Info • Symbiochloris reticulata Scotland extracted metagenome v1.0


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
protein length (aa) 377 307
exons per gene 6.85 6
# of gene models 12315


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.