Info • Scleroderma yunnanense jo. v1.0


[March 2022] The Scleroderma yunnanense jo. v1.0 genome was sequenced with PacBio, assembled with Flye, 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) 45.55
Sequencing read coverage depth 13.51x
# of contigs 308
# of scaffolds 308
# of scaffolds >= 2Kbp 308
Scaffold N50 17
Scaffold L50 (Mbp) 0.83
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 2.63, 2.05, 1.78

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 74049 70712 95.5%
Ests est.fasta 198453643 196272771 98.9%

Gene Models FilteredModels1
length (bp) of: average median
gene 1892 1586
transcript 1529 1269
exon 237 145
intron 68 55
protein length (aa) 453 358
exons per gene 6.46 5
# of gene models 10194


  • 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.