JGI S. moellendorffii v1.0 Info

Status

v1.0 (December 20, 2007): The Selaginella moellendorffii genome sequence assembly v1.0 was built with Arachne assembler from whole genome shotgun and paired end sequencing reads. The nuclear genome sequence from this draft assembly was annotated using the JGI Genome Annotation Pipeline and custom analyses.

Summary statistics for the S. moellendorffii v1.0 release:

Nuclear Genome Assembly¹	v1.0
Nuclear genome size (Mbp)	212.5
Sequencing read coverage depth	7.0x
Reported # of contigs	5,156
# of nuclear scaffolds	759
# of nuclear scaffolds >2 Kbp	726
Nuclear scaffold N/L50	38/1.7 Mbp
Three largest Scaffolds (Mbp)	7.0 6.2 4.5

[1] While the estimated genome size is 110Mb, we sequenced two divergent haplotypes of Selaginella so this assembly represents 212 Mb of genomic sequence. The statistics above include only nuclear scaffolds1kb or longer.

Gene Models²	v1.0 all scaffolds²	v1.0 non-redundant³
length (bp) of:	average	average
gene	1711.37	1701.63
transcript	1229.57	1193.81
exon	213.66	213.44
intron	103.33	112.56
description:
protein length (aa)	392.04	381.85
exons per gene	5.75	5.59
# of gene models	34,292	22,285

[2] FilteredModels2 gene model track
[3] FilteredModels3 gene model track

ESTs	Data set	# sequences total	# mapped to genome	# not mapped to genome	% mapped to genome
EST clusters	EstClusters_556_S_moellendorffii_Jgi20060227	19,871	17,514	2,357	88%
ESTs	Ests_naEstSelaginella_moellendorffiiAll20060227	93,812	89,049	4,763	95%

Collaborators

Links

The Selaginella community site

Funding

This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396.