Status
[December 2020] The Phyllosticta paracitricarpa CBS 141358 v1.0 genome was sequenced with PacBio, assembled with Flye, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.
Summary statistics for the Phyllosticta paracitricarpa CBS
141358 v1.0 release are below.
Genome Assembly | |
Genome Assembly size (Mbp) | 30.83 |
Sequencing read coverage depth | 38.45x |
# of contigs | 90 |
# of scaffolds | 90 |
# of scaffolds >= 2Kbp | 90 |
Scaffold N50 | 17 |
Scaffold L50 (Mbp) | 0.65 |
# of gaps | 0 |
% of scaffold length in gaps | 0.0% |
Three largest Scaffolds (Mbp) | 1.23, 1.15, 1.12 |
ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
EstClusters | ESTclusters | 34490 | 30927 | 89.7% |
Ests | est.fasta | 161307941 | 158411639 | 98.2% |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 1839 | 1583 |
transcript | 1674 | 1429 |
exon | 571 | 351 |
intron | 87 | 58 |
description: | ||
protein length (aa) | 474 | 387 |
exons per gene | 2.93 | 3 |
# of gene models | 10064 |
Collaborators
- Francis M. Martin, INRAE, France.
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
van Ingen-Buijs VA, van Westerhoven AC, Skiadas P, Zuijdgeest XCL, Haridas S, Daum C, Duffy K, Guo J, Hundley H, LaButti K, Lipzen A, Pangilinan J, Riley R, Wang J, Yan M, Martin F, Barry K, Grigoriev IV, Groenewald JZ, Crous PW, Seidl MF
Phyllosticta paracitricarpa is synonymous with the EU quarantine fungus P. Citricarpa based on phylogenomic analyses.
Fungal Genet Biol. 2024 Sep 5;():103925. doi: 10.1016/j.fgb.2024.103925
van Ingen-Buijs VA, van Westerhoven AC, Skiadas P, Zuijdgeest XCL, Haridas S, Daum C, Duffy K, Guo J, Hundley H, LaButti K, Lipzen A, Pangilinan J, Riley R, Wang J, Yan M, Martin F, Barry K, Grigoriev IV, Groenewald JZ, Crous PW, Seidl MF
Phyllosticta paracitricarpa is synonymous with the EU quarantine fungus P. Citricarpa based on phylogenomic analyses.
Fungal Genet Biol. 2024 Sep 5;():103925. doi: 10.1016/j.fgb.2024.103925
Links
- 1000 Fungal Genomes Project
- JGI PhyloGroup Portals: Fungi Dikarya Ascomycota Pezizomycotina Dothideomycetes Botryosphaeriales Phyllosticta
Funding
The work conducted by the U.S. Department of Energy Joint Genome
Institute, a DOE Office of Science User Facility, is supported by
the Office of Science of the U.S. Department of Energy under
Contract No. DE-AC02-05CH11231.