Info • Spirogloea muscicola CCAC 0214


The Spirogloea muscicola CCAC 0214 genome assembly and gene models have not been determined by the JGI, but were downloaded from the Cheng et al., 2019 genome supplemental data share at on November 21, 2019. In order to ensure this genome is comparable to those sequenced by the JGI, 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 the removal of 3,044 models and the generation of the FilteredModels1 (GeneCatalog) gene track. All published models are available in the ExternalModels track. Please note that this copy of the genome is not maintained by Cheng et al. and is therefore not automatically updated. In order to allow comparative analyses with other algal genomes sequenced by the JGI, a copy of this genome is incorporated into PhycoCosm. The JGI Annotation Pipeline was used to add functional annotation to the genes.

Published analysis of this genome indicates that S. muscicola has undergone a recent whole genome triplication event (Cheng et al. 2019). This is reflected in an assembly and annotation with a significant collection of segmental duplication gene pairs/triplets. To facilitate future analysis of this genome, all gene models from the three putative subgenomes have been preserved.

Genome Assembly
Genome Assembly size (Mbp) 171.14
Sequencing read coverage depth 354X
# of contigs 28742
# of scaffolds 19678
# of scaffolds >= 2Kbp 1735
Scaffold N50 94
Scaffold L50 (Mbp) 0.57
# of gaps 9064
% of scaffold length in gaps 8.2%
Three largest Scaffolds (Mbp) 2.32, 2.24, 1.80

Gene Models FilteredModels1
length (bp) of: average median
gene 3076 2393
transcript 1425 1122
exon 174 126
intron 232 193
protein length (aa) 475 374
exons per gene 8.19 7
# of gene models 24093

Genome Reference(s)


This project was not sequenced at the JGI.