ArticleG3 (Bethesda, Md.)2015
RNA-seq-Based Gene Annotation and Comparative Genomics of Four Fungal Grass Pathogens in the Genus Zymoseptoria Identify Novel Orphan Genes and Species-Specific Invasions of Transposable Elements.
Article in G3 (Bethesda, Md.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed.
- Interspecies hybridization as a route of accessory chromosome origin in fungal pathogens.mBio · 2026Article
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- An array of Zymoseptoria tritici effectors suppress plant immune responses.Molecular plant pathology · 2024Article
- Comparative Genomic Analyses ofJournal of fungi (Basel, Switzerland) · 2024Article
- Article
- Quantitative pathogenicity and host adaptation in a fungal plant pathogen revealed by whole-genome sequencing.Nature communications · 2024Article
- Comparative genomics of the extremophileFrontiers in fungal biology · 2024Article
- Genome-wide expression QTL mapping reveals the highly dynamic regulatory landscape of a major wheat pathogen.BMC biology · 2023Article
- The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogenMicrobial genomics · 2023Article
- H4K20me3 is important for Ash1-mediated H3K36me3 and transcriptional silencing in facultative heterochromatin in a fungal pathogen.PLoS genetics · 2023Article
- Article
- A secreted protease-like protein in Zymoseptoria tritici is responsible for avirulence on Stb9 resistance gene in wheat.PLoS pathogens · 2023Article
- A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen.Nature communications · 2023Article
- Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen.PLoS pathogens · 2023Article
- Fungal plant pathogen "mutagenomics" reveals tagged and untagged mutations inFrontiers in plant science · 2023Article
- Quantitative and qualitative plant-pathogen interactions call upon similar pathogenicity genes with a spectrum of effects.Frontiers in plant science · 2023Article
- Zymoseptoria tritici white-collar complex integrates light, temperature and plant cues to initiate dimorphism and pathogenesis.Nature communications · 2022Article
- Non-Mendelian transmission of accessory chromosomes in fungi.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2022Review
- Comparative genomic analysis reveals contraction of gene families with putative roles in pathogenesis in the fungal boxwood pathogens Calonectria henricotiae and C. pseudonaviculata.BMC ecology and evolution · 2022Article
- Comprehending the dynamism of B chromosomes in their journey towards becoming unselfish.Frontiers in cell and developmental biology · 2022Review
7 more citing papers are in PubMed but not listed here.
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The fungal pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola) is a prominent pathogen of wheat. The reference genome of the isolate IPO323 is one of the best-assembled eukaryotic genomes and encodes more than 10,000 predicted genes. However, a large proportion of the previously annotated gene models are incomplete, with either no start or no stop codons. The availability of RNA-seq data allows better predictions of gene structure. We here used two different RNA-seq datasets, de novo transcriptome assemblies, homology-based comparisons, and trained ab initio gene callers to generate a new gene annotation of Z. tritici IPO323. The annotation pipeline was also applied to re-sequenced genomes of three closely related species of Z. tritici: Z. pseudotritici, Z. ardabiliae, and Z. brevis. Comparative analyses of the predicted gene models using the four Zymoseptoria species revealed sets of species-specific orphan genes enriched with putative pathogenicity-related genes encoding small secreted proteins that may play essential roles in virulence and host specificity. De novo repeat identification allowed us to show that few families of transposable elements are shared between Zymoseptoria species while we observe many species-specific invasions and expansions. The annotation data presented here provide a high-quality resource for future studies of Z. tritici and its sister species and provide detailed insight into gene and genome evolution of fungal plant pathogens.
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