Status
[December 2020] The genome and transcriptome sequences were not determined by the Joint Genome Institute (JGI). The genome was sequenced with PacBio, assembled with Canu, and annotated with Braker2 by Aaron Oliver at the University of California San Diego. The transcriptome was sequenced with Illumina by Tyson Burch at the Colorado School of Mines, and then assembled with Trinity by Oliver. In order to ensure this genome is comparable to those sequenced by the JGI, the JGI Annotation Pipeline applied filters to remove: 1) transposable elements, 2) pseudogenes, 3) alternative transcripts and overlapping models, 4) alleles on secondary scaffolds and 5) unsupported short models. These removals generated the FilteredModels1 gene track. All of Oliver's original Braker2 models are available in the ExternalModels track. The JGI Annotation Pipeline was used to add functional annotation to this genome. The plastid and mitochondrial genomes were assembled by Oliver and are available on the Download page.
The genome is a polymorphic diploid, and this is reflected in an assembly and annotation with complete separation of alleles. Many of the scaffolds are very similar to larger scaffolds and are predicted to constitute an alternate or secondary haplotype. To represent these primary and secondary haplotypes in the Portal, we have created 'primary alleles' and 'secondary alleles' gene model tracks, comprising the models found on each haplotype. The goal of the GeneCatalog (GC) is to produce a non-redundant set of models which captures the full functional repertiore of the genome, and so the few secondary alleles that are unique were included in the GC, while all others were not.
Genome Assembly | |
Genome Assembly size (Mbp) | 99.71 |
Sequencing read coverage depth | |
# of contigs | 123 |
# of scaffolds | 123 |
# of scaffolds >= 2Kbp | 123 |
Scaffold N50 | 11 |
Scaffold L50 (Mbp) | 3.62 |
# of gaps | 0 |
% of scaffold length in gaps | 0.0% |
Three largest Scaffolds (Mbp) | 6.57, 6.36, 5.38 |
ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
Ests | est.fasta | 141617423 | 56602917 | 40.0% |
Other | UCSD_1010_lightADB | 72533 | 41201 | 56.8% |
Other | UCSD_control_A | 81778 | 41650 | 50.9% |
Other | UCSD_DarkC | 82799 | 40055 | 48.4% |
Other | UCSD_LowNitA | 79014 | 39357 | 49.8% |
Other | UCSD_NUrea_A | 78325 | 39993 | 51.1% |
Other | UCSD_TB19AM | 58335 | 21402 | 36.7% |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 1627 | 1336 |
transcript | 1513 | 1242 |
exon | 870 | 640 |
intron | 155 | 100 |
description: | ||
protein length (aa) | 504 | 414 |
exons per gene | 1.74 | 1 |
# of gene models | 17968 |
Collaborators
Genome Reference(s)
Oliver A, Podell S, Pinowska A, Traller JC, Smith SR, McClure R, Beliaev A, Bohutskyi P, Hill EA, Rabines A, Zheng H, Allen LZ, Kuo A, Grigoriev IV, Allen AE, Hazlebeck D, Allen EE
Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom.
Sci Rep. 2021 Aug 2;11(1):15592. doi: 10.1038/s41598-021-95106-3
Links
- JGI PhyloGroup Portals: Bacillariophyta Bacillariophyceae
- JGI EcoGroup Portal: Algae Oceanic phytoplankton