Status
[Mar 2016] This is a combined assembly, made using 13 individual single-cell Illumina libraries: two 1-cell, four 30-cell, and seven 100-cell. All scaffolds >= 2kb. Assembled using Spades v3.6.0.
Summary statistics for the Syncephalis pseudoplumigaleata
Benny S71-1 single-cell v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 16.27 |
| Sequencing read coverage depth | 1.0x |
| # of contigs | 3496 |
| # of scaffolds | 3317 |
| # of scaffolds >= 2Kbp | 3317 |
| Scaffold N50 | 757 |
| Scaffold L50 (Mbp) | 0.01 |
| # of gaps | 179 |
| % of scaffold length in gaps | 0.4% |
| Three largest Scaffolds (Mbp) | 0.10, 0.07, 0.04 |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1341 | 1103 |
| transcript | 1036 | 846 |
| exon | 248 | 144 |
| intron | 98 | 71 |
| description: | ||
| protein length (aa) | 345 | 282 |
| exons per gene | 4.18 | 3 |
| # of gene models | 6123 |
Collaborators
- Dr. Timothy Y. James, University of Michigan, USA
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Ahrendt SR, Quandt CA, Ciobanu D, Clum A, Salamov A, Andreopoulos B, Cheng JF, Woyke T, Pelin A, Henrissat B, Reynolds NK, Benny GL, Smith ME, James TY, Grigoriev IV
Leveraging single-cell genomics to expand the fungal tree of life.
Nat Microbiol. 2018 Dec;3(12):1417-1428. doi: 10.1038/s41564-018-0261-0
Ahrendt SR, Quandt CA, Ciobanu D, Clum A, Salamov A, Andreopoulos B, Cheng JF, Woyke T, Pelin A, Henrissat B, Reynolds NK, Benny GL, Smith ME, James TY, Grigoriev IV
Leveraging single-cell genomics to expand the fungal tree of life.
Nat Microbiol. 2018 Dec;3(12):1417-1428. doi: 10.1038/s41564-018-0261-0
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.
