Info • Melampsora americana R15-033-03 v1.0

Status

[August 2018] The Melampsora americana R15-033-03 genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina and assembled with Trinity. The mitochondrial genome was assembled separately and is available on the Download page.

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 americana R15-033-03 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 112.35
Sequencing read coverage depth 128.49x
# of contigs 389
# of scaffolds 389
# of scaffolds >= 2Kbp 383
Scaffold N50 34
Scaffold L50 (Mbp) 1.07
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 3.25, 3.10, 3.09


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 60136 55905 93.0%
Ests est.fasta 378939217 79269495 20.9%


Gene Models FilteredModels2
length (bp) of: average median
gene 1779 1547
transcript 1381 1173
exon 271 166
intron 99 81
description:
protein length (aa) 406 329
exons per gene 5.10 4
# of gene models 15984


Collaborators

Chris Smart, Cornell University, NY, USA

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.