Info • Lobaria pulmonaria Switzerland extracted metagenome v1.0


[March 2018] Assembly v1 is a 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 and the JGI Annotation Pipeline v1.10. The metatranscriptome was extracted by aligning the reads with the extracted mycobiont genome. The aligned Illumina reads were assemblied with Trinity.

Summary statistics for the Lobaria pulmonaria Switzerland v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 54.93
Sequencing read coverage depth 146.8x
# of contigs 1817
# of scaffolds 1405
# of scaffolds >= 2Kbp 1405
Scaffold N50 233
Scaffold L50 (Mbp) 0.07
# of gaps 412
% of scaffold length in gaps 0.4%
Three largest Scaffolds (Mbp) 0.44, 0.41, 0.35

ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 1053158095 1043740439 99.1%
Other JGI_RNA_contigs 120650 105565 87.5%

Gene Models FilteredModels1
length (bp) of: average median
gene 1512 1286
transcript 1342 1107
exon 455 276
intron 90 60
protein length (aa) 391 302
exons per gene 2.95 2
# of gene models 16426


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.