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Metagenomics

Prof:Rui Alvesralves@cmb.udl.es973702406Dept Ciencies Mediques Basiques,1st Floor, Room 1.08Website of the Course:http://web.udl.es/usuaris/pg193845/Courses/Bioinformatics_2007/ Course: http://10.100.14.36/Student_Server/

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 ProjectMeasuring 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 FileServerFarm

W E

B

PO

RT

AL

Traditional

User

Response

Request

DedicatedCompute Farm(1000 CPUs)

TeraGrid: Cyberinfrastructure Backplane(scheduled activities, e.g. all by all comparison)

(10000s of CPUs)

Data-BaseFarm

10 GigE Fabric

Calit2’s Direct Access Core Architecture Will Create Next Generation Metagenomics Server

Source: Phil Papadopoulos, SDSC, Calit2+

Web

Se

rvic

es

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

LocalEnvironment

DirectAccess LambdaCnxns

Marine Metagenomics

Who is there?

Drug discovery

Environmental surveyMicrobial genetic survey

Microbial genomic survey

Symbiosis

Organism discovery

Marine conservation

Evolution study

Bioenergy discovery

Endosymbiosis

Biogeochemistry mapping

Metabolic pathway discovery