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A new PacBio genome sequence of an Australian Pyrenophora tritici-repentis race 1 isolate

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 l...

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Autores principales: Moolhuijzen, Paula, See, Pao Theen, Moffat, Caroline S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6778365/
https://www.ncbi.nlm.nih.gov/pubmed/31585535
http://dx.doi.org/10.1186/s13104-019-4681-6
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author Moolhuijzen, Paula
See, Pao Theen
Moffat, Caroline S.
author_facet Moolhuijzen, Paula
See, Pao Theen
Moffat, Caroline S.
author_sort Moolhuijzen, Paula
collection PubMed
description 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.
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spelling pubmed-67783652019-10-07 A new PacBio genome sequence of an Australian Pyrenophora tritici-repentis race 1 isolate Moolhuijzen, Paula See, Pao Theen Moffat, Caroline S. BMC Res Notes Research Note 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. BioMed Central 2019-10-04 /pmc/articles/PMC6778365/ /pubmed/31585535 http://dx.doi.org/10.1186/s13104-019-4681-6 Text en © The Author(s) 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Note
Moolhuijzen, Paula
See, Pao Theen
Moffat, Caroline S.
A new PacBio genome sequence of an Australian Pyrenophora tritici-repentis race 1 isolate
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 Research Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6778365/
https://www.ncbi.nlm.nih.gov/pubmed/31585535
http://dx.doi.org/10.1186/s13104-019-4681-6
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