The evolution of microbial symbionts and their biosynthetic pathways through shotgun metagenomics

Project ID
FG-403
Project Categories
Life Science
Completed
Abstract
Symbiotic relationships between bacteria and eukaryotes are prevalent in nature.  The most fundamental of these symbiotic events resulted in modern eukaryotic cells containing mitochondria and chloroplasts descended from ancient endosymbionts.  These organelles are the end-points of symbiont evolution - they have extremely reduced and degraded genomes, and many of their vital functions are controlled and orchestrated by the host.  Although snapshots of intermediate stages of this reductive evolutionary process have been obtained through genomics of various insect symbionts, our picture of symbiont evolution is still incomplete.  We will be investigating symbiont evolution by examining various symbiotic systems from the marine environment, where symbionts are often implicated in the production of chemical defenses for sessile or ortherwise vulnerable invertebrates.  Because these symbionts are unculturable, their genomes will be assembled from environmental DNA obtained directly from their hosts.  Future Grid resources will be used to assemble such shotgun metagenomic sequence data.  Because of the complexity of these samples (i.e. they contain genomic DNA from a large number of different species), large amounts of memory and CPU power are required for assembly.
Use of FutureSystems
We will use Future Grid to assemble large metagenomic DNA sequence datasets with Velvet (http://www.ebi.ac.uk/~zerbino/velvet/). We will also do ancillary tasks in refining genome assemblies, such as carrying out large-scale BLAST searches.
Scale of Use
Each assembly run will require a single node with a large amount of memory (~200 GB), and typically takes 3-8 hours. In the past I have done similar runs on delta and bravo in project 149. Large scale blast searches will use multiple nodes, but will require less memory.