Moore Notes 10 27 09

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Group Call

  • JE is making an offer to Guillaume
  • Simulation discussion: schedule a skype call for this topic early next week, especially who is going to do what
  • Annual Meeting
    • Sessions can take different format
    • Feedback and planning, not just progress updates
    • Each postdoc should plan to lead a ~2 hour session
  • Progress report updates
    • Dongying:
      • GEBA Nature paper
        • tree-based selection of genomes for sequencing (100 initial genomes)
        • linear curve for new proteins - many more out there
        • greengenes db is "only the tip of the iceberg"
        • used protein-family identification pipeline (developed for iSEEM)
      • 63 Actinobacterial genomes (18 new from GEBA) as a test of ability to identify universal marker genes for a specific clade
        • 136 candidate markers for this clade
        • MCL clustering: all vs. all blast scores as distances
        • candidate markers: score each cluster (i.e. family) for evenness, universality (using HMM profile to search), phylogenetic informativeness (does taxa tree match gene tree?)
        • greedy (single-linkage) clustering algorithm to add a few more families
        • checked if actually one single copy per genome: most, but not all are
      • Discussion
        • JG: impact of phylogenetic breadth on studies of diversity, e.g. in plant studies
        • JE: could use it for a particular data set to extend the taxonomy (e.g. 16S tree)
        • next steps: apply to metagenomic data
        • TS: Don't yet know if these markers occur outside Actinobacteria, JE: idea is to score marker sets for informativeness in different clades (and not use them for clades where we don't expect them to work)
        • JG: How much Actinobacteria in GOS? JE: not a large fraction in most samples (different from Shewanella contamination issue)
        • JE: may help us look at the rare taxa, SK: yes, this will be helpful if we can normalize for different numbers of sequences
    • Steve: [has given updates on many previous calls, quick update/summary]
      • AMPHORA and RAxML to build phylogenetic tree for HOT/ALOHA depth series data
      • Measure diversity using phylogenetic diversity measure
        • taxanomic diversity does not vary with depth
        • PD does vary with depth (most diversity at intermediate depths)
        • also looked at beta-diversity with UNIFRAC (similar results)
        • results are quite robust (e.g. if use different bootstrap trees)
      • Future work ideas
        • See if Actinobacteria marker genes show a similar pattern
        • See if extended AMPHORA marker gene sets show a similar pattern
        • TS: are there more photosynthetic organisms in the shallow samples?, SK: yes, especially Prochlorococcus, TS: could check if photosynthetic proteins (rather than taxa) show a similar pattern