Status
v2.0 (May 2010): The assembly release version 2.0 of 454 and Sanger
sequencing reads was constructed with the Newbler assembler and
post-processed using JGI gapResolution software with targeted
finishing of the mat A chromosome. This genome assembled into 81
main genome scaffolds totaling 39.1 Mbp. Roughly half of the genome
is contained in 3 scaffolds all at least 5.7 Mbp in length.
v.1.0 (February, 2009): The assembly release version 1.0 of whole genome shotgun reads was constructed with the Arachne assembler, using paired end sequencing reads at a coverage of ~8.30X. After trimming for vector and quality, this genome assembled into 155 main genome scaffolds totaling 37.8 Mbp. Roughly half of the genome is contained in 13 scaffolds all at least 976.6 Kbp in length.
v.1.0 (February, 2009): The assembly release version 1.0 of whole genome shotgun reads was constructed with the Arachne assembler, using paired end sequencing reads at a coverage of ~8.30X. After trimming for vector and quality, this genome assembled into 155 main genome scaffolds totaling 37.8 Mbp. Roughly half of the genome is contained in 13 scaffolds all at least 976.6 Kbp in length.
| Nuclear Genome Assembly: | Neurospora tetrasperma FGSC 2508 mat A v2.0 |
Neurospora tetrasperma FGSC 2508 mat A v1.0 |
Neurospora tetrasperma FGSC 2509 mat a v1.0 |
| Sequencing platform: | Hybrid 454/Sanger | Sanger | Hybrid 454/Sanger |
| Scaffold count: | 81 | 155 | 307 |
| All Contig count: | 551 | 542 | 861 |
| Scaffold sequence bases total: | 39.1 Mb | 37.8 Mb | 39.1 Mb |
| Scaffolded (Large) Contig sequence bases total: | 38.5 Mb | 37.5 Mb | 38.1 Mb |
| Estimated % sequence bases in gaps: | 1.7% | 0.5% | 2.5% |
| Scaffold N50 / L50: | 3 / 5.7 Mb | 13 / 976.6 Kb | 3 / 5.7 Mb |
| Contig N50 / L50: | 89 / 134.9 Kb | 69 / 162.5 Kb | 117 / 99.8 Kb |
| Number of scaffolds > 50.0 Kb: | 7 | 74 | 7 |
| % in scaffolds > 50.0 Kb: | 99.2% | 97% | 98.2% |
v2.0 (May 2010): The assembly was annotated with the JGI Annotation
Pipeline, using a variety of homology-based and ab initio gene
predictors. After filtering for EST support, completeness, and
homology support, a total of 10,380 genes were structurally and
functionally annotated.
v1.0 (February 2009): The assembly was annotated with the JGI Annotation Pipeline, using a variety of homology-based and ab initio gene predictors. After filtering for EST support, completeness, and homology support, a total of 10,640 genes were structurally and functionally annotated.
v1.0 (February 2009): The assembly was annotated with the JGI Annotation Pipeline, using a variety of homology-based and ab initio gene predictors. After filtering for EST support, completeness, and homology support, a total of 10,640 genes were structurally and functionally annotated.
| Nuclear Genome Annotation: | Neurospora tetrasperma FGSC 2508 mat A v2.0 |
Neurospora tetrasperma FGSC 2508 mat A v1.0 |
Neurospora tetrasperma FGSC 2509 mat a v2.0 |
| # gene models: | 10,380 | 10,640 | 11,192 |
| Gene density: | 265 | 281 | 286 |
| Avg.gene length: | 1836 | 1780 | 1800 |
| Avg. protein length: | 468 | 462 | 443 |
| Avg. exon frequency: | 2.72 exons/gene | 2.8 exons/gene | 2.7 exons/gene |
| Avg. exon length: | 579 | 558 | 548 |
| Avg. intron length: | 154 | 131 | 152 |
| % complete gene models (with start and stop codons): | 94% | 94% | 92% |
| % genes with homology support: | 91% | 87% | 87% |
| % genes with Pfam domains: | 50% | 42% | 46% |
Collaborators
- John Taylor, Department of Plant and Microbial Biology, University of California, Berkeley
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Ellison CE, Stajich JE, Jacobson DJ, Natvig DO, Lapidus A, Foster B, Aerts A, Riley R, Lindquist EA, Grigoriev IV, Taylor JW
Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma.
Genetics. 2011 Sep;189(1):55-69. doi: 10.1534/genetics.111.130690
Ellison CE, Stajich JE, Jacobson DJ, Natvig DO, Lapidus A, Foster B, Aerts A, Riley R, Lindquist EA, Grigoriev IV, Taylor JW
Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma.
Genetics. 2011 Sep;189(1):55-69. doi: 10.1534/genetics.111.130690
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.
