Info • Capnodiales sp. MNA-CCFEE 6580 v1.0


[December 2022] The Capnodiales sp. MNA-CCFEE 6580 v1.0 genome was sequenced with Illumina, assembled with SPAdes, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

Capnodiales sp. MNA-CCFEE 6580 is likely a diploid/dikaryotic genome, and this is reflected in an assembly and annotation with significant separation of alleles. Many of the smaller 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 repertoire 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) 44.61
Sequencing read coverage depth 187.94x
# of contigs 1985
# of scaffolds 1971
# of scaffolds >= 2Kbp 1733
Scaffold N50 314
Scaffold L50 (Mbp) 0.04
# of gaps 14
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.32, 0.20, 0.17

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 52051 48472 93.1%
Ests est.fasta 214475142 205026411 95.6%

Gene Models FilteredModels1
length (bp) of: average median
gene 1755 1518
transcript 1632 1416
exon 672 396
intron 88 60
protein length (aa) 460 376
exons per gene 2.43 2
# of gene models 11911



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.