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