Status
Assembly v1 (June 2015) is a standard draft assembly of Illumina gDNA reads using AllPathsLG.
Annotation v1 (April 2016) is a standard draft annotation using Illumina RNA-Seq reads assembled with Trinity and modeled and filtered by the JGI Annotation Pipeline.
Summary statistics for the Usnea florida ATCC18376 v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 44.32 |
| Sequencing read coverage depth | 87.6x |
| # of contigs | 1774 |
| # of scaffolds | 274 |
| # of scaffolds >= 2Kbp | 195 |
| Scaffold N50 | 29 |
| Scaffold L50 (Mbp) | 0.50 |
| # of gaps | 1500 |
| % of scaffold length in gaps | 5.9% |
| Three largest Scaffolds (Mbp) | 1.34, 1.02, 1.02 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 58417 | 55842 | 95.6% |
| Ests | est.fasta | 109440685 | 105175194 | 96.1% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1722 | 1464 |
| transcript | 1549 | 1296 |
| exon | 501 | 299 |
| intron | 84 | 60 |
| description: | ||
| protein length (aa) | 454 | 366 |
| exons per gene | 3.09 | 3 |
| # of gene models | 12649 |
Collaborators
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Mondo SJ, He G, Sharma A, Ciobanu D, Riley R, Andreopoulos WB, Lipzen A, Kuo A, LaButti K, Pangilinan J, Salamov A, Salamon H, Shu L, Gladden J, Magnuson J, Aime MC, O'Malley R, Grigoriev IV
Consecutive low-frequency shifts in A/T content denote nucleosome positions across microeukaryotes.
iScience. 2025 May 16;28(5):112472. doi: 10.1016/j.isci.2025.112472
Mondo SJ, He G, Sharma A, Ciobanu D, Riley R, Andreopoulos WB, Lipzen A, Kuo A, LaButti K, Pangilinan J, Salamov A, Salamon H, Shu L, Gladden J, Magnuson J, Aime MC, O'Malley R, Grigoriev IV
Consecutive low-frequency shifts in A/T content denote nucleosome positions across microeukaryotes.
iScience. 2025 May 16;28(5):112472. doi: 10.1016/j.isci.2025.112472
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.
