Info • Rhamphospora nymphaeae CBS 172.38 v1.0


[January 2019] The Rhamphospora nymphaeae CBS 172.38 genome was sequenced with PacBio, assembled with Falcon unzip version 0.4.0, 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 diploid/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 Rhamphospora nymphaeae CBS 172.38 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 46.12
Sequencing read coverage depth 214.6x
# of contigs 834
# of scaffolds 834
# of scaffolds >= 2Kbp 831
Scaffold N50 36
Scaffold L50 (Mbp) 0.35
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.82, 1.23, 1.21

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 56553 50756 89.7%
Ests est.fasta 251234424 239071683 95.2%

Gene Models FilteredModels1
length (bp) of: average median
gene 2426 2125
transcript 1837 1506
exon 399 227
intron 165 130
protein length (aa) 529 412
exons per gene 4.61 4
# of gene models 7715


Dr. Catherine Aime, Purdue University, IN

Dr. Joseph Spatafora, Oregon State University, OR


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.