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Info • Heterobasidion annosum v2.0

Status

Assembly

v2.0 (June 2010) The assembly release version 2.0 is an Arachne assembly that was improved with finishing reads and gap closure. The v2.0 assembly is now in 15 scaffolds at least 10 of which represent nearly complete chromosomes. Roughly half of the genome is contained in 6 scaffolds all at least 2.6 Mb in length.

v1.0 (June 2009) The assembly release version 1.0 of whole shotgun reads was constructed with the Arachne assembler using paired end sequencing reads at a coverage of 8.23x.

Nuclear Genome Assembly v1.0 v2.0
Scaffold count 39 15
All Contig count 630 18
Scaffold sequence bases total 33.7 Mb 33.1 Mb
Scaffolded (Large) Contig sequence bases total 33.1 Mb 33.6 Mb
Estimated % sequence bases in gaps 1.9% 0.0%
Scaffold N50/L50 6/2.2 Mb 6/2.6 Mb
Contig N50/L50 82/127.0 Kb 6/2.3 Mb
Number of scaffolds > 50.0 Kb 18 14
% in scaffolds > 50.0 Kb 99.7% 100.0%

Annotation

v2.0 (June 2010) of the v2.0 assembly was produced by the JGI Annotation Pipeline, using a variety of homology-based and ab initio gene predictors. The v1.0 gene catalog along with its manual curations was mapped to the v2.0 assembly and included in filtering. After filtering for EST support, completeness and homology support, a total of 13,405 genes were structurally and functionally annotated.

v1.0 (June 2009) of the v1.0 assembly was produced by the JGI Annotation Pipeline, using a variety of homology-based and ab initio gene predictors. After filtering for homology support, a total of 12,270 genes were structurally and functionally annotated.

Nuclear Genome Annotation v1.0 v2.0
# gene models 12,270 13,405
Gene density 364.09 399.02
Avg.gene length 1618 nt 1601 nt
Avg. protein length 382 aa 379 aa
Avg. exon frequency 5.54 exons/gene 5.39 exons/gene
Avg. exon length 529 nt 561 nt
Avg. intron length 83 nt 82 nt
% complete gene models (with start and stop codons) 88% 86%
% genes with homology support 54% 70%
% genes with Pfam domains 34% 44%

Collaborators

Jan Stenlid Swedish University of Agricultural Sciences, Uppsala, Sweden

Genome Reference(s)

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.