Info • Melampsora x columbiana Clatskanie v1.0


[July 2019] The Melampsora x columbiana Clatskanie 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. Please note: this lineage is a known hybrid between M. medusae and M. occidentalis. Consequently, there are a substantial number of duplicated genes that are highy diverged from one another. Therefore, these were left in the filtered model set to more fully represent the functional capabilities of M. columbiana. Also, we detected that scaffold_889 is potentially of mitochondrial origin. However, coverage and GC content on this scaffold were similar to the main assembly. Therefore, models were removed from the Gene Catalog but were kept in downloadable content so they can be removed at your discretion.

Summary statistics for the Melampsora x columbiana Clatskanie v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 184.87
Sequencing read coverage depth 124.25x
# of contigs 1366
# of scaffolds 1366
# of scaffolds >= 2Kbp 1366
Scaffold N50 196
Scaffold L50 (Mbp) 0.30
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.16, 0.99, 0.96

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 90629 54346 60.0%
Ests est.fasta 100794332 77077458 76.5%

Gene Models FilteredModels1
length (bp) of: average median
gene 1599 1341
transcript 1218 992
exon 266 164
intron 108 80
protein length (aa) 370 295
exons per gene 4.59 4
# of gene models 37633



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.