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Bacteriophage Gene Clustering and PhylogenyNicholas CelmsSan Diego State UniversityFunded in part byNSF 0827278 UBM Interdisciplinary Training in Biology and Mathematics.1

1GoalBuild a method for making taxonomic groupings of bacteriophages based on sets of protein-encoding genes (PEGs)

22Bacteriophages

3Viruses that infect bacteria~24-200 nm longHorizontal gene transferShort, highly-diverse genomesTypically have a head/capsid, tail, and a base plate

3GoalBuild a method for making taxonomic groupings of bacteriophages based on sets of protein-encoding genes (PEGs) Define clusters of protein-encoding genes that differentiate strains of bacteriophages into subdivisions called clansDefine super-groups of clans called componentsExamine components and clans for: phylogenyClassification of new strainsUse PEG clusters to:Improve functional annotationsDefine lifestyle indicatorsFind horizontally-transferred groups of genes4Build a method for making taxonomic groupings of bacteriophages based on sets of protein-encoding genes (PEGs) Define clusters of protein-encoding genes that differentiate strains of bacteriophages into subdivisions called clansDefine super-groups of clans called componentsExamine components and clans for: phylogenyClassification of new strainsUse PEG clusters to:Improve functional annotationsDefine lifestyle indicatorsFind horizontally-transferred groups of genes

4Clustering Strains5We cluster our strains into natural subdivisions

5Focusing on one clan66Image Cluster: PEG set associated with clan7Each clan has a signature PEG-Family setWe call it the clans module788Image Cluster vs. ClustersImage cluster: generic PEG set associated with a clanCluster: a phages specific set of PEG orthologs of the image cluster 991010Data120 phages, 8558 PEGsFiltered: 2512 contributive PEGs (appear in a cluster)335 clans (interrelated groupings of phages) forming 14 components111112Note that of our original 120 phages, 19 appear in zero clans! 12Results13Propensity of hypothetical and phage protein is certainly a standing problem in phage research. However, it is also one of the prime benefits of this process. When poorly annotated proteins are grouped with well-annotated proteins, we find strong suggestion for replacing the poor annotation, or experimentally validating doing so. 13FutureBroadening our analysis to all available phages~700 phages, ~55,000 PEGsPhage phylogenyExperimentally-validating suggested functional annotations14Annotation usagesNew ones

14Questions?151516TermDefinitionComponentGroup of clans. A strain cannot appear in more than one component.ClanGroup of interrelated strains. A strain can exist in multiple clansPEGProtein-encoding gene.PEG-FamilySet of highly-similar PEGs.Image ClusterGeneric PEG set associated with a clan.ClusterA phages equivalent set of PEGs to its clans image clusterBacteriophageVirus that infects bacteria.16