Improved Gene Annotation of the Fungal Wheat Pathogen <i>Zymoseptoria tritici</i> Based on Combined Iso-Seq and RNA-Seq Evidence
Despite large omics datasets, the prediction of eukaryotic genes is still challenging. We have developed a new method to improve the prediction of eukaryotic genes and demonstrate its utility using the genome of the fungal wheat pathogen <i>Zymoseptoria tritici</i>. From 10,933 to 13,260 genes were predicted by four previous annotations, but only one third were identical. A novel bioinformatics suite, InGenAnnot, was developed to improve <i>Z</i>. <i>tritici</i> gene annotation using Iso-Seq full-length transcript sequences. The best gene models were selected among different ab initio gene predictions, according to transcript and protein evidence. Overall, 13,414 reannotated gene models (RGMs) were predicted, improving previous annotations. Iso-Seq transcripts outlined 5' and 3' untranslated regions for 73% of the RGMs and alternative transcripts mainly due to intron retention. Our results showed that the combination of different ab initio gene predictions and evidence-driven curation improved gene annotation of a eukaryotic genome. It also provided new insights into the transcriptional landscape of this fungus. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Authors
- Justine Sucher (ORCID: https://orcid.org/0000-0002-9580-1315)
- Igor V. Grigoriev (ORCID: https://orcid.org/0000-0002-3136-8903)
- Yohann Petit (ORCID: https://orcid.org/0000-0003-4806-8349)
- Andrei Stecca Steindorff (ORCID: https://orcid.org/0000-0002-2052-2848)
- Robert C. King (ORCID: https://orcid.org/0000-0003-1828-9490)
- Lucie Lamothe
- James K. Hane (ORCID: https://orcid.org/0000-0002-7651-0977)
- Mélanie Appertet
- Stephen B. Goodwin (ORCID: https://orcid.org/0000-0001-5708-9729)
- Daniel Croll (ORCID: https://orcid.org/0000-0002-2072-380X)
- J. J. Rudd (ORCID: https://orcid.org/0000-0002-4743-1401)
- G.H.J. Kema (ORCID: https://orcid.org/0000-0002-2732-6911)
- Alice Feurtey (ORCID: https://orcid.org/0000-0001-6315-9631)
- Alison Renwick
- Marc‐Henri Lebrun (ORCID: https://orcid.org/0000-0003-1562-1902)
- Camille Delude
- Leen Abraham (ORCID: https://orcid.org/0000-0002-9122-6456)
- Nicolas Lapalu (ORCID: https://orcid.org/0000-0002-9773-4611)
- Daniel P. Smith (ORCID: https://orcid.org/0000-0003-3158-3969)
- Anne Génissel (ORCID: https://orcid.org/0000-0001-7120-181X)
- Eva Stukenbrock
- Gabriel Scalliet
Institutions
- Agricultural Research Service (US)
- Institut National de la Recherche Agronomique (MA)
- Lawrence Berkeley National Laboratory (US)
- Joint Genome Institute (US)
- Curtin University (AU)
- Université Paris-Saclay (FR)
- Rothamsted Research (GB)
- Christian-Albrechts-Universität zu Kiel (DE)
- ETH Zurich (CH)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Cropping Systems Research Laboratory (US)
- Max Planck Institute for Evolutionary Biology (DE)
- University of Neuchâtel (CH)
- Epigenomics (Germany) (DE)
- Syngenta (Switzerland) (CH)
- Wageningen University & Research (NL)
- University of California, Berkeley (US)
Publication Details
- Journal
- Molecular Plant-Microbe Interactions
- Published
- 2025-01-01
- DOI
- https://doi.org/10.1094/mpmi-07-25-0077-ta
- Citations
- 5
- Primary Topic
- Mycotoxins in Agriculture and Food
- Type
- article
- Field-Weighted Citation Impact
- 8.75
Funders
- U.S. Department of Energy
- Joint Genome Institute
- Agence Nationale de la Recherche
- Région Occitanie Pyrénées-Méditerranée
- Directorate for Biological Sciences
- Office of Science
- Biotechnology and Biological Sciences Research Council