Christian Gauthier to speak

Christian Gauthier - Hatfull Lab

Pham assembly with MMseqs2 enables rapid, sensitive exploration of diverse sequence space: new insights into phage diversity and evolution

Friday, March 19, 2021

12:10 PM

Virtual Zoom seminar

Abstract: 

Bacteriophages (phages) are viruses that infect bacteria.  They are the most numerous biological entities we know of, with a global population estimated around 1031.  The extent of phage diversity, scale of phage evolutionary time and the prominent role horizontal gene transfer has played in that evolution mean that protein sequence similarity is our most robust means of identifying relationships between phages.  Assortment of phage gene products into “phamilies” (phams) of putative homologs is thus a routine task in the Hatfull Lab, where the quality of the resultant phams is vital to our success in 1) properly cataloging phage genetic diversity, 2) examining the spread of genes throughout the population, and 3) identifying novel aspects of phage biology to probe experimentally.  Known false positives and the deprecation (and slow runtimes) of earlier tools used for pham assembly, have prompted the development of a new pham assembly pipeline with MMseqs2 at its core. 

The new pipeline is remarkably quick, quite sensitive, and appears to construct functionally congruent phams (where functions are known).  Thus far, we’ve used the new pham data to identify previously unknown “superclusters” of distantly related groups of Actinobacteriophages.  We’re in the process of studying diverse serine integrase phams, with the goal of ultimately creating a library of integration-proficient plasmids that can be combined in the same genome - presently only a handful of these plasmids exist, and many are mutually exclusive.  We are also in the process of using a subset of mycobacteriophage phams to create a new bioinformatic tool for quickly and accurately identifying prophages (phage genomes integrated into host chromosome) in the genomes of sequenced Mycobacteria.  Future plans include a search for novel phage-encoded toxin-antitoxin systems and mobile genetic elements, and exploring relationships between the Actinobacteriophages and phages infecting hosts from other phyla.

Date

19 Mar 2021

News or Events

Events
Graduate Student Presentations