Info • Scleroderma citrinum hr. v1.0


[January 2021] The Scleroderma citrinum hr. v1.0 genome was sequenced with PacBio, assembled with hicanu, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

We identified polymorphic content, 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.

Genome Assembly
Genome Assembly size (Mbp) 77.47
Sequencing read coverage depth 26.21x
# of contigs 169
# of scaffolds 169
# of scaffolds >= 2Kbp 169
Scaffold N50 16
Scaffold L50 (Mbp) 1.19
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 3.79, 3.68, 3.64

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 76173 72022 94.6%
Ests est.fasta 168110001 167311594 99.5%

Gene Models FilteredModels1
length (bp) of: average median
gene 1790 1523
transcript 1446 1212
exon 229 142
intron 67 55
protein length (aa) 428 342
exons per gene 6.31 5
# of gene models 10323


  • Francis Martin at INRAE, France (National Research Institute for Agriculture, Food and Environment)


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.