Info • Tetradesmus deserticola SNI-2 v1.1


The Tetradesmus deserticola SNI-2 v1.1 genome was sequenced with PacBio, assembled with MECAT, and annotated using the JGI Annotation Pipeline. In contrast to the v1.0 portal, this annotation has been improved through the addition of Iso-Seq data to the original RNAseq transcriptome.

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.

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 672278454 667374185 99.3%
Other IsoSeq_reads 169700 165248 97.4%
Other JGI_RNA_contigs 239748 198719 82.9%

Gene Models FilteredModels2
length (bp) of: average median
gene 4366 3644
transcript 2174 1920
exon 332 170
intron 397 311
protein length (aa) 422 319
exons per gene 6.55 5
# of gene models 17197



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.