Hemileia vastatrix Genome Analysis
The coffee rust, Hemileia vastatrix, is the most damaging pathogen of coffee and is now present in every coffee producing region in the world, except Hawaii. As part of Cenicafe Genome project we are studying the genome of this pathogen and we are collaborating with scientists from Universidad de los Andes in Bogotá in the annotation of the genome and transcriptome sequence. The lab heads at Universidad de los Andes in this project are Dr. Harold Castro at Department of Computational Engineering and Dr. Silvia Restrepo at The Mycology and Plant Pathology Laboratory (LAMFU).
We have obtained around 500,000 genomic 454 sequences from H. vastatrix clustered in 45,224 contigs by Newbler assembler. A total of 5,629 contigs were annotated with BlastX using Uniref 100 (Release Nov 2009) and annotation statistics can be viewed here. We are currently testing PCR amplification of 100 SSR primers that were developed from the genomic sequences to study the evolution of this pathogen in Colombia.
Annotation of the H. vastatrix genome is being currently performed and includes: Installation of the MAKER software as a pipeline for genome annotation, MIRA assembly, gene prediction with Augustus, SNPs prediction by GygaBytes software, secreted proteins prediction by TargetP and SignalP algorithms, and a pipeline for de novo transposable elements search with the programs RepeatScouts and RepeatMasker.
As we are expecting additional transcriptome and genome sequences in the next few weeks, we will have preliminary results of a draft genome sequence of rust in the near future.
The Genome sequencing is a project financed by Ministerio de Agricultura y Desarrollo Rural and the genome annotation is partially financed by Colciencias.
Major Fungi Genomics Projects are taking place at:
DOE JOINT GENOME INSTITUTE: http://www.jgi.doe.gov/genome-projects/
BROAD INSTITUTE: http://www.broadinstitute.org/science/data#
BGI (formerly known as Beijing Genomics Institute): http://www.genomics.cn/en/index.php
The genome of a rust, Melampsora laricis-populina, has been completed http://genome.jgi-psf.org/Mellp1/Mellp1.download.ftp.html