Info • Nitzschia inconspicua GAI-293 v2.0


[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.

Summary statistics for the Nitzschia inconspicua GAI-293 v2.0 release are below.
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
protein length (aa) 504 414
exons per gene 1.74 1
# of gene models 17968

Genome Reference(s)



This project was not sequenced at the JGI.