Status
The genome of Septoria populicola was not sequenced by the Joint Genome Institute, but by Phil Tanguay (Research Scientist), Laurentian Forestry Centre (Canadian Forest Service), Succ.Sainte-Foy (Quebec) and Richard Hamelin (University of British Columbia, Canada) using Illumina technology. The reads were assembled with Newbler. The JGI fungal genome annotation pipeline was used to predict and annotate genes and other genomic features. Since no ESTs are available for S. populicola, ESTs from the closely related species S. musiva were used to assist in gene prediction.
Summary statistics for the Septoria populicola v1.0
release are below.
Genome Assembly | |
Genome Assembly size (Mbp} | 33.19 |
Sequencing read coverage depth | 18x |
# of contigs | 2827 |
# of scaffolds | 502 |
# of scaffolds >= 2Kbp | 502 |
Scaffold N50 | 41 |
Scaffold L50 (Mbp) | 0.26 |
# of gaps | 2325 |
% of scaffold length in gaps | 3.2% |
Three largest Scaffolds (Mbp) | 1.07, 0.90, 0.84 |
ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
Other | EST_Sepmu1 | 10652 | 5521 | 51.8% |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 1572 | 1314 |
transcript | 1408 | 1161 |
exon | 557 | 260 |
intron | 109 | 68 |
description: | ||
protein length (aa) | 449 | 367 |
exons per gene | 2.53 | 2 |
# of gene models | 9739 |
Collaborators
- Richard Hamelin, University of British Columbia, Canada
- Igor Grigoriev, Joint Genome Institute
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, Barry KW, Condon BJ, Copeland AC, Dhillon B, Glaser F, Hesse CN, Kosti I, LaButti K, Lindquist EA, Lucas S, Salamov AA, Bradshaw RE, Ciuffetti L, Hamelin RC, Kema GH, Lawrence C, Scott JA, Spatafora JW, Turgeon BG, de Wit PJ, Zhong S, Goodwin SB, Grigoriev IV
Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi.
PLoS Pathog. 2012;8(12):e1003037. doi: 10.1371/journal.ppat.1003037
Dhillon B, Feau N, Aerts AL, Beauseigle S, Bernier L, Copeland A, Foster A, Gill N, Henrissat B, Herath P, LaButti KM, Levasseur A, Lindquist EA, Majoor E, Ohm RA, Pangilinan JL, Pribowo A, Saddler JN, Sakalidis ML, de Vries RP, Grigoriev IV, Goodwin SB, Tanguay P, Hamelin RC
Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen.
Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):3451-6. doi: 10.1073/pnas.1424293112
Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, Barry KW, Condon BJ, Copeland AC, Dhillon B, Glaser F, Hesse CN, Kosti I, LaButti K, Lindquist EA, Lucas S, Salamov AA, Bradshaw RE, Ciuffetti L, Hamelin RC, Kema GH, Lawrence C, Scott JA, Spatafora JW, Turgeon BG, de Wit PJ, Zhong S, Goodwin SB, Grigoriev IV
Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi.
PLoS Pathog. 2012;8(12):e1003037. doi: 10.1371/journal.ppat.1003037
Dhillon B, Feau N, Aerts AL, Beauseigle S, Bernier L, Copeland A, Foster A, Gill N, Henrissat B, Herath P, LaButti KM, Levasseur A, Lindquist EA, Majoor E, Ohm RA, Pangilinan JL, Pribowo A, Saddler JN, Sakalidis ML, de Vries RP, Grigoriev IV, Goodwin SB, Tanguay P, Hamelin RC
Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen.
Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):3451-6. doi: 10.1073/pnas.1424293112
Links
- Septoria musiva
- Cochliobolus heterostrophus C5
- Mycosphaerella fijiensis v2.0
- Mycosphaerella graminicola v2.0
- Alternaria brassicicola
- Pyrenophora tritici-repentis
- Stagonospora nodorum SN15
- Dothistroma septosporum
- Leptosphaeria maculans
- Hysterium pulicare
- Rhytidhysteron rufulum
- Setosphaeria turcica
- Baudoinia compniacensis
Funding
This project was not sequenced at the JGI.