Fusarium oxysporum Assembly and Gene Annotation

About Fusarium oxysporum f. sp. lycopersici

Fusarium oxysporum, an ascomycete fungus, comprises all the species, varieties and forms recognized by Wollenweber and Reinking within an infrageneric grouping called section Elegans. It is part of the family Nectriaceae.

Picture credit: Public domain via Wikimedia Commons (Image source) Taxonomy ID 660025

(Text from Wikipedia.)

More information General information about this species can be found in Wikipedia

Variation Data

Fusarium oxysporum exhibits genetic plasticity which makes it a destructive pathogen across a wide range of crops. We constructed a variation database comparing 27 different strains of this species. Sequence read data was downloaded from ENA Short Read Archive and mapped against the Fusarium oxysporum f.sp. lycopersici genome using Burrows-Wheeler Alignment Tool (Li H.and Durbin R.Bioinformatics 2010) and variation calling was done using SAMtools (Li H.et.al Bioinfomratics 2009).

References

1. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium.
   Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B et al. 2010. Nature. 464:367-373.
2. Identification of genes up-regulated during conidiation of Fusarium oxysporum through expressed sequence tag analysis.
   Iida Y, Ohara T, Tsuge T. 2006. Fungal Genet. Biol.. 43:179-189.

Picture credit: Picture credit: Keith Weller

Other Data

• Non coding RNA genes have been 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.
• 'Expressed Sequence Tags' (ESTs) from dbEST are aligned to the genome using Exonerate.

More information

General information about this species can be found in Wikipedia.