Info • Chlamydomonas reinhardtii CC-4532 v6.1


The genome sequence and gene models of Chlamydomonas reinhardtii CC-4532 v6.1 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 16,484 models from C. reinhardtii CC-4532 v6.1 (mainly TE-related or alternative isoforms) and generation of the FilteredModels1 gene track. All original Phytozome models are available in the PhytozomeModels track. JGI tools were used to automatically annotate predicted proteins.

Genome Assembly
Genome Assembly size (Mbp) 114.04
Sequencing read coverage depth 176x
# of contigs 120
# of scaffolds 57
# of scaffolds >= 2Kbp 57
Scaffold N50 7
Scaffold L50 (Mbp) 6.95
# of gaps 63
% of scaffold length in gaps 0.8%
Three largest Scaffolds (Mbp) 9.95, 9.29, 8.91

Note: transcriptome contigs produced for the v6.1 Phytozome annotation were aligned to the genome with BLAT
ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters pertranContigs 287891 281175 97.7%

Gene Models FilteredModels1
length (bp) of: average median
gene 5343 4444
transcript 3164 2654
exon 349 150
intron 272 232
protein length (aa) 766 542
exons per gene 9.05 7
# of gene models 16090


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.