Info • Tribonema minus UTEX B 3156 v1.0

Status

[December 2020] The genome and transcriptome sequences were not determined by the Joint Genome Institute (JGI). The genome was sequenced with PacBio and Illumina, and then assembled with Canu by Krissy Mahan at Sandia National Laboratories. The transcriptome was sequenced with Illumina by Krissy, and then assembled with Trinity by JGI. Subsequently, all of the above data were inputted into the JGI Annotation Pipeline, which produced a final structural and functional annotation. The plastid and mitochondrial genomes were assembled separately by Krissy and are available on the Download page.

Summary statistics for the Tribonema minus UTEX B 3156 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 158.35
Sequencing read coverage depth
# of contigs 557
# of scaffolds 557
# of scaffolds >= 2Kbp 557
Scaffold N50 66
Scaffold L50 (Mbp) 0.77
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 2.45, 2.12, 2.11


ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 261340568 7107713 2.7%
Other JGI_RNA_contigs 170431 24096 14.1%


Gene Models FilteredModels1
length (bp) of: average median
gene 5210 3242
transcript 1501 1128
exon 253 157
intron 754 617
description:
protein length (aa) 469 342
exons per gene 5.93 4
# of gene models 18290


Genome Reference(s)

Please cite the following publication(s) if you use the data from this genome in your research:

Mahan KM, Polle JEW, McKie-Krisberg Z, Lipzen A, Kuo A, Grigoriev IV, Lane TW, Davis AK
Annotated Genome Sequence of the High-Biomass-Producing Yellow-Green Alga Tribonema minus.
Microbiol Resour Announc. 2021 Jun 17;10(24):e0032721. doi: 10.1128/MRA.00327-21

Davis AK, Anderson RS, Spierling R, Leader S, Lesne C, Mahan K, Lundquist T, Benemann JR, Lane T, Polle JEW
Characterization of a novel strain of Tribonema minus demonstrating high biomass productivity in outdoor raceway ponds.
Bioresour Technol. 2021 Jul;331():125007. doi: 10.1016/j.biortech.2021.125007

Links

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.