Status
Assembly v3 (October 2013) is an improved assembly. Solexa gDNA reads were assembled using AllPathsLG, then gaps were closed using PacBio gDNAs and PBJelly, and finally bacterial contaminant scaffolds were removed.
Summary statistics for the Trichoderma citrinoviride v4.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 33.22 |
| Sequencing read coverage depth | 63.1x |
| # of contigs | 699 |
| # of scaffolds | 533 |
| # of scaffolds >= 2Kbp | 200 |
| Scaffold N50 | 7 |
| Scaffold L50 (Mbp) | 1.85 |
| # of gaps | 166 |
| % of scaffold length in gaps | 0.2% |
| Three largest Scaffolds (Mbp) | 3.29, 2.90, 2.85 |
RNASeq reads were extracted from a mixed culture of Trichoderma
longibrachiatum and T. citrinioviride, predominatantly
the former.
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | JGI_RNA_contigs | 28133 | 1192 | 4.2% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1702 | 1406 |
| transcript | 1481 | 1227 |
| exon | 477 | 255 |
| intron | 107 | 72 |
| description: | ||
| protein length (aa) | 484 | 399 |
| exons per gene | 3.10 | 3 |
| # of gene models | 9737 |
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Druzhinina IS, Chenthamara K, Zhang J, Atanasova L, Yang D, Miao Y, Rahimi MJ, Grujic M, Cai F, Pourmehdi S, Salim KA, Pretzer C, Kopchinskiy AG, Henrissat B, Kuo A, Hundley H, Wang M, Aerts A, Salamov A, Lipzen A, LaButti K, Barry K, Grigoriev IV, Shen Q, Kubicek CP
Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts.
PLoS Genet. 2018 Apr;14(4):e1007322. doi: 10.1371/journal.pgen.1007322
Druzhinina IS, Chenthamara K, Zhang J, Atanasova L, Yang D, Miao Y, Rahimi MJ, Grujic M, Cai F, Pourmehdi S, Salim KA, Pretzer C, Kopchinskiy AG, Henrissat B, Kuo A, Hundley H, Wang M, Aerts A, Salamov A, Lipzen A, LaButti K, Barry K, Grigoriev IV, Shen Q, Kubicek CP
Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts.
PLoS Genet. 2018 Apr;14(4):e1007322. doi: 10.1371/journal.pgen.1007322
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.
