Status
The assembly release of whole genome shotgun reads was constructed with the JGI assembler, JAZZ.
The short summary of the 8x Trichoderma atroviride genome is as follows:
Main Genome Total Reads in the assembly:
430,655
Main Genome Total Number of Scaffolds: 50
Main Genome Total Number of Contigs: 350
Main Genome Scaffold Sequence Total: 36.1 MB
Main Genome Contig Total: 36.0 MB (->0.16% gap)
Main Genome Scaffold N/L50: 6/2.00 MB
Main Genome Contig N/L50: 46/252 KB
Main Genome Depth: 8.26 +/-0.03
The current draft release, version 1.0, includes a total of 11,100 gene models predicted and functionally annotated using the JGI annotation pipeline.
Collaborators
- US Department of Energy Joint Genome Institute (JGI)
- Scott Baker, PNNL
- Christian Kubicek, Vienna University of Technology, Austria
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA, Mukherjee PK, Mukherjee M, Kredics L, Alcaraz LD, Aerts A, Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F, Deshpande N, von Döhren H, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gómez-RodrÃguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernández-Oñate M, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lübeck M, Lübeck PS, Margeot A, Metz B, Misra M, Nevalainen H, Omann M, Packer N, Perrone G, Uresti-Rivera EE, Salamov A, Schmoll M, Seiboth B, Shapiro H, Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A, Wilkinson HH, Zhang M, Coutinho PM, Kenerley CM, Monte E, Baker SE, Grigoriev IV
Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma.
Genome Biol. 2011;12(4):R40. doi: 10.1186/gb-2011-12-4-r40
Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA, Mukherjee PK, Mukherjee M, Kredics L, Alcaraz LD, Aerts A, Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F, Deshpande N, von Döhren H, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gómez-RodrÃguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernández-Oñate M, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lübeck M, Lübeck PS, Margeot A, Metz B, Misra M, Nevalainen H, Omann M, Packer N, Perrone G, Uresti-Rivera EE, Salamov A, Schmoll M, Seiboth B, Shapiro H, Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A, Wilkinson HH, Zhang M, Coutinho PM, Kenerley CM, Monte E, Baker SE, Grigoriev IV
Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma.
Genome Biol. 2011;12(4):R40. doi: 10.1186/gb-2011-12-4-r40
Funding
This work was performed under the auspices of the US Department of
Energy's Office of Science, Biological and Environmental Research
Program, and by the University of California, Lawrence Berkeley
National Laboratory under contract No. DE-AC02-05CH11231, Lawrence
Livermore National Laboratory under Contract No. DE-AC52-07NA27344,
and Los Alamos National Laboratory under contract No.
DE-AC02-06NA25396.
