quentin C. Santana verfasserin aut Stephanie van Wyk verfasserin aut Kyle S. Leeuwendaal verfasserin aut Brenda D. Wingfield verfasserin aut Emma T. Steenkamp verfasserin aut In Pathogens MDPI AG, 2012 13(2024), 1, p 70 (DE-627)732627885 (DE-600)2695572-6 20760817 nnns volume:13 year:2024 number:1, p 70 https://doi.org/10.3390/pathogens13010070 kostenfrei https://doaj.org/article/cd1f09946a1c47e2a68604f3567716c6 kostenfrei https://www.mdpi.com/2076-0817/13/1/70 kostenfrei https://doaj.org/toc/2076-0817 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2024 1, p 70 |
| language |
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Chromosome-Level Assemblies for the Pine Pitch Canker Pathogen <i<Fusarium circinatum</i< |
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The pine pitch canker pathogen, <i<Fusarium circinatum</i<, 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 <i<F. circinatum</i<, 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 <i<F. circinatum</i< 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 <i<F. circinatum</i< strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of <i<F. circinatum</i< 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. |
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The pine pitch canker pathogen, <i<Fusarium circinatum</i<, 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 <i<F. circinatum</i<, 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 <i<F. circinatum</i< 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 <i<F. circinatum</i< strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of <i<F. circinatum</i< 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. |
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The pine pitch canker pathogen, <i<Fusarium circinatum</i<, 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 <i<F. circinatum</i<, 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 <i<F. circinatum</i< 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 <i<F. circinatum</i< strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of <i<F. circinatum</i< 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. |
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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 <i<F. circinatum</i<, 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 <i<F. circinatum</i< 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 <i<F. circinatum</i< strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of <i<F. circinatum</i< and its relatives. 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