View Category:Genomics -> Projects -> Hemileia vastatrix Genome Project
The aims of this project are:
1. Construction of the first draft of the H. vastatrix genome.
2. Development of a Web-based information system for the search and visualization of the H. vastatrix genome.
3. Development and evaluation of SSR markers for diversity studies of the coffee rust evolution in Colombia.
4. Analysis of methods for the estimation of genome size and chromosome number in the coffee rust.
5. Evaluation of algorithms for the characterization of the spatial distribution of H. vastatrix populations in Colombia.
This project is in collaboration with scientists from Universidad de los Andes in Bogota and is financed by Colciencias-Renata.
The most damaging pathogen of coffee is Hemileia vastatrix Berk. and Br. (Uredinales), or coffee rust. In 1869, the fungus appeared in Ceylon (now Sri Lanka) and within ten years it devastated the entire coffee industry. H. vastatrix is now present in every coffee producing region in the world, except Hawaii.
H. vastatrix Sequencing
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. More information http://quimbaya.cenicafe.org/SI/genomicAssembly/HVastatrixProject.php
1. Cristancho, MA; Escobar C 2008 Transferability of SSRs markers from related Uredinales species to the coffee rust (Hemileia vastatrix). Genetics and Molecular Research 7(4): 1186-1192.
2. Cristancho, MA; Escobar C; Ocampo JD. 2007 Evolution of races of Hemileia vastatrix in Colombia. Cenicafe 58(4): 165-174.
3. GRASSO V.; SIEROTZKI H.; GARIBALDI A.; GISI U. Relatedness Among Agronomically important Rusts Based on Mitochondrial Cytochrome b Gene and Ribosomal ITS Sequences. J. Phytopathology 154: 110-118. 2006.
4. GOUVEIA M., M.C.; RIBEIRO, A.; VARZEA, V.M.P.; RODRIGUES JR, C. J. Genetic diversity in Hemileia vastatrix based on RAPD markers. Mycologia, 97: 396-404. 2005. 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.
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