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Volume 8, Issue 4

A chromosome-scale genome assembly of the tomato pathogen reveals a compartmentalized genome architecture and the presence of a dispensable chromosome Open Access

Abstract

is a fungal pathogen that causes leaf mould of tomato. The reference genome of this pathogen was released in 2012 but its high repetitive DNA content prevented a contiguous assembly and further prohibited the analysis of its genome architecture. In this study, we combined third generation sequencing technology with the Hi-C chromatin conformation capture technique, to produce a high-quality and near complete genome assembly and gene annotation of a Race 5 isolate of . The resulting genome assembly contained 67.17 Mb organized into 14 chromosomes (Chr1-to-Chr14), all of which were assembled telomere-to-telomere. The smallest of the chromosomes, Chr14, is only 460 kb in size and contains 25 genes that all encode hypothetical proteins. Notably, PCR assays revealed that Chr14 was absent in 19 out of 24 isolates of a world-wide collection of , indicating that Chr14 is dispensable. Thus, is currently the second species of Capnodiales shown to harbour dispensable chromosomes. The genome of Race 5 is 49.7 % repetitive and contains 14 690 predicted genes with an estimated completeness of 98.9%, currently one of the highest among the Capnodiales. Genome structure analysis revealed a compartmentalized architecture composed of gene-dense and repeat-poor regions interspersed with gene-sparse and repeat-rich regions. Nearly 39.2 % of the Race 5 genome is affected by Repeat-Induced Point (RIP) mutations and evidence of RIP leakage toward non-repetitive regions was observed in all chromosomes, indicating the RIP plays an important role in the evolution of this pathogen. Finally, 345 genes encoding candidate effectors were identified in Race 5, with a significant enrichment of their location in gene-sparse regions, in accordance with the ‘two-speed genome’ model of evolution. Overall, the new reference genome of presents several notable features and is a valuable resource for studies in plant pathogens.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Accessory chromosome , effectors , fungal pathogen evolution , gene duplication , repeat-induced point mutation and two-speed genome
Funding
This study was supported by the:
  • University of California, Davis (Award Dean’s Distinguished Graduate Fellowship (DDGF) program)
    • Principle Award Recipient: AlexZanella Zaccaron
  • USDA-NIFA (Award CA-D-PPA-2185-H)
    • Principle Award Recipient: IoannisStergiopoulos
  • Directorate for Biological Sciences (Award 1557995)
    • Principle Award Recipient: IoannisStergiopoulos
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2022-04-26
2024-05-13
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http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000819
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A chromosome-scale genome assembly of the tomato pathogen Cladosporium fulvum reveals a compartmentalized genome architecture and the presence of a dispensable chromosome
M Gen 8, 000819 (2022); https://doi.org/10.1099/mgen.0.000819
/content/journal/mgen/10.1099/mgen.0.000819
/content/journal/mgen/10.1099/mgen.0.000819
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