Info • Coccomyxa subellipsoidea C-169 v3.0


[September 2022] The Coccomyxa subellipsoidea C-169 v3.0 updated assembly and annotation project began with the v2.0 (25 Sep 2009) improved assembly, originally produced by the JGI Finishing Pipeline, based on v1.0 JGI whole genome shotgun sequencing, assembled by Jazz 2.10.1 and Arachne. The v2.0 assembly was scanned for potential organellar or bacterial contamination, resulting in removal of 14 short scaffolds, devoid of v2.0 gene models and totalling less than 100kb, and the filtered set was treated as the v3.0 assembly. A new annotation was produced using the JGI Annotation Pipeline.

The v2.0 chloroplast and mitochondrial genomes were assembled separately and are available in the downloads section.

Genome Assembly
Genome Assembly size (Mbp) 48.85
# of contigs 31
# of scaffolds 31
# of scaffolds >= 2Kbp 31
Scaffold N50 9
Scaffold L50 (Mbp) 1.96
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 4.04, 3.86, 3.06

v2.0 Sanger EST cDNAs (2009) were combined with JGI RNA-seq and Iso-Seq sequencing from 2021/2022.
ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 162193412 160806962 99.1%
Ests v2_ESTs 7984 7464 93.5%
Other IsoSeq_hq_reads 102456 101424 99.0%
Other RNAseq_contigs 66315 63861 96.3%

Gene Models FilteredModels1
length (bp) of: average median
gene 3834 3119
transcript 1932 1707
exon 226 161
intron 254 223
protein length (aa) 447 369
exons per gene 8.53 7
# of gene models 10893


v3.0 Transcriptomics and Revised Annotation

v2.0 Prior Release

  • James Van Etten, University of Nebraska, Lincoln, Department of Plant Pathology
  • Michael V. Graves, University of Massachusetts-Lowell
  • Takashi Yamada, Hiroshima University
  • Tae-Jin Choi, Pukyong National University, Korea
  • Rosevelt L. Pardy, University of Nebraska
  • Jean-Michel Claverie, Structural and Genomic Information Lab, CNRS, Marseille, France

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.