Verticillium dahliae JR2 Assembly and Gene Annotation

About the Verticillium dahliae JR2 genome

Verticillium dahliae is one of the causal agent of vascular wilt in numerous economically important plants causing wilting of all or only parts of the host. The most common hosts are trees and shrubs, including olive and maple, and vegetables, including cotton, tomatoes and potatoes and also ornamentals. This soilborn fungus persists in the soil for many years under the form of tiny and black resting bodies called microsclerotia. These germinate in the presence of the host plant roots when the external conditions are beneficial. The resulting hyphae invades the plant roots into the the vascular tissue.

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

1. 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.