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Laccaria

Laccaria. Phanerochaete v2. Cryptococcus / Ustilago. Whiterot -> Laccaria 1e-10: 43702 hits representing 7258 proteins in Whiterot and 8153 in Laccaria . 50% coverage: 4275 hits representing 1863 proteins in Whiterot and 1992 proteins in Laccaria. Laccaria -> Whiterot

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Laccaria

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  1. Laccaria Phanerochaete v2 Cryptococcus / Ustilago

  2. Whiterot -> Laccaria 1e-10: 43702 hits representing 7258 proteins in Whiterot and 8153 in Laccaria. 50% coverage: 4275 hits representing 1863 proteins in Whiterot and 1992 proteins in Laccaria Laccaria -> Whiterot 1e-10: 44686 hits representing 7237 proteins in Whiterot and 8247 in Laccaria 50% coverage: 7911 hits representing 3548 proteins in Whiterot and 3794 om Laccaria Finding the homologues

  3. Average sequence lenghts (aa): • Laccaria: 375 (19202 proteins) • Whiterot v1: 282 (11776 proteins) • Whiterot v2: 455 (10048 proteins)

  4. i-ADHoRe thresholds • Gap size: 15 • Gene duplicate gap size: 7 • Probability cutoff: 0.001 • Q-value (linearity): 0.9 • Cluster gap size: 20

  5. Laccaria internal conserved gene order Scaffold 69: gene 65-81 Scaffold 69 end Scaffold 69: gene 12-39

  6. Laccaria, Scaffold 69, 81 genes

  7. No hit Ambigious Ribosomal Protein S10 Plasma membrane ATP-ase Hypothetical Pectinmethyl-esterase Laminarinase Hypothetical Hypothetical No hit No hit Ribosomal Protein S10 Plasma membrane ATP-ase Ambigious Pectinmethyl-esterase Laminarinase Hypothetical Hypothetical Gene segments, scaffold 16

  8. Laccaria internal conserved gene order Scaffold 69 Scaffold 45 Scaffold 69

  9. Laccaria internal conserved gene order Scaffold 5: gene 741-746 Scaffold 95: gene 12-16

  10. Only whiterot Only whiterot Hypothetical No hit Only whiterot Only whiterot Putative glucoamylase Hypothetical No hits Only whiterot Gene segments, scaffold 5 and 95 Scaffold 95 Scaffold 5

  11. Laccaria and Phanerochaete conserved gene order Laccaria Scaffold 1: gene 417-439 Phanerochaete Scaffold 25: gene 44-66

  12. GDP dissociation inhibitor Membrane protein Ubiquitin-conjugating Beta glucan synthesis Hypothetical GDP dissociation inhibitor Hypothetical Ubiquitin-conjugating Beta glucan synthesis Muscle segmentation homeobox?! Gene segments Laccaria, scaffold 1 Phanerochaete, scaffold 25

  13. Laccaria Laccaria and Phanerochaete conserved gene order Scaffold 2: gene 892-926 Phanerochaete Scaffold 3: gene 98-134

  14. Peroxisomal enoyl CoA Hypothetical Hypothetical Adaptor related Hypothetical Transcription initiation Hypothetical Hypothetical Peroxisomal enoyl CoA Transcription factor Hypothetical Adaptor related Hypothetical Transcription initiation Hypothetical Hypothetical Gene segments Laccaria, scaffold 2 Phanerochaete, scaffold 3

  15. Laccaria Laccaria and Phanerochaete conserved gene order Scaffold 1: gene 1102-1140 Phanerochaete Scaffold 11: gene 68-109

  16. Thiosulfat sulfurtransferase Hypothetical Zink finger Threonine aldolase Peroxisomal membrane Hypothetical Hypothetical Peroxisomal membrane DNA repair Thiosulfat sulfurtransferase Hypothetical Hypothetical Threonine aldolase Peroxisomal membrane Hypothetical Hypothetical Peroxisomal membrane Hypothetical Gene segments Laccaria, scaffold 1 Phanerochaete, scaffold 11 + Succinyl CoA ligase

  17. Tandem gene arrays

  18. Largest tandem gene repeats • Ankyrin, 13 genes • Ankyrin, 12 genes • No hit / weak hit, 11 genes • No hit / weak hit, 11 genes

  19. Ankyrin / WD / NACHT domain containing genes in tandem

  20. Conclusions • Low gene order conservation between Laccaria and other basidiomycetes • Low gene order conservation within basidiomycetes • Many genes are not annotated • Large fraction of tandem repeat genes • Improvement of assembly may change the result

  21. ”Bacterial endosymbiont” • Either a β- or γ-proteo bacterium (no rRNAs) Burkholderia?? • But also a Lambda-likevirus (Siphoviridae) • In total 10538 reads • 927 reads have homology (1e-10) against Uniprot

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