Status
[June 2016] The Rhodosporidium toruloides APA 2687 genome was sequenced with Illumina, assembled with AllPathsLG, and annotated with the JGI Annotation pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.
Summary statistics for the Rhodosporidium toruloides APA
2687 v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 20.29 |
| Sequencing read coverage depth | 129.2x |
| # of contigs | 172 |
| # of scaffolds | 163 |
| # of scaffolds >= 2Kbp | 142 |
| Scaffold N50 | 18 |
| Scaffold L50 (Mbp) | 0.38 |
| # of gaps | 9 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 0.99, 0.87, 0.70 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 257698825 | 250064934 | 97.0% |
| Ests | Trinity_assembled_Illumina_ESTs | 31376 | 29855 | 95.2% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 2147 | 1798 |
| transcript | 1739 | 1441 |
| exon | 282 | 171 |
| intron | 81 | 64 |
| description: | ||
| protein length (aa) | 516 | 412 |
| exons per gene | 6.17 | 5 |
| # of gene models | 8235 |
Collaborators
John Gladden, Joint Bioenergy Institute (JBEI)
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
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
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.
