Status
Assembly v1 is a minimal draft assembly extracted from a lichen metagenome by aligning the reads with the reference photobiont genome. The aligned Illumina gDNAs were assembled with Velvet and then AllPathsLG. The mitochondrial and chloroplast assemblies are available on the Download page.
Annotation v1 is a draft annotation using an extracted metatranscriptome and the JGI Annotation Pipeline v1.10. The metatranscriptome was extracted by aligning the reads with the extracted photobiont genome. The aligned Illumina reads were assemblied with Trinity.
Summary statistics for the Symbiochloris reticulata
Scotland v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 59.36 |
| Sequencing read coverage depth | 98.9x |
| # of contigs | 2348 |
| # of scaffolds | 1970 |
| # of scaffolds >= 2Kbp | 1970 |
| Scaffold N50 | 334 |
| Scaffold L50 (Mbp) | 0.06 |
| # of gaps | 378 |
| % of scaffold length in gaps | 0.6% |
| Three largest Scaffolds (Mbp) | 0.28, 0.26, 0.26 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 4986566 | 4381578 | 87.9% |
| Other | JGI_RNA_contigs | 29815 | 28010 | 93.9% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 2812 | 2199 |
| transcript | 1298 | 1110 |
| exon | 189 | 156 |
| intron | 261 | 246 |
| description: | ||
| protein length (aa) | 377 | 307 |
| exons per gene | 6.85 | 6 |
| # of gene models | 12315 |
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.
