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COMPARATIVE GENOMICS ROYA VS Melampsora laricis-populina
The poplar leaf rust fungus Melampsora is the most devastating and widespread pathogen of poplars, and has limited the use of poplars for environmental and wood production goals in many parts of the world. Almost all known poplar cultivars are susceptible to Melampsora laricis-populina, and new virulent strains are continuously developing. This disease therefore has a strong potential impact on current and future poplar plantations used for production of forest products (principally pulp and consolidated wood products), carbon sequestration, biofuels production, and bioremediation. There is a pressing need to develop a thorough understanding of the Melampsora species that are poplar pathogens so that new control approaches can be established.
To elucidate the genetic basis of the Melampsora-Populus interaction, JGI have sequenced the hundred million base-pair genome of the dicaryotic strain 98AG31 to high draft using a whole genome shotgun method. This is the first genome of a tree pathogen to be sequenced. Details at: http://genome.jgi-psf.org/Mellp1/Mellp1.home.html
Roya 454 Contigs Vs Melampsora laricis-populina Assembled scaffolds
About 1444 Rust 454 Contigs were mapped over 147 Melampsora Scaffolds.
Command : blastall -p blastx -i 454AllContigs.fna -d Melampsora_laricis_populina -e 1e-5 -F T -o RoyaVsMelam.bn -a 8&
Roya 454 Contigs Vs Melampsora laricis-populina Clustered ESTs
About 157 Rust 454 Contigs present significant hits over 143 Melampsora EST Clusters.
Command : blastall -p blastx -i 454AllContigs.fna -d Mlaricis_populina_ESTclusters -e 1e-5 -F T -o RoyaVsMelamEstclus.bn -a 8&
Roya 454 Contigs Vs Melampsora laricis-populina Filtered Protein Models
About 1936 Rust 454 Contigs present a significant hits over 2175 Melampsora Protein Models.
Command : blastall -p blastx -i 454AllContigs.fna -d Mlaricis_populina.FilteredModels3 -e 1e-5 -F T -o RoyaVsMelamAA.bx -a 8&