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Volume 9, Issue 11

The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Open Access

Abstract

Long non-coding RNAs (lncRNAs) are regulatory molecules interacting in a wide array of biological processes. lncRNAs in fungal pathogens can be responsive to stress and play roles in regulating growth and nutrient acquisition. Recent evidence suggests that lncRNAs may also play roles in virulence, such as regulating pathogenicity-associated enzymes and on-host reproductive cycles. Despite the importance of lncRNAs, only a few model fungi have well-documented inventories of lncRNA. In this study, we apply a recent computational pipeline to predict high-confidence lncRNA candidates in an important global pathogen of wheat impacting global food production. We analyse genomic features of lncRNAs and the most likely associated processes through analyses of expression over a host infection cycle. We find that lncRNAs are frequently expressed during early infection, before the switch to necrotrophic growth. They are mostly located in facultative heterochromatic regions, which are known to contain many genes associated with pathogenicity. Furthermore, we find that lncRNAs are frequently co-expressed with genes that may be involved in responding to host defence signals, such as oxidative stress. Finally, we assess pangenome features of lncRNAs using four additional reference-quality genomes. We find evidence that the repertoire of expressed lncRNAs varies substantially between individuals, even though lncRNA loci tend to be shared at the genomic level. Overall, this study provides a repertoire and putative functions of lncRNAs in enabling future molecular genetics and functional analyses in an important pathogen.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): expression analyses , long non-coding RNA , pangenomes , plant pathogen and Zymoseptoria tritici
Funding
This study was supported by the:
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Award 205401)
    • Principle Award Recipient: DanielCroll
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2023-11-22
2024-04-27
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The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Zymoseptoria tritici
M Gen 9, 001136 (2023); https://doi.org/10.1099/mgen.0.001136
/content/journal/mgen/10.1099/mgen.0.001136
/content/journal/mgen/10.1099/mgen.0.001136
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