Info • Cladochytrium replicatum JEL 714 v1.0

Status

[March 2020] The Cladochytrium replicatum JEL 714 v1.0 genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

This genome was identified to have substantial amount of segmental duplication (~70% of assembly duplicated). Amino acid identity between copies is low, ~83%. As alleles in diploid/dikaryotic fungi tend to be >95% identical, the nature of this duplication event is unclear. Given the substantial divergence observed, duplicated content may also carry unique functions. Therefore, all gene models were retained in the Gene Catalog. A mapping file of primary and secondary copies was added to downloads in case separating content is desirable.

Summary statistics for the Cladochytrium replicatum JEL 714 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 50.67
Sequencing read coverage depth 230.35x
# of contigs 216
# of scaffolds 216
# of scaffolds >= 2Kbp 216
Scaffold N50 42
Scaffold L50 (Mbp) 0.39
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.50, 0.93, 0.84


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 55244 51547 93.3%
Ests est.fasta 196380767 190747412 97.1%


Gene Models FilteredModels1
length (bp) of: average median
gene 1852 1562
transcript 1565 1296
exon 297 168
intron 69 58
description:
protein length (aa) 458 365
exons per gene 5.27 4
# of gene models 16307


Collaborators

Genome Reference(s)

Please cite the following publication(s) if you use the data from this genome in your research:

Amses KR, Simmons DR, Longcore JE, Mondo SJ, Seto K, Jerônimo GH, Bonds AE, Quandt CA, Davis WJ, Chang Y, Federici BA, Kuo A, LaButti K, Pangilinan J, Andreopoulos W, Tritt A, Riley R, Hundley H, Johnson J, Lipzen A, Barry K, Lang BF, Cuomo CA, Buchler NE, Grigoriev IV, Spatafora JW, Stajich JE, James TY
Diploid-dominant life cycles characterize the early evolution of Fungi.
Proc Natl Acad Sci U S A. 2022 Sep 6;119(36):e2116841119. doi: 10.1073/pnas.2116841119

Funding

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.