Workshop Agenda

8:30 AM

Registration

Session I - Introduction to JGI

09:00 - 09:15

Welcome and Overview of the Workshop

Nikos Kyrpides

09:15 - 09:45

Introduction to the JGI

The powerful high-throughput DNA sequencing technologies catalyzed by the Human Genome Project, which have contributed to dramatic advances in biomedicine, are now being directed to characterizing the genomes of plants and microbes. Leading this effort is the US Department of Energy (DOE) Joint Genome Institute (JGI), a national user facility that unites the expertise of five national laboratories to advance genomics in support of the DOE mission areas of bioenergy, carbon cycling, and bioremediation.

Jim Bristow

09:45 - 10:15

New Sequencing Technologies

JGI’s future depends on new sequencing technologies.  Currently, we are under the process of evaluating, validating, and developing applications for three next-generation sequencing technologies, namely Roche’s GS FLX, Illumina’s Genome Analyzer, and AB’s SOLiD system.  Introduction to all three technologies will be given and advantages and disadvantages will be compared and discussed.  Examples of applications in genomic research for these new technologies will be presented. 

Feng Chen

10:15 - 10:45

Microbial Genome Assembly and Finishing

The US DOE Joint Genome Institute's mission is to provide the scientific community with high-quality finished genomes. Approximately 400 microbial genomes are currently in the JGI pipeline and to date, 166 have been completed. The value of a totally complete microbial genome was recognized and “appreciated” by scientists. Finished genomes allow, for example, the study of genome-level evolution, while the draft sequences are usually of sufficient quality to determine the basic genetic and metabolic parameters of an organism. Some interesting traits can be lost when only working from draft. Computational and lab approaches will be discussed

Alla Lapidus

10:45 - 11:00

Break

11:00 - 11:30

Single cell genomics

The bulk of finished microbial genomes to date are derived from bacteria and archaea that can be readily grown in culture. However, the vast majority of microorganisms on this planet elude current culturing attempts, severely limiting access to their genomes. While various enrichment methods as well as metagenomic approaches have been successfully applied to aid the genome analysis of such non-cultivable environmental microbes, these methodologies are not suitable for countless community members of interest. Single cell genomics is a new approach which aims to access the genome from an individual microbial cell. Single cells can be isolated from the community using optical tweezers, micromanipulators, flow-sorting, or serial dilutions. After cell lysis, the microbial genome is amplified using multiple displacement amplification (MDA), allowing random genome shotgun sequencing.  The advantages as well problems associated with the single cell genomics approach will be discussed.

Tanja Woyke

and

Jan-Fang Cheng

11:30 - 12:00

JGI Eukaryotic Microbial Annotation of Eukaryotic Genomes

Over 50 eukaryotic genomes from different taxonomic groups are annotated at JGI using JGI Annotation pipeline. The pipeline integrates several gene prediction, annotation, and analysis tools to annotate a diverse set of genomes in high-throughput but genome-specific manner. To address gene prediction challenges in eukaryotes that often display high repeat content, low gene density, and complex gene structure, we combine different gene predictors with available experimental data and comparative genomics analysis. JGI Eukaryotic Portal provides web-based tools for user communities to enable comprehensive genome analysis and manual curation of predicted genes and functions.

Igor Grigoriev

12:00 - 13:00

Lunch - JGI Facilities Tour

Session II - JGI Science Projects

13:00 - 13:30

Microbial Genomics

Since the release of the first completely sequenced microbial genome, more than decade ago, the genomics world has been changing rapidly as large amounts of microbial sequencing data have been accumulating at exponential rate. Microbial Genomics, fueled by recent advancements in sequencing technology, are now playing a central role in medicine and biotechnology and have greatly expanded our understanding of the available phylogenetic and metabolic complexity. Where are we going next? The past, present and future of microbial genomics will be discussed.

Nikos Kyrpides

13:30 - 14:00

Archaeal Genomics

Archaea is the least well characterized organisms of the three domains of life. Yet, they share many important features with eukaryotes and are the key in understanding the origins and nature of the last common ancestor. JGI has a strong interest in Archaea due to their broad biotechnological applications as well as their relevance in Energy production, and therefore a large number of archaeal sequencing projects are currently under way. The analysis of two Crenarchaeal genomes that have been completely sequenced will be presented. Examples will be shown of how unique genes and genes uniquely missing from these genomes can be identified and characterized.

Iain Anderson

14:00 - 14:30

Phylogenomics

Clarifying the relationships among bacterial lineages is important to provide a phylogenetic framework on which to trace the evolution of bacterial diversity. The large number of complete genomes now available from numerous bacterial lineages has greatly augmented the power of phylogenetic analyses. Large-scale protein alignments and other approaches are revealing the topology of many areas of the bacterial tree, although others still remain controversial. We’ll discuss how to use genomic information to investigate bacterial phylogeny, in spite of horizontal transfer and other phenomena that entangle phylogenetic reconstruction, and how the phylogenies obtained can advance our understanding of genome evolution in bacteria.

Pilar Francino

14:30-15.00

Break

15:00 - 15:30

Introduction to Metagenomics

Metagenomics, the application of high throughput sequencing to environmental samples is an emerging field that is rapidly advancing our understanding of how microbial communities function and evolve. This introductory talk with trace the roots of metagenomics, it's current practice and speculate on future developments in the field

Phil Hugenholtz

 15:30 - 16:00

Metagenomics of Hypersaline mats

The Guerrero Negro hypersaline microbial mat in Baja California is one of the most complex and diverse microbial communities yet described.. We have generated shotgun sequence of 10 successive layers of a ~6 cm thick mat core for comparative analysis. Millimeter-scale functional gradients were inferred from gene and pathway frequency distributions that often tracked with the physicochemical profile of the mat. The environment and the results of the metagenome analysis will be presented and discussed

Victor Kunin

16:00 - 16:30

Discovery of feedstock-targeted glycosyl hydrolases by Metatranscriptomics

Highly active and stable cellulolytic enzymes are major bottlenecks for the efficient large-scale production of biofuels from lignocellulose, Complex microbial habitats such as the bovine foregut are known to harbor fibrolytic microbes and represent promising sources of novel biocatalysts for lignocellulose degradation. We employed high-throughput pyrosequencing to identify feedstock-targeted enzymes within the transcriptome of bovine rumen microbial communities.

Matthias Hess

16:30 - 17:00

Pre-processing of metagenomic datasets

The rapid increase of metagenomic projects is leading to an exponential growth of the sequence data, which in turn creates new challenges related to efficient data storage and analysis. This problem is expected to become more prominent as new sequencing technologies are adopted and large scale sequencing projects are carried out (e.g. HMP, GOS). The Genome Biology Group at the DOE-JGI is developing methods to address these challenges in metagenomic projects, which allow efficient compression of the datasets and representation without loss of sequence, contextual and functional information. These methods include the metafolds and proxygene clusters for Sanger and 454 based metagenomic datasets respectively. In many occasions these approaches allow the extraction of information that was previously undetected such as genomic variations and relationships between members of a group.

Kostas Mavrommatis

OnLine Tools

IMG

IMG/M

IMG-ER

IMG-EDU

Artemis

VISTA

Greengenes

ARB

GOLD

BLAST

ClustalX

COGs

EBI

Eukaryotic Portal

InterPro

KEGG

NCBI/GenBank

Pfam

PIR

Sequencher