Info • Rhodotorula graminis strain WP1 v1.1


v1.1 (September 2010):The Rhodotorula graminis strain WP1 genome sequence assembly v1.0 was built with the 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.Note that the v1.1 data is a reannotation of the v1.0 assembly, but using newly available EST data for gene modeling and annotation.

Summary statistics for the Rhodotorula graminis strain WP1 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp} 21.01
Sequencing read coverage depth 8.55x
# of contigs 323
# of scaffolds 26
# of scaffolds >= 2Kbp 25
Scaffold N50 7
Scaffold L50 (Mbp) 1.42
# of gaps 297
% of scaffold length in gaps 1.1%
Three largest Scaffolds (Mbp) 2.37, 1.72, 1.61
ESTs Data set # sequences total # mapped to genome % mapped to genome Notes
EstClusters EstClusters* 19126 6692 35.0% JGI cluster consensus sequences for the JGI 454 ESTs
Ests ESTs* 1880475 844124 44.9% 454 ESTs sequenced by JGI
*The Est data appear to contain contamination from a different species, possibly switchgrass; this is the likely cause of the low % mapping to the genome for this data
Gene Models FilteredModels2
length (bp) of: average median
gene 2126 1773
transcript 1585 1308
exon 254 155
intron 105 79
protein length (aa) 501 407
exons per gene 6.24 5
# of gene models 7283

Genome Reference(s)


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.