Status
Version 2.0 (November 2011) This improved draft assembly was produced using Roche (454), Sanger Fosmid, and shredded consensus from Velvet assembled Illumina data. One round of automated gap closure with Gap Resolution closed 47 gaps in version 1.0 of the main genome. In addition to this, several misassemblies have been corrected.
Summary statistics for the Pichia membranifaciens v2.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 11.58 |
| Sequencing read coverage depth | 38.95x |
| # of contigs | 279 |
| # of scaffolds | 11 |
| # of scaffolds >= 2Kbp | 11 |
| Scaffold N50 | 3 |
| Scaffold L50 (Mbp) | 1.68 |
| # of gaps | 134 |
| % of scaffold length in gaps | 1.3% |
| Three largest Scaffolds (Mbp) | 2.70, 2.68, 1.68 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | Assembled Illumina ESTs | 10376 | 8840 | 85.2% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1630 | 1341 |
| transcript | 1578 | 1318 |
| exon | 1285 | 1056 |
| intron | 226 | 111 |
| description: | ||
| protein length (aa) | 482 | 399 |
| exons per gene | 1.23 | 1 |
| # of gene models | 5560 |
Collaborators
- Igor Grigoriev, JGI
- Thomas Jeffries, USDA Forest Service, Forest Products Laboratory
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
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.
