Status
The Klebsormidium nitens NIES-2285 v1.0 genome sequence and v1.1 gene models have not been determined by the JGI, but were downloaded from the Klebsormidium nitens NIES-2285 genome sequencing project on May 10, 2023. 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, 4) alleles on secondary scaffolds and 5) unsupported short models. This resulted in the removal of 1487 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 the Klebsormidium nitens NIES-2285 genome sequencing project 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. Chloroplast and mitochondrial genomes were assembled separately by the Klebsormidium nitens NIES-2285 genome sequencing project, and are available on the download portal.
Genome Assembly | |
Genome Assembly size (Mbp) | 103.92 |
Sequencing read coverage depth | 40x |
# of contigs | 3364 |
# of scaffolds | 1812 |
# of scaffolds >= 2Kbp | 1812 |
Scaffold N50 | 229 |
Scaffold L50 (Mbp) | 0.13 |
# of gaps | 1552 |
% of scaffold length in gaps | 1.0% |
Three largest Scaffolds (Mbp) | 0.54, 0.53, 0.52 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 5078 | 4270 |
transcript | 2077 | 1770 |
exon | 295 | 176 |
intron | 499 | 429 |
description: | ||
protein length (aa) | 550 | 428 |
exons per gene | 7.04 | 6 |
# of gene models | 15568 |
Genome Reference(s)
Hori K, Maruyama F, Fujisawa T, Togashi T, Yamamoto N, Seo M, Sato S, Yamada T, Mori H, Tajima N, Moriyama T, Ikeuchi M, Watanabe M, Wada H, Kobayashi K, Saito M, Masuda T, Sasaki-Sekimoto Y, Mashiguchi K, Awai K, Shimojima M, Masuda S, Iwai M, Nobusawa T, Narise T, Kondo S, Saito H, Sato R, Murakawa M, Ihara Y, Oshima-Yamada Y, Ohtaka K, Satoh M, Sonobe K, Ishii M, Ohtani R, Kanamori-Sato M, Honoki R, Miyazaki D, Mochizuki H, Umetsu J, Higashi K, Shibata D, Kamiya Y, Sato N, Nakamura Y, Tabata S, Ida S, Kurokawa K, Ohta H
Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation.
Nat Commun. 2014 May 28;5():3978. doi: 10.1038/ncomms4978
Links
- JGI Algae EcoGroup Portal
- JGI PhyloGroup Portals: Viridiplantae Streptophyta Klebsormidiophyceae