Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating-type locus

Research output: Contribution to journalArticleResearchpeer review

Authors

  • Sophie Richter
  • Sabine Kind
  • Thomas Wolfgang Oberhänsli
  • Michael Schneider
  • Natalia Nenasheva
  • Katharina Hoff
  • Jens Keilwagen
  • Il Kweon Yeon
  • Vincent Philion
  • Shigeki Moriya
  • Henryk Flachowsky
  • Andrea Patocchi
  • Thomas Wolfgang Wöhner

External Research Organisations

  • Julius Kühn Institute - Federal Research Centre for Cultivated Plants (JKI)
  • Research Institute of Organic Agriculture (FiBL)
  • University of Greifswald
  • Gyeongsangbuk-do Agricultural Research and Extension Services (GBARES)
  • Research and Development Institute for the Agri-Environment (IRDA)
  • National Agricultural Research Centers Japan
  • Agroscope
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Details

Original languageEnglish
Article number1437132
Number of pages16
JournalFrontiers in Plant Science
Volume15
Publication statusPublished - 18 Oct 2024
Externally publishedYes

Abstract

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.

Keywords

    apple blotch, D. coronariae, genome sequence, long reads, Malus, mating types, short reads

ASJC Scopus subject areas

Cite this

Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating-type locus. / Richter, Sophie; Kind, Sabine; Oberhänsli, Thomas Wolfgang et al.
In: Frontiers in Plant Science, Vol. 15, 1437132, 18.10.2024.

Research output: Contribution to journalArticleResearchpeer review

Richter, S, Kind, S, Oberhänsli, TW, Schneider, M, Nenasheva, N, Hoff, K, Keilwagen, J, Yeon, IK, Philion, V, Moriya, S, Flachowsky, H, Patocchi, A & Wöhner, TW 2024, 'Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating-type locus', Frontiers in Plant Science, vol. 15, 1437132. https://doi.org/10.3389/fpls.2024.1437132
Richter, S., Kind, S., Oberhänsli, T. W., Schneider, M., Nenasheva, N., Hoff, K., Keilwagen, J., Yeon, I. K., Philion, V., Moriya, S., Flachowsky, H., Patocchi, A., & Wöhner, T. W. (2024). Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating-type locus. Frontiers in Plant Science, 15, Article 1437132. https://doi.org/10.3389/fpls.2024.1437132
Richter S, Kind S, Oberhänsli TW, Schneider M, Nenasheva N, Hoff K et al. Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating-type locus. Frontiers in Plant Science. 2024 Oct 18;15:1437132. doi: 10.3389/fpls.2024.1437132
Richter, Sophie ; Kind, Sabine ; Oberhänsli, Thomas Wolfgang et al. / Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating-type locus. In: Frontiers in Plant Science. 2024 ; Vol. 15.
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title = "Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating-type locus",
abstract = "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.",
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AU - Richter, Sophie

AU - Kind, Sabine

AU - Oberhänsli, Thomas Wolfgang

AU - Schneider, Michael

AU - Nenasheva, Natalia

AU - Hoff, Katharina

AU - Keilwagen, Jens

AU - Yeon, Il Kweon

AU - Philion, Vincent

AU - Moriya, Shigeki

AU - Flachowsky, Henryk

AU - Patocchi, Andrea

AU - Wöhner, Thomas Wolfgang

N1 - Publisher Copyright: Copyright © 2024 Richter, Kind, Oberhänsli, Schneider, Nenasheva, Hoff, Keilwagen, Yeon, Philion, Moriya, Flachowsky, Patocchi and Wöhner.

PY - 2024/10/18

Y1 - 2024/10/18

N2 - 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.

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KW - D. coronariae

KW - genome sequence

KW - long reads

KW - Malus

KW - mating types

KW - short reads

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DO - 10.3389/fpls.2024.1437132

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JO - Frontiers in Plant Science

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