Status
[May 2014] The Phoma tracheiphila genome was sequenced
using the Illumina platform and assembled with AllPathsLG release
version R47710 (Gnerre
et al., 2010).
Mitochondrial genome was assembled separately and is available in
the downloads section.
Summary statistics for the Phoma tracheiphila IPT5 v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 34.24 |
| Sequencing read coverage depth | 98.6x |
| # of contigs | 431 |
| # of scaffolds | 273 |
| # of scaffolds >= 2Kbp | 231 |
| Scaffold N50 | 20 |
| Scaffold L50 (Mbp) | 0.53 |
| # of gaps | 158 |
| % of scaffold length in gaps | 0.5% |
| Three largest Scaffolds (Mbp) | 1.52, 1.52, 1.30 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | RNNotator assembled Illumina ESTs | 25313 | 24354 | 96.2% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1692 | 1452 |
| transcript | 1555 | 1330 |
| exon | 583 | 371 |
| intron | 84 | 57 |
| description: | ||
| protein length (aa) | 441 | 362 |
| exons per gene | 2.67 | 2 |
| # of gene models | 13209 |
Collaborators
Joseph
Spatafora, Oregon State
University, USA
David Ezra, Agricultural Research
Organization, The Volcani Center at Bet-Dagan, Israel.
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Haridas S, Albert R, Binder M, Bloem J, LaButti K, Salamov A, Andreopoulos B, Baker SE, Barry K, Bills G, Bluhm BH, Cannon C, Castanera R, Culley DE, Daum C, Ezra D, González JB, Henrissat B, Kuo A, Liang C, Lipzen A, Lutzoni F, Magnuson J, Mondo SJ, Nolan M, Ohm RA, Pangilinan J, Park HJ, Ramírez L, Alfaro M, Sun H, Tritt A, Yoshinaga Y, Zwiers LH, Turgeon BG, Goodwin SB, Spatafora JW, Crous PW, Grigoriev IV
101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens.
Stud Mycol. 2020 Jun;96():141-153. doi: 10.1016/j.simyco.2020.01.003
Haridas S, Albert R, Binder M, Bloem J, LaButti K, Salamov A, Andreopoulos B, Baker SE, Barry K, Bills G, Bluhm BH, Cannon C, Castanera R, Culley DE, Daum C, Ezra D, González JB, Henrissat B, Kuo A, Liang C, Lipzen A, Lutzoni F, Magnuson J, Mondo SJ, Nolan M, Ohm RA, Pangilinan J, Park HJ, Ramírez L, Alfaro M, Sun H, Tritt A, Yoshinaga Y, Zwiers LH, Turgeon BG, Goodwin SB, Spatafora JW, Crous PW, Grigoriev IV
101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens.
Stud Mycol. 2020 Jun;96():141-153. doi: 10.1016/j.simyco.2020.01.003
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.
