Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating-type locus
Diplocarpon coronariae is a fungal pathogen that is prevalent in low-input apple production. Over the past 15 years, it has become increasingly distributed in Europe. However, comprehensive insights into its biology and pathogenicity remain limited. One particular aspect is the rarity of the sexual...
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Frontiers Media S.A.
2024-10-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1437132/full |
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| author | Sophie Richter Sophie Richter Sabine Kind Thomas Oberhänsli Michael Schneider Natalia Nenasheva Katharina Hoff Jens Keilwagen Il-Kweon Yeon Vincent Philion Shigeki Moriya Henryk Flachowsky Andrea Patocchi Thomas Wolfgang Wöhner |
| author_facet | Sophie Richter Sophie Richter Sabine Kind Thomas Oberhänsli Michael Schneider Natalia Nenasheva Katharina Hoff Jens Keilwagen Il-Kweon Yeon Vincent Philion Shigeki Moriya Henryk Flachowsky Andrea Patocchi Thomas Wolfgang Wöhner |
| author_sort | Sophie Richter |
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| description | Diplocarpon coronariae is a fungal pathogen that is prevalent in low-input apple production. Over the past 15 years, it has become increasingly distributed in Europe. However, comprehensive insights into its biology and pathogenicity remain limited. One particular aspect is the rarity of the sexual morph of this pathogen, a phenomenon hitherto unobserved in Europe. Diplocarpon coronariae reproduces through a heterothallic mating system requiring at least two different mating types for sexual reproduction. Genes determining the mating types are located on the mating-type locus. In this study, D. coronariae strain DC1_JKI from Dresden, Germany, was sequenced and used to unravel the structure of the mating type locus. Using short-read and long-read sequencing methods, the first gapless and near-complete telomere-to-telomere genome assembly of D. coronariae was achieved. The assembled genome spans 51.2 Mbp and comprises 21 chromosome-scale contigs of high completeness. The generated genome sequence was used to in silico elucidate the structure of the mating-type locus, identified as MAT1-2. Furthermore, an examination of MAT1-1 and MAT1-2 frequency across a diverse set of samples sourced from Europe and Asia revealed the exclusive presence of MAT1-2 in European samples, whereas both MAT loci were present in Asian counterparts. Our findings suggest an explanation for the absence of the sexual morph, potentially linked to the absence of the second mating idiomorph of D. coronariae in European apple orchards. |
| format | Article |
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| issn | 1664-462X |
| language | English |
| publishDate | 2024-10-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj-art-07a5dc0a441c428fadbb63ad366eff1e2025-08-20T01:56:52ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2024-10-011510.3389/fpls.2024.14371321437132Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating-type locusSophie Richter0Sophie Richter1Sabine Kind2Thomas Oberhänsli3Michael Schneider4Natalia Nenasheva5Katharina Hoff6Jens Keilwagen7Il-Kweon Yeon8Vincent Philion9Shigeki Moriya10Henryk Flachowsky11Andrea Patocchi12Thomas Wolfgang Wöhner13Institute for Breeding Research on Fruit Crops, Julius Kühn-Institute (JKI) – Federal Research Centre for Cultivated Plants, Dresden, GermanyInstitute for Plant Genetics, Leibniz University Hannover, Hanover, GermanyInstitute for Plant Protection in Fruit Crops and Viticulture, Julius Kühn Institute (JKI) Federal Research Centre for Cultivated Plants, Dossenheim, GermanyDepartment of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, SwitzerlandDepartment of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, SwitzerlandInstitute of Mathematics and Computer Science and Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, GermanyInstitute of Mathematics and Computer Science and Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, GermanyInstitute for Biosafety in Plant Biotechnology, Julius Kühn-Institute (JKI) – Federal Research Centre for Cultivated Plants, Quedlinburg, GermanyGyeongsangbuk-do Agricultural Research and Extension Services (GBARES), Daegu, Republic of KoreaResearch and Development Institute for the Agri-Environment (IRDA), Québec, QC, CanadaInstitute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Morioka, JapanInstitute for Breeding Research on Fruit Crops, Julius Kühn-Institute (JKI) – Federal Research Centre for Cultivated Plants, Dresden, Germany0Research Division Plant Breeding, Agroscope, Waedenswil, SwitzerlandInstitute for Breeding Research on Fruit Crops, Julius Kühn-Institute (JKI) – Federal Research Centre for Cultivated Plants, Dresden, GermanyDiplocarpon coronariae is a fungal pathogen that is prevalent in low-input apple production. Over the past 15 years, it has become increasingly distributed in Europe. However, comprehensive insights into its biology and pathogenicity remain limited. One particular aspect is the rarity of the sexual morph of this pathogen, a phenomenon hitherto unobserved in Europe. Diplocarpon coronariae reproduces through a heterothallic mating system requiring at least two different mating types for sexual reproduction. Genes determining the mating types are located on the mating-type locus. In this study, D. coronariae strain DC1_JKI from Dresden, Germany, was sequenced and used to unravel the structure of the mating type locus. Using short-read and long-read sequencing methods, the first gapless and near-complete telomere-to-telomere genome assembly of D. coronariae was achieved. The assembled genome spans 51.2 Mbp and comprises 21 chromosome-scale contigs of high completeness. The generated genome sequence was used to in silico elucidate the structure of the mating-type locus, identified as MAT1-2. Furthermore, an examination of MAT1-1 and MAT1-2 frequency across a diverse set of samples sourced from Europe and Asia revealed the exclusive presence of MAT1-2 in European samples, whereas both MAT loci were present in Asian counterparts. Our findings suggest an explanation for the absence of the sexual morph, potentially linked to the absence of the second mating idiomorph of D. coronariae in European apple orchards.https://www.frontiersin.org/articles/10.3389/fpls.2024.1437132/fullapple blotchD. coronariaeMalusgenome sequenceshort readslong reads |
| spellingShingle | Sophie Richter Sophie Richter Sabine Kind Thomas Oberhänsli Michael Schneider Natalia Nenasheva Katharina Hoff Jens Keilwagen Il-Kweon Yeon Vincent Philion Shigeki Moriya Henryk Flachowsky Andrea Patocchi Thomas Wolfgang Wöhner Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating-type locus Frontiers in Plant Science apple blotch D. coronariae Malus genome sequence short reads long reads |
| title | Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating-type locus |
| title_full | Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating-type locus |
| title_fullStr | Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating-type locus |
| title_full_unstemmed | Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating-type locus |
| title_short | Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating-type locus |
| title_sort | genome sequence of a european diplocarpon coronariae strain and in silico structure of the mating type locus |
| topic | apple blotch D. coronariae Malus genome sequence short reads long reads |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1437132/full |
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