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Info • Melampsora medusae f. sp. tremuloidae Mmt05Ida529 v1.0

Status

[January 2019] The Melampsora medusae f. sp. tremuloidae Mmt05Ida529 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. tremuloidae Mmt05Ida529 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 145.19
Sequencing read coverage depth 235.69x
# of contigs 1794
# of scaffolds 1794
# of scaffolds >= 2Kbp 1773
Scaffold N50 143
Scaffold L50 (Mbp) 0.24
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.72, 1.47, 1.45


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 65787 44638 67.9%
Ests est.fasta 291539372 283764472 97.3%


Gene Models FilteredModels2
length (bp) of: average median
gene 1598 1322
transcript 1223 993
exon 265 165
intron 106 80
description:
protein length (aa) 369 292
exons per gene 4.62 4
# of gene models 22850


Collaborators

Richard Hamelin, University of British Columbia, Canada

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

Funding

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.