Status
[June 2013] The Pleomassaria siparia genome was sequenced using
the Illumina platform and assembled with AllPathsLG
release version R44849 (Gnerre
et al., 2010).
Mitochondrial genome was assembled separately with AllPathsLG to
produce an assembly with 8 scaffolds, 95 Kb scaffold N50, 184714 bp
total scaffold and is available in the downloads section.
Summary statistics for the Pleomassaria siparia CBS 279.74
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 43.18 |
| Sequencing read coverage depth | 87.3x |
| # of contigs | 1023 |
| # of scaffolds | 193 |
| # of scaffolds >= 2Kbp | 132 |
| Scaffold N50 | 8 |
| Scaffold L50 (Mbp) | 1.89 |
| # of gaps | 830 |
| % of scaffold length in gaps | 1.3% |
| Three largest Scaffolds (Mbp) | 4.56, 4.46, 2.74 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | RNNotator assembled Illumina ESTs | 30225 | 29325 | 97.0% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1666 | 1418 |
| transcript | 1474 | 1251 |
| exon | 524 | 319 |
| intron | 108 | 60 |
| description: | ||
| protein length (aa) | 426 | 349 |
| exons per gene | 2.81 | 2 |
| # of gene models | 13486 |
Collaborators
Joseph Spatafora, Oregon State University, USA.
Pedro Crous and Manfred Binder at CBS-KNAW, Netherlands.
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, RamÃrez 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, RamÃrez 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.
