ArticleBMC genomics2017
Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed, 119 citations in OpenAlex.
- Chromosome-Level Genome Assembly and Annotation of theJournal of fungi (Basel, Switzerland) · 2026Article
- SDrecall: a sensitive approach for variant detection in segmental duplications.Genome biology · 2026Article
- Evolutionary History of the DD41D Family of Tc1/Mariner Transposons in Two Mayetiola Species.Biochemical genetics · 2025Article
- Integrated genome and transcriptome analysis reveals pathogenic mechanisms of Calonectria eucalypti in Eucalyptus leaf blight.BMC genomics · 2025Article
- Phylogenomics and adaptive evolution of the Colletotrichum gloeosporioides species complex.Communications biology · 2025Article
- Uncovering the Host Range-Lifestyle Relationship in the Endophytic and Anthracnose Pathogenic GenusMicroorganisms · 2025Review
- Comparative Genomics Reveals Sources of Genetic Variability in the Asexual Fungal Plant Pathogen Colletotrichum lupini.Molecular plant pathology · 2024Article
- Comparative Genomic Analyses ofJournal of fungi (Basel, Switzerland) · 2024Article
- Complete genome of the Medicago anthracnose fungus,Microbial genomics · 2024Article
- The Molecular Genetics and Genomics of Plant-Pathogen Interactions.International journal of molecular sciences · 2024Article
- Genome comparisons reveal accessory genes crucial for the evolution of apple Glomerella leaf spot pathogenicity in Colletotrichum fungi.Molecular plant pathology · 2024Article
- Genome Comparisons betweenJournal of fungi (Basel, Switzerland) · 2024Article
- Comparative Genomic Analysis ofJournal of fungi (Basel, Switzerland) · 2023Article
- The Hidden Truths of Fungal Virulence and Adaptation on Hosts: Unraveling the Conditional Dispensability of Minichromosomes in the HemibiotrophicInternational journal of molecular sciences · 2023Review
- Efficient multiple gene knockout in Colletotrichum higginsianum via CRISPR/Cas9 ribonucleoprotein and URA3-based marker recycling.Molecular plant pathology · 2023Article
- Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi.Nature communications · 2023Article
- Article
- CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes.Scientific reports · 2023Article
- Chromosome-level analysis of theFrontiers in microbiology · 2023Article
- Fungal Secondary Metabolites and Small RNAs Enhance Pathogenicity during Plant-Fungal Pathogen Interactions.Journal of fungi (Basel, Switzerland) · 2022Review
Corrections and comments
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Authors and funding
19 authors at 10 institutions in 7 countries.
Funding
Abstract
backgroundThe ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing errors in the prediction of protein-coding genes and preventing the analysis of repetitive sequences and genome architecture.
resultsHere, we re-sequenced the genome using single-molecule real-time (SMRT) sequencing technology and, in combination with optical map data, this provided a gapless assembly of all twelve chromosomes except for the ribosomal DNA repeat cluster on chromosome 7. The more accurate gene annotation made possible by this new assembly revealed a large repertoire of secondary metabolism (SM) key genes (89) and putative biosynthetic pathways (77 SM gene clusters). The two mini-chromosomes differed from the ten core chromosomes in being repeat- and AT-rich and gene-poor but were significantly enriched with genes encoding putative secreted effector proteins. Transposable elements (TEs) were found to occupy 7% of the genome by length. Certain TE families showed a statistically significant association with effector genes and SM cluster genes and were transcriptionally active at particular stages of fungal development. All 24 subtelomeres were found to contain one of three highly-conserved repeat elements which, by providing sites for homologous recombination, were probably instrumental in four segmental duplications.
conclusionThe gapless genome of C. higginsianum provides access to repeat-rich regions that were previously poorly assembled, notably the mini-chromosomes and subtelomeres, and allowed prediction of the complete SM gene repertoire. It also provides insights into the potential role of TEs in gene and genome evolution and host adaptation in this asexual pathogen.
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