Coding gene evolution

From AAAWiki

Contents 1 Ka/Ks - Based Analyses 2 Codon Usage Analyses 3 Some possible areas to work on 4 People interested in Coding Gene analysis

Ka/Ks - Based Analyses

• Analysis at individual genes
• Branch-specific analysis
  • Melanogaster-group species (n = 6, dsim, dsec, dmel, dyak, dere, dana)
    • using consensus (6939) models that have 1:1 orthologs in all 6 species
  • All 12 Drosophila species (n = 12, dsim, dsec, dmel, dyak, dere, dana, dpse, dper, dwil, dmoj, dvir, dgri)
    • using consensus (4760) models that have 1:1 orthologs in all 12 species
• Analysis in different functional categories (based on GO)
  • Identification of categories with high and low constraints
  • Constraint differences across lineages.

Pre-consensus results and consensus datafiles: Ka/Ks analyses

Codon Usage Analyses

Codon Usage Across Ten Species of Drosophila from Saverio Vicario & Jeff Powell

Some possible areas to work on

• Alignments of protein-coding genes (at amino acid and CDS level)
• GO annotations for all genes
• Gene gains and losses in all lineages
  • Representation of different GO categories in gains and losses
  • Consider an approach to identify lineages with unexpected changes using a model of family evolution like Hahn et al.

One effort to identify species changes in GO categories is available at DroSpeGe: gene-GO-function-association. This uses fruitfly and three other proteomes, and indicates potentially interesting phylogenetic effects for genes in binding, catalytic activity, morphogenesis, cell cycle, transcription and others.

• which families are fast evolving?
• representation of GO categories in these families
• "Hidden class" models for amino acid evolution (e.g. sites that go from being slow-evolving to fast-evolving)
• Genes that are expected to be evolving very fast (also gene fusion/splitting events): immune response, olfaction, sex/courtship/behavior
• Can we bin Drosophila proteins (or regions of proteins) by evolutionary rate? Where do the well-studied examples fall? Can we use this info to identify new interesting genes?
• Relationship of coding divergence and their proximity to inversion breakpoints. D. pseudoobscura and D. persimilis have three fixed inversion differences, which will allow this issue to be addressed.
• Opportunities for detailed phylogeny
• Evidence for ancestral lineage sorting?
• Drosophila-specific stories

People interested in Coding Gene analysis

Julio Rozas and colleagues - Ka/Ks ratios across lineages and GO categories using paml and HyPhy.

Mohamed Noor and Stephen Schaeffer are interested in coding divergence versus inversion breakpoint position.

Andreas Heger and Chris Ponting - codon bias, ka/ks