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Conserved gene order in Basidiomycetes
An investigation of synteny within and between:
Laccaria bicolorCoprinopsis cinerea
Phanerochaete chrysosporium
Björn Canbäck
Methods
BLAST: E-value: 1e-10
i-ADHoRe Gap size: 15 Cluster gap size: 20 Probability: 0.001 Gene pairs: 5
Internal duplications, gene view
Laccaria bicolor Phanerochaete chrysosporium
Coprinopsis cinereus0
5000
10000
15000
20000
25000
Gene modelsGenes in segmentsGene pairs
Example duplication in Laccaria bicolor
Scaffold 69 Scaffold 39
Best BLAST hit against UniProt
1. Hypothetical protein
2. Queuosine biosynthesis protein
3. Guanine nucleotide-binding protein
4. Hypothetical protein
5. Prolyl-tRNA synthetase
6. Copper radical oxidase
7. Predicted protein
8. Putative membrane glycoprotein
1. Predicted protein
2. Wsv360
3. Guanine nucleotide-binding protein
4. Hypothetical protein
5. Chromosome 14 wgs
6. Copper radical oxidase
7. Predicted protein
8. Putative membrane glycoprotein
Scaffold 69 Scaffold 39
Laccaria bicolor scaffold 17
Internal duplications, segment view
Duplicated segments Average genes / segement
Genes in largest segment0
10
20
30
40
50
60
Laccaria bicolorPhanerochaete chrysosporiumCoprinopsis cinerea
Note: Half of the duplicated segments are
in the same scaffold
Duplications between genomes
Laccaria vs. Phanerochaete
Laccaria vs. Coprinopsis
Phanerochaete vs. Coprinopsis
All three0
0.05
0.1
0.15
0.2
0.25
Fraction of genes in duplicated segments
Laccaria bicolorPhanerochaete chrysosporiumCoprinopsis cinereus
Duplications between genomes
Genes/segment Max. segmentLaccaria 16 111
Phanerochaete Phanerochaete 15 124
Genes/segment Max. segmentLaccaria 13 113
Coprinopsis Coprinopsis 14 124
Genes/segment Max. segmentPhanerochaete Phanerochaete 13 46
Coprinopsis 14 66
Laccaria vs.
Laccaria vs.
vs. Coprinopsis
Laccaria - Phanerochaete
Phanerochaetescaffold 11
Laccariascaffold 1
Laccaria - Coprinopsis
Coprinopsis25
Laccariascaffold 1
Phanerochaete - Coprinopsis
Coprinopsis23
Phanerochaetescaffold 11
All three genomes
Coprinopsis24
Laccariascaffold 1
Phanerochaetescaffold 11
Conclusions
Very limited amount of detectable duplications in Laccaria bicolor despite large genome size
Internal duplications should be traceable because it can be detected between basidiomycetes
Large amount of conserved duplications in the ancestor of the three basidiomycetes
This contrasts with reports from ascomycetes
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