Info • Chlamydomonas reinhardtii CC-503 v5.6


The genome sequence and gene models of Chlamydomonas reinhardtii were downloaded from Phytozome, the Joint Genome Institute (JGI) Plant genomics portal. In order to allow comparative analyses with other algal genomes sequenced by the JGI, a copy of this genome is incorporated into PhycoCosm. 

We applied filters to remove if present: 1) transposable elements, 2) pseudogenes, 3) alternative transcripts and overlapping models, and 4) unsupported short models. This resulted in removal of 3,123 models from C. reinhardtii v5.6 and generation of the FilteredModels1 gene track. All published models are available in the ExternalModels track. JGI tools were used to automatically annotate predicted proteins.

Summary statistics for the Chlamydomonas reinhardtii v5.6 release are below.
Genome Assembly
Genome Assembly size (Mbp) 111.10
Sequencing read coverage depth 13x
# of contigs 1495
# of scaffolds 54
# of scaffolds >= 2Kbp 54
Scaffold N50 7
Scaffold L50 (Mbp) 7.78
# of gaps 1441
% of scaffold length in gaps 3.6%
Three largest Scaffolds (Mbp) 9.73, 9.22, 9.22

Gene Models FilteredModels1
length (bp) of: average median
gene 5482 4444
transcript 3318 2618
exon 367 155
intron 271 230
protein length (aa) 762 522
exons per gene 9.05 7
# of gene models 16403

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.