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Evolution and diversification of duplicated genes in Laccaria bicolor

Evolution and diversification of duplicated genes in Laccaria bicolor. Dag Ahrén Microbial Ecology Lund University. Outline. Duplications in Laccaria bicolor GC content of the Laccaria genome Metabolic reconstruction of L. bicolor. Gene duplications. Evolution of duplications

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Evolution and diversification of duplicated genes in Laccaria bicolor

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  1. Evolution and diversification of duplicated genes in Laccaria bicolor Dag Ahrén Microbial Ecology Lund University

  2. Outline • Duplications in Laccaria bicolor • GC content of the Laccaria genome • Metabolic reconstruction of L. bicolor

  3. Gene duplications Evolution of duplications Nonfunctionalization Pseudogene Subfunctionalization Neofunctionalization

  4. Gene duplications Events leading to duplications Whole Genome Duplications (WGD) Segmental Duplications Tandem Duplications

  5. Laccaria Gene duplications Whole genome duplications: 0 (B. Canbäck) Segmental duplications: 39 segments (B. Canbäck) 117 gene duplications Tandem duplications: 953 gene duplications (F. Martin)

  6. Gene duplications Dn vs Ds Selection pressure Calculated through Dn/Ds ratio of gene duplications n=nonsynonymous substitutions s=synonymous substitutions Positive selection (Adaptation) Dn/Ds>1 Neutral selection (Relaxed) Dn/Ds=1 Negative selection (Purifying) Dn/Ds<1

  7. 10 pairs Dn/Ds>1 Recently duplicated Duplications that have gone to fixation Gene duplications Dn vs Ds Dn Tandem duplications Ds

  8. Gene duplications Dn vs Ds Dn Segmental duplications 6 pairs Dn/Ds>1 Ds

  9. Gene duplications Functional annotation of duplications with positive selection

  10. Gene duplications Duplications with positive selection

  11. Gene duplications Conclusions: • More than 1000 gene duplications have been evaluated. • 16 gene duplications are under positive selection • Mostly hypothetical proteins but with known domains. • WD40 Repeats common in genes under positive selection (5 pairs compared to 148 matches in the entire genome)

  12. GC Percent GC content Isochore: A region of genomic DNA sequence in which G+C compositions are relatively uniform. (Nature glossary) Gene density Recombination

  13. GC GC content in Laccaria Coprinus Phanerochaete Entire genome 47% 52% 57% All genes 50% 53% 59% Tandem duplications 50% - - Segmental duplications 51% - -

  14. Laccaria bicolor Coprinus cinereus Phanerochaete chrysosporium

  15. GC

  16. GC & GC3 in basidiomycetes B. Rajashekar

  17. Coprinus Ustilago Laccaria Phanerochaete ENC vs GC3 in basidiomycetes B. Rajashekar

  18. Length distribution Ustilago Coprinus Phanerochaete Laccaria B. Rajashekar

  19. GC Conclusions: • Laccaria has a low %GC compared to the other basidiomycete genomes • Laccaria has isochores with lower %GC content than the rest of the genome • %GC is correlated with gene density and conservation between organisms • Genes tend to have a higher %GC than average • Laccaria have larger fraction genes of length <1000 • No correlation between GC3 and ENC is found in Laccaria

  20. Laccaria metabolic map -Overview Compared with Coprinus metabolism

  21. Laccaria metabolic map Use of metabolic map of Laccaria Web Resource: • Comparative genomics against metabolism of other basidiomycete genomes • Custom pathways Add/Remove/Modify • Microarray data • Missing genes

  22. Laccaria metabolic map -Overview Compared with Coprinus metabolism

  23. Laccaria metabolic map -Pathway page

  24. Laccaria metabolic map -Gene page

  25. Laccaria metabolic map Laccaria bicolor

  26. Laccaria metabolic map

  27. Comparison with Cryptococcus neoformans • Differences in 85 pathways • 34 unique in C. neoformans • 51 unique in L. bicolor • Gained/Lost pathways • Variants of pathways • False positives/negatives • Needs to be checked manually! Ongoing

  28. Laccaria metabolic web page http://mycor.nancy.inra.fr/LaccariaGenome/

  29. Metabolic map -microarray analysis

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