Status
[March 2018] Assembly v1 is a minimal draft assembly extracted from a lichen metagenome by aligning the reads with the reference mycobiont genome. The aligned Illumina gDNAs were assembled with Velvet and then AllPathsLG. The mitochondrial assembly is available on the Download page.
Annotation v1 is a draft annotation, using an extracted metatranscriptome, the reference mycobiont transcriptome, and the JGI Annotation Pipeline v1.10. The metatranscriptome was extracted by aligning the Illumina reads with the extracted mycobiont genome. The metatranscriptome and the reference transcriptome were each assemblied separately with Trinity.
Summary statistics for the Lobaria pulmonaria Scotland
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 55.85 |
| Sequencing read coverage depth | 144.8x |
| # of contigs | 1603 |
| # of scaffolds | 1189 |
| # of scaffolds >= 2Kbp | 1189 |
| Scaffold N50 | 184 |
| Scaffold L50 (Mbp) | 0.08 |
| # of gaps | 414 |
| % of scaffold length in gaps | 0.4% |
| Three largest Scaffolds (Mbp) | 0.49, 0.47, 0.46 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 371979111 | 365166762 | 98.2% |
| Other | JGI_met_RNA_contigs | 88215 | 80443 | 91.2% |
| Other | JGI_ref_RNA_contigs | 103899 | 78854 | 75.9% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1553 | 1327 |
| transcript | 1384 | 1150 |
| exon | 469 | 291 |
| intron | 88 | 60 |
| description: | ||
| protein length (aa) | 392 | 306 |
| exons per gene | 2.95 | 2 |
| # of gene models | 16471 |
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.
