A new PacBio genome sequence of an Australian Pyrenophora tritici-repentis race 1 isolate
Abstract Objectives The necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) is the causal agent of tan spot a major disease of wheat. We have generated a new genome resource for an Australian Ptr race 1 isolate V1 to support comparative ‘omics analyses. In particular, the V1 PacBio Biosc...
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| Format: | Article |
| Language: | English |
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BMC
2019-10-01
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| Series: | BMC Research Notes |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13104-019-4681-6 |
| _version_ | 1818552745622241280 |
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| author | Paula Moolhuijzen Pao Theen See Caroline S. Moffat |
| author_facet | Paula Moolhuijzen Pao Theen See Caroline S. Moffat |
| author_sort | Paula Moolhuijzen |
| collection | DOAJ |
| description | Abstract Objectives The necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) is the causal agent of tan spot a major disease of wheat. We have generated a new genome resource for an Australian Ptr race 1 isolate V1 to support comparative ‘omics analyses. In particular, the V1 PacBio Biosciences long-read sequence assembly was generated to confirm the stability of large-scale genome rearrangements of the Australian race 1 isolate M4 when compared to the North American race 1 isolate Pt-1C-BFP. Results Over 1.3 million reads were sequenced by PacBio Sequel small-molecule real-time sequencing (SRMT) cell to yield 11.4 Gb for the genome assembly of V1 (285X coverage), with median and maximum read lengths of 8959 bp and 72,292 bp respectively. The V1 genome was assembled into 33 contiguous sequences with a of total length 40.4 Mb and GC content of 50.44%. A total of 14,050 protein coding genes were predicted and annotated for V1. Of these 11,519 genes were orthologous to both Pt-1C-BFP and M4. Whole genome alignment of the Australian long-read assemblies (V1 to M4) confirmed previously identified large-scale genome rearrangements between M4 and Pt-1C-BFP and presented small scale variations, which included a sequence break within a race-specific region for ToxA, a well-known necrotrophic effector gene. |
| first_indexed | 2024-12-12T09:17:11Z |
| format | Article |
| id | doaj.art-54ac8462e04c4346b0e3ce5c84ff4704 |
| institution | Directory Open Access Journal |
| issn | 1756-0500 |
| language | English |
| last_indexed | 2024-12-12T09:17:11Z |
| publishDate | 2019-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Research Notes |
| spelling | doaj.art-54ac8462e04c4346b0e3ce5c84ff47042022-12-22T00:29:21ZengBMCBMC Research Notes1756-05002019-10-011211510.1186/s13104-019-4681-6A new PacBio genome sequence of an Australian Pyrenophora tritici-repentis race 1 isolatePaula Moolhuijzen0Pao Theen See1Caroline S. Moffat2Centre for Crop Disease and Management, School of Molecular Life Sciences, Curtin UniversityCentre for Crop Disease and Management, School of Molecular Life Sciences, Curtin UniversityCentre for Crop Disease and Management, School of Molecular Life Sciences, Curtin UniversityAbstract Objectives The necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) is the causal agent of tan spot a major disease of wheat. We have generated a new genome resource for an Australian Ptr race 1 isolate V1 to support comparative ‘omics analyses. In particular, the V1 PacBio Biosciences long-read sequence assembly was generated to confirm the stability of large-scale genome rearrangements of the Australian race 1 isolate M4 when compared to the North American race 1 isolate Pt-1C-BFP. Results Over 1.3 million reads were sequenced by PacBio Sequel small-molecule real-time sequencing (SRMT) cell to yield 11.4 Gb for the genome assembly of V1 (285X coverage), with median and maximum read lengths of 8959 bp and 72,292 bp respectively. The V1 genome was assembled into 33 contiguous sequences with a of total length 40.4 Mb and GC content of 50.44%. A total of 14,050 protein coding genes were predicted and annotated for V1. Of these 11,519 genes were orthologous to both Pt-1C-BFP and M4. Whole genome alignment of the Australian long-read assemblies (V1 to M4) confirmed previously identified large-scale genome rearrangements between M4 and Pt-1C-BFP and presented small scale variations, which included a sequence break within a race-specific region for ToxA, a well-known necrotrophic effector gene.http://link.springer.com/article/10.1186/s13104-019-4681-6Pyrenophora tritici-repentisGenome assemblyPacBio sequelComparative analysisToxATan spot |
| spellingShingle | Paula Moolhuijzen Pao Theen See Caroline S. Moffat A new PacBio genome sequence of an Australian Pyrenophora tritici-repentis race 1 isolate BMC Research Notes Pyrenophora tritici-repentis Genome assembly PacBio sequel Comparative analysis ToxA Tan spot |
| title | A new PacBio genome sequence of an Australian Pyrenophora tritici-repentis race 1 isolate |
| title_full | A new PacBio genome sequence of an Australian Pyrenophora tritici-repentis race 1 isolate |
| title_fullStr | A new PacBio genome sequence of an Australian Pyrenophora tritici-repentis race 1 isolate |
| title_full_unstemmed | A new PacBio genome sequence of an Australian Pyrenophora tritici-repentis race 1 isolate |
| title_short | A new PacBio genome sequence of an Australian Pyrenophora tritici-repentis race 1 isolate |
| title_sort | new pacbio genome sequence of an australian pyrenophora tritici repentis race 1 isolate |
| topic | Pyrenophora tritici-repentis Genome assembly PacBio sequel Comparative analysis ToxA Tan spot |
| url | http://link.springer.com/article/10.1186/s13104-019-4681-6 |
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