Status
[September 2016] The Lophiotrema nucula CBS 627.86 genome was sequenced with Illumina, assembled with AllPathsLG, and annotated with the JGI Annotation pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.
Summary statistics for the Lophiotrema nucula v1.0 release
are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 48.64 |
| Sequencing read coverage depth | 138.8x |
| # of contigs | 251 |
| # of scaffolds | 187 |
| # of scaffolds >= 2Kbp | 168 |
| Scaffold N50 | 18 |
| Scaffold L50 (Mbp) | 0.98 |
| # of gaps | 64 |
| % of scaffold length in gaps | 0.1% |
| Three largest Scaffolds (Mbp) | 2.11, 1.87, 1.71 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 37078 | 36596 | 98.7% |
| Ests | est.fasta | 135665108 | 132763715 | 97.9% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1605 | 1372 |
| transcript | 1477 | 1254 |
| exon | 565 | 359 |
| intron | 82 | 57 |
| description: | ||
| protein length (aa) | 438 | 363 |
| exons per gene | 2.61 | 2 |
| # of gene models | 18117 |
Collaborators
Jon Magnuson at the Pacific Northwest National Laboratory
Joseph Spatafora, Oregon State University, USA
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.
