Maximum-Likelihood phylogeny generated by FastTree for Chloropicon primus and other Viridiplantae

The Chloropicon primus CCMP1205 genome assembly and gene models have not been determined by the JGI, but were downloaded from NCBI on October 31, 2019. All published models are available as ExternalModels. In order to ensure this genome is comparable to those sequenced annotated by the JGI, we applied standard filters to ExternalModels to produce the initial GeneCatalog. A total of 135 external models were excluded based on one of the following classifications: 1) association with repetitive elements, 2) pseudogenes with internal stop codons, 3) alternative isoforms or overlapping transcript models, 4) alleles on secondary scaffolds, and 5) short models lacking functional annotation. Please note that this copy of the genome is not maintained by NCBI 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 this genome.

Chloropicon primus (Phylum Chlorophyta, Class Chloropicophyceae) is the first published genome for this class of unicellular green picoalgae, closely related to Mamiellophyceae. The compact 17.4 Mb genome for strain CCMP1205 has an surprisingly diploid structure to its nuclear genome, higher than expected polymorphism (averaging 0.54 variants per kb), high gene density (averaging 0.50 genes per kb), and 4% repeat content. Several interesting metabolic pathways have been described in this species, including the complete set of enzymes for proprionate degradation. (Lemieux C. et al., 2019)