Info • Rhizoclosmatium globosum JEL800 v1.0


[December 2015] The Rhizoclosmatium globosum JEL800 genome was sequenced using the PacBio platform and assembled together with Falcon version 20150310 ( and improved with finisherSC version 2.0 (Lam et al., 2014), then polished with Quiver version
smrtanalysis_2.3.0.140936 (Chin et al., 2013).


Rhizoclosmatium hyalinus JEL800 was determined to be a diploid/heterokaryon assembly. 326 of the 437 scaffolds (40.4% of total assembly) displayed significant similarity to larger scaffolds and thus were predicted to belong to the alternate haplotype. These have been designated 'secondary scaffolds'. To be a secondary scaffold, >50% of the scaffold had to be at least 95% identical to a larger scaffold. In the case of Rhizoclosmatium, on average 91.3% of the secondary scaffold was at least 95% identical to a larger scaffold. As a result, we created two new tracks, the 'primary alleles' and 'secondary alleles' tracks, which highlight the models which are 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 thus models unique to the secondary scaffolds were included in the GC, while others were removed.

Summary statistics for the Rhizoclosmatium hyalinus JEL800 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 57.02
Sequencing read coverage depth
# of contigs 437
# of scaffolds 437
# of scaffolds >= 2Kbp 435
Scaffold N50 51
Scaffold L50 (Mbp) 0.29
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.02, 0.95, 0.94

ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests RNNotator_assembled_Illumina_ESTs 40307 38300 95.0%

Gene Models FilteredModels1
length (bp) of: average median
gene 1530 1235
transcript 1319 1070
exon 330 211
intron 73 55
protein length (aa) 395 312
exons per gene 4.00 3
# of gene models 16990


Jason Stajich, UC Riverside, California

Joey Spatafora, Oregon State, Oregon

Genome Reference(s)


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.