Status
[April 2016] The Lineolata rhizophorae ATCC 16933
genome was sequenced using the Illumina platform and assembled with
AllPathsLG release version R49403 (Gnerre et al.,
2011).
Mitochondrial genome was assembled separately and is available in
the downloads section.
Summary statistics for the Lineolata rhizophorae v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 31.14 |
| Sequencing read coverage depth | 97.8x |
| # of contigs | 426 |
| # of scaffolds | 68 |
| # of scaffolds >= 2Kbp | 58 |
| Scaffold N50 | 11 |
| Scaffold L50 (Mbp) | 1.11 |
| # of gaps | 358 |
| % of scaffold length in gaps | 1.9% |
| Three largest Scaffolds (Mbp) | 2.16, 1.61, 1.58 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 38553 | 37125 | 96.3% |
| Ests | est.fasta | 117112025 | 114091378 | 97.4% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1720 | 1444 |
| transcript | 1524 | 1251 |
| exon | 522 | 322 |
| intron | 104 | 72 |
| description: | ||
| protein length (aa) | 433 | 339 |
| exons per gene | 2.92 | 3 |
| # of gene models | 10230 |
Collaborators
Jon
Magnuson, Pacific Northwest National Laboratory, USA
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.
