Symbiochloris reticulata Africa extracted metagenome v1.0

Status

[March 2018] Assembly v1 is a 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 Africa v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 58.57
Sequencing read coverage depth 100.1x
# of contigs 2634
# of scaffolds 2281
# of scaffolds >= 2Kbp 2281
Scaffold N50 379
Scaffold L50 (Mbp) 0.05
# of gaps 353
% of scaffold length in gaps 0.6%
Three largest Scaffolds (Mbp) 0.29, 0.23, 0.22


ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 34307668 33837642 98.6%
Other JGI_RNA_contigs 59943 55400 92.4%


Gene Models FilteredModels1
length (bp) of: average median
gene 2805 2198
transcript 1346 1152
exon 200 160
intron 256 243
description:
protein length (aa) 374 302
exons per gene 6.73 6
# of gene models 12720


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.