Status
This draft release was produced by combining shredded consensus from Velvet-assembled Illumina data, Roche (454) standard and Roche (454) paired end, which were then assembled with Newbler. Gap closure with gapResolution closed 226 gaps (30%) in initial assembly. The genome was annotated with the JGI annotation pipeline and custom analyses.
Summary statistics for the Metschnikowia bicuspidata NRRL
YB-4993 v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 16.06 |
| Sequencing read coverage depth | 16.08 |
| # of contigs | 421 |
| # of scaffolds | 48 |
| # of scaffolds >= 2Kbp | 48 |
| Scaffold N50 | 3 |
| Scaffold L50 (Mbp) | 2.54 |
| # of gaps | 373 |
| % of scaffold length in gaps | 2.3% |
| Three largest Scaffolds (Mbp) | 5.39, 2.56, 2.54 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| RNAseq contigs | RNAseq contigs | 10706 | 9849 | 92.0% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1497 | 1224 |
| transcript | 1443 | 1187 |
| exon | 1140 | 922 |
| intron | 204 | 92 |
| description: | ||
| protein length (aa) | 438 | 355 |
| exons per gene | 1.27 | 1 |
| # of gene models | 5851 |
Collaborators
Thomas Jeffries, University of Wisconsin Igor Grigoriev, DOE Joint Genome Institute
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, Deshpande S, Douglass AP, Hanson SJ, Klenk HP, LaButti KM, Lapidus A, Lindquist EA, Lipzen AM, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW
Comparative genomics of biotechnologically important yeasts.
Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9882-7. doi: 10.1073/pnas.1603941113
Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, Deshpande S, Douglass AP, Hanson SJ, Klenk HP, LaButti KM, Lapidus A, Lindquist EA, Lipzen AM, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW
Comparative genomics of biotechnologically important yeasts.
Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9882-7. doi: 10.1073/pnas.1603941113
Links
Thomas Jeffries laboratory, University of Wisconsin
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.
