Status
The genome sequence and gene prediction of Colletotrichum tropicale CgS9275 have not been determined by the Joint Genome Institute (JGI), but were downloaded from NCBI on Oct 20, 2024. All published models are available as ExternalModels. In order to ensure this genome is comparable to those sequenced and annotated by the JGI, we applied standard filters to ExternalModels to produce the initial GeneCatalog. A total of 367 ExternalModels were excluded based on one of the following classifications: 1) association with repetitive elements, 2) pseudogenes with internal stop codons, 3) alternative isoforms or overlapping transcript models, 4) alleles on secondary scaffolds, and 5) short models lacking functional annotation. Please note that this copy of the genome is not maintained by NCBI and is therefore not automatically updated. In order to allow comparative analyses with other fungal genomes sequenced by the JGI, a copy of this genome is incorporated into Mycocosm. The JGI Annotation Pipeline was used to add functional annotation to the genes.
Genome Assembly | |
Genome Assembly size (Mbp) | 55.76 |
Sequencing read coverage depth | 494.1x |
# of contigs | 837 |
# of scaffolds | 778 |
# of scaffolds >= 2Kbp | 168 |
Scaffold N50 | 24 |
Scaffold L50 (Mbp) | 0.69 |
# of gaps | 59 |
% of scaffold length in gaps | 0.0% |
Three largest Scaffolds (Mbp) | 2.64, 2.04, 1.81 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 1615 | 1389 |
transcript | 1457 | 1239 |
exon | 499 | 276 |
intron | 84 | 60 |
description: | ||
protein length (aa) | 486 | 413 |
exons per gene | 2.92 | 2 |
# of gene models | 14427 |
Genome Reference(s)
Gan P, Hiroyama R, Tsushima A, Masuda S, Shibata A, Ueno A, Kumakura N, Narusaka M, Hoat TX, Narusaka Y, Takano Y, Shirasu K
Telomeres and a repeat-rich chromosome encode effector gene clusters in plant pathogenic Colletotrichum fungi.
Environ Microbiol. 2021 Oct;23(10):6004-6018. doi: 10.1111/1462-2920.15490
Links
- JGI PhyloGroup Portals: Fungi Dikarya Ascomycota Pezizomycotina Sordariomycetes Hypocreomycetidae Glomerellaceae Colletotrichum
- JGI EcoGroup Portals: Plant Pathogens