Status
Assembly v1 (January 2016) is a standard draft assembly, using Pacbio and Illumina gDNAs assembled with Falcon, improved with finisherSC, and polished with quiver.
Suillua pictus EM44 is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. 716 of the 1400 scaffolds are very similar to larger scaffolds and are predicted to constitute an alternate or secondary haplotype. To represent these primary and secondary haplotypes in the Portal, we have created 'primary alleles' and 'secondary alleles' gene model tracks, comprising the models found on each haplotype. The goal of the GeneCatalog (GC) is to produce a non-redundant set of models which captures the full functional repertiore of the genome, and so the few secondary alleles that are unique were included in the GC, while all others were not.
Genome Assembly | |
Genome Assembly size (Mbp) | 87.09 |
Sequencing read coverage depth | 73.85x |
# of contigs | 1400 |
# of scaffolds | 1400 |
# of scaffolds >= 2Kbp | 1395 |
Scaffold N50 | 186 |
Scaffold L50 (Mbp) | 0.13 |
# of gaps | 0 |
% of scaffold length in gaps | 0.0% |
Three largest Scaffolds (Mbp) | 0.77, 0.75, 0.71 |
ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
EstClusters | ESTclusters | 67526 | 43614 | 64.6% |
Ests | est.fasta | 193436861 | 188087975 | 97.2% |
Gene Models | FilteredModels2 | |
length (bp) of: | average | median |
gene | 1481 | 1196 |
transcript | 1187 | 939 |
exon | 214 | 139 |
intron | 67 | 55 |
description: | ||
protein length (aa) | 342 | 261 |
exons per gene | 5.54 | 4 |
# of gene models | 19349 |
Collaborators
Genome Reference(s)
Lofgren LA, Nguyen NH, Vilgalys R, Ruytinx J, Liao HL, Branco S, Kuo A, LaButti K, Lipzen A, Andreopoulos W, Pangilinan J, Riley R, Hundley H, Na H, Barry K, Grigoriev IV, Stajich JE, Kennedy PG
Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi.
New Phytol. 2021 Apr;230(2):774-792. doi: 10.1111/nph.17160