Status
Assembly v1.0 (November 2015) . Elsinoe ampelina CECT 20119 genome was sequenced using Illumina HiSeq platform and assembled with AllPathsLG to produce a main assembly with 161 scaffolds and 28.27 Mb. ESTs were assembled using Trinity.
Summary statistics for the Elsinoe ampelina v1.0 release
are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 28.27 |
| Sequencing read coverage depth | 100.2x |
| # of contigs | 503 |
| # of scaffolds | 161 |
| # of scaffolds >= 2Kbp | 125 |
| Scaffold N50 | 7 |
| Scaffold L50 (Mbp) | 1.53 |
| # of gaps | 342 |
| % of scaffold length in gaps | 1.2% |
| Three largest Scaffolds (Mbp) | 3.31, 2.76, 2.27 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 94912225 | 92254222 | 97.2% |
| Other | Assembled_EST_contigs | 20375 | 19809 | 97.2% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1693 | 1467 |
| transcript | 1594 | 1373 |
| exon | 676 | 416 |
| intron | 75 | 53 |
| description: | ||
| protein length (aa) | 451 | 373 |
| exons per gene | 2.36 | 2 |
| # of gene models | 10209 |
Collaborators
Joseph
Spataphora, Oregon State
University
Lucía
Ramírez, Public Universiy of
Navarre
Antonio G. Pisabarro,
Public Universiy of Navarre
Manuel Alfaro,
Public University of Navarre
Raúl
Castanera, Public University of Navarre
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.
