The first genome assembly of fungal pathogen Pyrenophora tritici-repentis race 1 isolate using Oxford Nanopore MinION sequencing
Objectives: The assembly of fungal genomes using short-reads is challenged by long repetitive and low GC regions. However, long-read sequencing technologies, such as PacBio and Oxford Nanopore, are able to overcome many problematic regions, thereby providing an opportunity to improve fragmented geno...
| Main Authors: | , , |
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| Format: | Journal Article |
| Language: | English |
| Published: |
2021
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| Subjects: | |
| Online Access: | http://hdl.handle.net/20.500.11937/87625 |
| _version_ | 1848764929923874816 |
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| author | Moolhuijzen, Paula See, Pao Theen Moffat, Caroline |
| author_facet | Moolhuijzen, Paula See, Pao Theen Moffat, Caroline |
| author_sort | Moolhuijzen, Paula |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | Objectives: The assembly of fungal genomes using short-reads is challenged by long repetitive and low GC regions. However, long-read sequencing technologies, such as PacBio and Oxford Nanopore, are able to overcome many problematic regions, thereby providing an opportunity to improve fragmented genome assemblies derived from short reads only. Here, a necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) isolate 134 (Ptr134), which causes tan spot disease on wheat, was sequenced on a MinION using Oxford Nanopore Technologies (ONT), to improve on a previous Illumina short-read genome assembly and provide a more complete genome resource for pan-genomic analyses of Ptr.
Results: The genome of Ptr134 sequenced on a MinION using ONT was assembled into 28 contiguous sequences with a total length of 40.79 Mb and GC content of 50.81%. The long-read assembly provided 6.79 Mb of new sequence and 2846 extra annotated protein coding genes as compared to the previous short-read assembly. This improved genome sequence represents near complete chromosomes, an important resource for large scale and pan genomic comparative analyses. |
| first_indexed | 2025-11-14T11:27:10Z |
| format | Journal Article |
| id | curtin-20.500.11937-87625 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| language | eng |
| last_indexed | 2025-11-14T11:27:10Z |
| publishDate | 2021 |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-876252022-03-03T01:09:28Z The first genome assembly of fungal pathogen Pyrenophora tritici-repentis race 1 isolate using Oxford Nanopore MinION sequencing Moolhuijzen, Paula See, Pao Theen Moffat, Caroline Comparative analysis Genome assembly MinION Oxford Nanopore Pyrenophora tritici-repentis Tan spot ToxA Yellow spot Ascomycota Genome, Fungal High-Throughput Nucleotide Sequencing Nanopores Objectives: The assembly of fungal genomes using short-reads is challenged by long repetitive and low GC regions. However, long-read sequencing technologies, such as PacBio and Oxford Nanopore, are able to overcome many problematic regions, thereby providing an opportunity to improve fragmented genome assemblies derived from short reads only. Here, a necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) isolate 134 (Ptr134), which causes tan spot disease on wheat, was sequenced on a MinION using Oxford Nanopore Technologies (ONT), to improve on a previous Illumina short-read genome assembly and provide a more complete genome resource for pan-genomic analyses of Ptr. Results: The genome of Ptr134 sequenced on a MinION using ONT was assembled into 28 contiguous sequences with a total length of 40.79 Mb and GC content of 50.81%. The long-read assembly provided 6.79 Mb of new sequence and 2846 extra annotated protein coding genes as compared to the previous short-read assembly. This improved genome sequence represents near complete chromosomes, an important resource for large scale and pan genomic comparative analyses. 2021 Journal Article http://hdl.handle.net/20.500.11937/87625 10.1186/s13104-021-05751-0 eng http://creativecommons.org/licenses/by/4.0/ fulltext |
| spellingShingle | Comparative analysis Genome assembly MinION Oxford Nanopore Pyrenophora tritici-repentis Tan spot ToxA Yellow spot Ascomycota Genome, Fungal High-Throughput Nucleotide Sequencing Nanopores Moolhuijzen, Paula See, Pao Theen Moffat, Caroline The first genome assembly of fungal pathogen Pyrenophora tritici-repentis race 1 isolate using Oxford Nanopore MinION sequencing |
| title | The first genome assembly of fungal pathogen Pyrenophora tritici-repentis race 1 isolate using Oxford Nanopore MinION sequencing |
| title_full | The first genome assembly of fungal pathogen Pyrenophora tritici-repentis race 1 isolate using Oxford Nanopore MinION sequencing |
| title_fullStr | The first genome assembly of fungal pathogen Pyrenophora tritici-repentis race 1 isolate using Oxford Nanopore MinION sequencing |
| title_full_unstemmed | The first genome assembly of fungal pathogen Pyrenophora tritici-repentis race 1 isolate using Oxford Nanopore MinION sequencing |
| title_short | The first genome assembly of fungal pathogen Pyrenophora tritici-repentis race 1 isolate using Oxford Nanopore MinION sequencing |
| title_sort | first genome assembly of fungal pathogen pyrenophora tritici-repentis race 1 isolate using oxford nanopore minion sequencing |
| topic | Comparative analysis Genome assembly MinION Oxford Nanopore Pyrenophora tritici-repentis Tan spot ToxA Yellow spot Ascomycota Genome, Fungal High-Throughput Nucleotide Sequencing Nanopores |
| url | http://hdl.handle.net/20.500.11937/87625 |