Status
v1.2 (June 2011). The Pachysolen tannophilus NRRL Y-2460 v1.0 hybrid draft release genome sequence assembly was built using the Newbler assembler (Release 2.4pre), and 392 gaps were subsequently closed by automated gap resolution. The draft assembly and gap resolution input reads consist of Roche (454), Illumina (Solexa), and fosmid (Sanger) data. The nuclear genome sequence from this draft assembly was annotated using the JGI Genome Annotation Pipeline and custom analyses. For this v1.2 annotation, the alternate yeast nuclear code (translation table 12) was used. This v1.2 portal consists of the assembly data from the v1.0 portal plus ESTs (see table below) used for gene modeling to produce the Pacta1_2 updated annotation release.
Summary statistics for the Pachysolen tannophilus NRRL
Y-2460 v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 12.60 |
| Sequencing read coverage depth | 90.65x |
| # of contigs | 583 |
| # of scaffolds | 198 |
| # of scaffolds >= 2Kbp | 28 |
| Scaffold N50 | 3 |
| Scaffold L50 (Mbp) | 1.75 |
| # of gaps | 385 |
| % of scaffold length in gaps | 1.9% |
| Three largest Scaffolds (Mbp) | 2.51, 2.19, 1.75 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | EstClusters | 13973 | 13103 | 93.8% |
| Gene Models | Filteredmodels2 | |
| length (bp) of: | average | median |
| gene | 1638 | 1383 |
| transcript | 1586 | 1354 |
| exon | 1193 | 978 |
| intron | 162 | 98 |
| description: | ||
| protein length (aa) | 480 | 396 |
| exons per gene | 1.33 | 1 |
| # of gene models | 5675 |
Collaborators
- PI: Igor Grigoriev (JGI)
- Thomas Jeffries, USDA Forest Products Lab, Madison, WI.
- Meredith Blackwell, Louisiana State University, Baton Rouge, Louisiana
- Cletus P. Kurtzman, USDA National Center for Agricultural Utilization Research, Peoria, IL
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.
