Status
[November 2019] The Trichoderma endophyticum SZMC 28010 genome was sequenced with Illumina, assembled with SPAdes, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina and assembled with Trinity. Mitochondrial genome was assembled separately and is available in the downloads section.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 39.40 |
| Sequencing read coverage depth | 106.44x |
| # of contigs | 185 |
| # of scaffolds | 175 |
| # of scaffolds >= 2Kbp | 134 |
| Scaffold N50 | 9 |
| Scaffold L50 (Mbp) | 1.75 |
| # of gaps | 10 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 3.45, 2.46, 2.24 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 38313 | 36704 | 95.8% |
| Ests | est.fasta | 175144176 | 174290027 | 99.5% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1955 | 1700 |
| transcript | 1793 | 1555 |
| exon | 631 | 399 |
| intron | 90 | 67 |
| description: | ||
| protein length (aa) | 484 | 393 |
| exons per gene | 2.84 | 2 |
| # of gene models | 12947 |
Collaborators
- Randy Berka, Archer Daniels Midland Company, CA, USA
- Irina Druzhinina, Nanjing Agricultural University, Jiangsu, PRC
- Adrian Tsang, Concordia University, Quebec, Canada
Links
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.
