Info • Melampsora larici-populina v2.0


[December 2015] The Melampsora larici-populina v2.0 genome was assembled using ARACHNE. Misassemblies were identified using a map provided by Uffe Helsten which was based on 85 offspring, and has map position information at 29,168 unique positions in the genome.  Scaffold breaks were identified using an abrupt change in the linkage group.  A total of 62 breaks were made. Scaffolds were then oriented, ordered, and joined together using the map and assembled into 18 chromosomes.  A total of 186 joins were made during this process.

Summary statistics for the Melampsora larici-populina v2.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 109.88
Sequencing read coverage depth 7.47x
# of contigs 4520
# of scaffolds 511
# of scaffolds >= 2Kbp 486
Scaffold N50 8
Scaffold L50 (Mbp) 5.82
# of gaps 4009
% of scaffold length in gaps 5.8%
Three largest Scaffolds (Mbp) 8.57, 8.00, 7.40

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters SangerESTclusters 11535 8470 73.4%
Ests est.fasta 522244426 491776833 94.2%
Other Trinity_assembled_transcripts 57498 33208 57.8%

Gene Models FilteredModels1
length (bp) of: average median
gene 1468 1156
transcript 1110 846
exon 254 153
intron 108 81
protein length (aa) 339 255
exons per gene 4.37 3
# of gene models 19550

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.