Status
The Triparma laevis f. inornata genome sequence and gene models have not been determined by the JGI, but were downloaded from NCBI on November 04, 2024. 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 601 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 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) | 42.57 |
Sequencing read coverage depth | NA |
# of contigs | 4469 |
# of scaffolds | 902 |
# of scaffolds >= 2Kbp | 666 |
Scaffold N50 | 204 |
Scaffold L50 (Mbp) | 0.08 |
# of gaps | 3567 |
% of scaffold length in gaps | 2.9% |
Three largest Scaffolds (Mbp) | 0.33, 0.20, 0.19 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 2036 | 1395 |
transcript | 1498 | 1053 |
exon | 370 | 289 |
intron | 179 | 146 |
description: | ||
protein length (aa) | 499 | 351 |
exons per gene | 4.04 | 3 |
# of gene models | 12794 |
Genome Reference(s)
Ban H, Sato S, Yoshikawa S, Yamada K, Nakamura Y, Ichinomiya M, Sato N, Blanc-Mathieu R, Endo H, Kuwata A, Ogata H
Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs.
Commun Biol. 2023 Jul 7;6(1):697. doi: 10.1038/s42003-023-05002-x
Links
- JGI PhyloGroup Portals: Heterokonta Ochrophyta Bolidophyta
- JGI EcoGroup Portal: Algae Oceanic phytoplankton