
Verticillium dahliae JR2 Assembly and Gene Annotation
About Verticillium dahliae JR2
Verticillium dahliae is a fungal plant pathogen. It causes verticillium wilt in many plant species, causing leaves to curl and discolor. It may cause death in some plants. Over 400 plant species are affected by Verticillium complex.
Picture credit: Creative Commons Attribution 3.0 via Wikimedia Commons (Image source) Taxonomy ID 1202531
(Text from Wikipedia.)
More information General information about this species can be found in Wikipedia
Assembly
The draft genome sequence of the JR2 strain was assembled by the Laboratory of Phytopathology, Wageningen University, using 250X coverage PacBio and optical mapping solved using MapSolve. The assembly has been submitted to the INSDC archives as GCA_000400815.2.
Annotation
Protein coding gene annotation was generated by the Laboratory of Phytopathology, Wageningen University. The genome was annotated using Maker2 software supported by RNA-seq reads, assembled RNA-seq data that were used as EST evidence, 35 different fungal proteomes and two ab-intio gene predictors (Augustus and SNAP). The predicted genes were manually curated using WebApollo software.
The set of non-coding RNA genes available comprises a set of gene models [annotated by the Laboratory of Phytopathology, Wageningen University, plus an additional set annotated using tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997), RFAM (Griffiths-Jones et al 2005), and RNAmmer (Lagesen K.,et al 2007); additional analysis tools have also been applied.
Expression Data
RNA-seq expression data of Verticillum dahliae strain JR2 infecting Nicotiana benthamiana at 4, 8, 12 and 16 days post inoculation were mapped to the genome using Tophat2 software by Laboratory of Phytopathology, Wageningen University. This data can be viewed as a track in the browser.
Variation
The variation data was provided by the Laboratory of Phytopathology, Wageningen University, by calling SNPs from 10 resequenced strains aligned to the Verticillium dahliae JR2 reference strain.
References
- Tomato immune receptor Ve1 recognizes effector of multiple fungal
pathogens uncovered by genome and RNA
sequencing.
de Jonge R, van Esse HP, Maruthachalam K, Bolton MD, Santhanam P, Saber MK, Zhang Z, Usami T, Lievens B, Subbarao KV et al. 2012. Proc. Natl. Acad. Sci. U.S.A.. 109:5110-5115.
Picture credit: Infection by Verticillium dahliae on sunflower. Source: Howard F. Schwartz, Colorado State University, Bugwood.org.
More information
General information about this species can be found in Wikipedia.
Statistics
Summary
Assembly | VDAG_JR2v.4.0, INSDC Assembly GCA_000400815.2, Sep 2014 |
Database version | 115.1 |
Golden Path Length | 36,150,287 |
Genebuild by | LPPWU |
Genebuild method | Import |
Data source | Laboratory of Phytopathology, Wageningen University |
Gene counts
Coding genes | 11,426 |
Non coding genes | 211 |
Small non coding genes | 211 |
Gene transcripts | 11,650 |
Other
Short Variants | 384,900 |