Info • Melampsora medusae f. sp. Deltoidae Mmd05TRE539 v1.0


[August 2018] The Melampsora medusae f. sp. Deltoidae Mmd05TRE539 v1.0 genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

The genome is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. Many of the scaffolds are very similar to larger scaffolds and are predicted to constitute an alternate or secondary haplotype. To represent these primary and secondary haplotypes in the Portal, we have created 'primary alleles' and 'secondary alleles' gene model tracks, comprising the models found on each haplotype. The goal of the GeneCatalog (GC) is to produce a non-redundant set of models which captures the full functional repertiore of the genome, and so the few secondary alleles that are unique were included in the GC, while all others were not.

Summary statistics for the Melampsora medusae f. sp. Deltoidae Mmd05TRE539 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 139.73
Sequencing read coverage depth 90.94x
# of contigs 2952
# of scaffolds 2952
# of scaffolds >= 2Kbp 2920
Scaffold N50 400
Scaffold L50 (Mbp) 0.10
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.54, 0.52, 0.50

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 50544 38169 75.5%
Ests est.fasta 200808227 190367492 94.8%

Gene Models FilteredModels1
length (bp) of: average median
gene 1638 1382
transcript 1247 1027
exon 258 162
intron 104 80
protein length (aa) 374 295
exons per gene 4.83 4
# of gene models 20491


Richard Hamelin, University of British Columbia, Canada

Philippe Tanguay and Marie-Josée Bergeron, Canadian Forest Service, Laurentian Forestry Centre


The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.