Info • Nannochloropsis salina CCMP1776

Status

The Nannochloropsis salina CCMP1776 genome sequence and gene models have not been determined by the JGI, but were downloaded from the Los Alamos National Laboratory (LANL) Greenhouse portal on October 31, 2019. All published models are available as ExternalModels. In order to ensure this genome is comparable to those sequenced and annotated by the JGI, we applied standard filters to ExternalModels to produce the initial GeneCatalog. A total of 357 of 8,927 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 LANL 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.

Genome Assembly
Genome Assembly size (Mbp) 27.76
Sequencing read coverage depth NA
# of contigs 1212
# of scaffolds 196
# of scaffolds >= 2Kbp 188
Scaffold N50 13
Scaffold L50 (Mbp) 0.83
# of gaps 1016
% of scaffold length in gaps 0.4%
Three largest Scaffolds (Mbp) 1.56, 1.46, 1.38


Gene Models FilteredModels1
length (bp) of: average median
gene 2077 1641
transcript 1609 1269
exon 499 173
intron 212 179
description:
protein length (aa) 536 423
exons per gene 3.22 2
# of gene models 8570


Genome Reference(s)

Funding

This project was not sequenced at the JGI.