Info • Rhodosporidium toruloides IFO0880 v4.0

Status

[June 2017] [May 2017] The Rhodosporidum toruloides IFO0880 genome was sequenced externally in the lab of Dr. Jeffrey Skerker using PacBio, assembled with HGAP, then annotated with the JGI annotation pipeline. This assembly improves upon the v3.0 by separating the mitochondria from the main genome assembly, which is now provided separately in the downloads section. Additionally, the default analysis track was updated to reflect manual curations done by the Skerker lab on the previous version (R. toruloides v3.0).

Summary statistics for the Rhodosporidium toruloides IFO0880 v4.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 20.68
Sequencing read coverage depth
# of contigs 30
# of scaffolds 30
# of scaffolds >= 2Kbp 30
Scaffold N50 6
Scaffold L50 (Mbp) 1.39
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 2.22, 1.97, 1.86


ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 257698825 255759050 99.2%
Ests RNNotator_assembled_Illumina_ESTs 31376 30074 95.9%


Gene Models FrozenGeneCatalog
length (bp) of: average median
gene 2083 1783
transcript 1699 1432
exon 283 171
intron 78 64
description:
protein length (aa) 500 406
exons per gene 6.01 5
# of gene models 8490


Collaborators

John Gladden, Joint Bioenergy Institute (JBEI)
Jeffrey Skerker, UC Berkeley

Genome Reference(s)

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

Coradetti ST, Pinel D, Geiselman GM, Ito M, Mondo SJ, Reilly MC, Cheng YF, Bauer S, Grigoriev IV, Gladden JM, Simmons BA, Brem RB, Arkin AP, Skerker JM
Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides.
Elife. 2018 Mar 9;7():. doi: 10.7554/eLife.32110

Funding

This project was not sequenced at the JGI.