Info • Tetradesmus deserticola SNI-2 v1.0

Status

[September 2020] The Tetradesmus deserticola SNI-2 v1.0 genome was sequenced with PacBio, assembled with MECAT, and annotated using the JGI Annotation Pipeline. The mitochondrial and chloroplast genomes were assembled separately and are available in the downloads section.

The genome is likely a diploid sample, and this is reflected in an assembly and annotation with significant 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 Tetradesmus deserticola SNI-2 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 198.16
Sequencing read coverage depth 339.39x
# of contigs 126
# of scaffolds 126
# of scaffolds >= 2Kbp 126
Scaffold N50 14
Scaffold L50 (Mbp) 5.31
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 10.58, 9.08, 7.88


ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 669325395 664456389 99.3%
Other JGI_RNA_contigs 239748 198628 82.8%


Gene Models FilteredModels2
length (bp) of: average median
gene 4110 3242
transcript 2026 1654
exon 323 171
intron 397 310
description:
protein length (aa) 388 294
exons per gene 6.27 5
# of gene models 18507


Collaborators

Funding

The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.