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Metagenomics Prof:Rui Alves Dept Ciencies Mediques Basiques, 1st Floor, Room 1.08 Website of the Course: Course:

Studying an organism …ACTG… >Dna MAACTG… >DNA Pol MTC… Stress Measure Response Find signatures for physiological dynamics in genomic data

Diversity of Life on Earth Described species: ~1.5 millions Predicted to exist: >30 millions Cultivate in the lab: ~thousands How do we know the genome of the species we can not cultivate? How can we know if the genes that are expressed in nature follow the same patterns as those in the lab?

Metagenomics Metagenomics (also Environmental Genomics, Ecogenomics or Community Genomics) is the study of genetic material recovered directly from environmental samples.

Sampling in Metagenomics Take a sample off of the environment Isolate and amplify DNA/mRNA Sequence it

Shotgun Sequencing Restriction Enzymes

Computer assembly ACT…GTC CTA …ATC … …GGGG How do we know which genes belong to which genome???? How do we assemble them???

The Best Case Scenario Coverage is enough to assemble independent genomes

What normally happens Coverage is not enough and assembly is fragmentary Worst Case Scenario: Some fragments can not be assigned

Down Side of Metagenomics Often fragmentary Often highly divergent Rarely any known activity No chromosomal placement No organism of origin Ab initio ORF predictions Huge data

Marine Metagenomics Microbes account for more than 90% of ocean biomass, mediate all biochemical cycles in the oceans and are responsible for 98% of primary production in the sea. Metagenomics is a breakthrough sequencing approach to examine the open-space microbial species without the need for isolation and lab cultivation of individual species.

PI Larry Smarr Paul Gilna Ex. Dir. PI Larry Smarr

Marine Genome Sequencing Project Measuring the Genetic Diversity of Ocean Microbes Sorcerer II Data from this area has already reach to 10% of GenBank. The Entire Data Will Double Number of Proteins in Embank !

Sample Metadata from GOS Site Metadata  Location (lat/long, water depth)  Site characterization (finite list of types plus “other”)  Site description (free text)  Country Sampling Metadata  Sample collection date/time  Sampling depth  Conditions at time of sampling (e.g., stormy, surface temperature)  Sample physical/chemical measurements (T (oC), S (ppt), chl a (mg m-3), etc)  “author” Experimental Parameters  Filter size  Insert size

Flat File Server Farm W E B PORTAL Traditional User Response Request Dedicated Compute Farm (1000 CPUs) TeraGrid: Cyberinfrastructure Backplane (scheduled activities, e.g. all by all comparison) (10000s of CPUs) Data- Base Farm 10 GigE Fabric Calit2’s Direct Access Core Architecture Will Create Next Generation Metagenomics Server Source: Phil Papadopoulos, SDSC, Calit2 + Web Services Sargasso Sea Data Sorcerer II Expedition (GOS) JGI Community Sequencing Project Moore Marine Microbial Project NASA Goddard Satellite Data Community Microbial Metagenomics Data Web (other service) Local Cluster Local Environment Direct Access Lambda Cnxns

Marine Metagenomics Who is there? Drug discovery Environmental survey Microbial genetic survey Microbial genomic survey Symbiosis Organism discovery Marine conservation Evolution study Bioenergy discovery Endosymbiosis Biogeochemistry mapping Metabolic pathway discovery