MGM Agenda

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.

JGIʼs future depends on new sequencing technologies and applications developed based on these technologies. With multiple sequencing platforms available, JGIʼs R&D team has been aimed to develop sequencing applications based on the strength provided by different platforms. Our areas of development lie in de novo whole genome shotgun sequencing, transcriptome sequencing, and metagenomic sample diversity study. Examples of JGIʼs available sequencing applications in genomic research will be discussed.

Genome assembly is the process of inferring the full DNA sequence of a microbial, viral, or eukaryotic chromosome, from many shorter pieces, known as reads.  While the reads produced by current sequencing technologies are getting longer, they still fall short of the full lengths of chromosomes, or even annotatable genomic features such as genes, operons, or biosynthetic gene clusters.  Computational methods for genome assembly are therefore a crucial part of genome sequencing and analysis.  I will give an overview of the theory and practice of genome assembly with applications to both short and long read data.

The Genomes Online Database (GOLD) is data management system that catalogs sequencing projects and their associated metadata from around the world. There are three different sources of projects in GOLD: internal projects from the Department of Energy Joint Genome Institute (DOE JGI) that are entered automatically, external projects entered by GOLD users and projects from public databases such as NCBI. GOLD serves as the entry point for projects submitted for analysis to the IMG data management system and ensures that projects are correctly defined along with their necessary metadata. This presentation will provide an overview of the commonly used GOLD terminologies,  a description of its four-level organization system and a tutorial on how to enter sequencing projects in GOLD.

Annotation of microbial genomes usually starts with finding the genes coding for stable RNAs (rRNA and tRNA) and protein-coding genes (CDSs). The principles underlying gene prediction in microbial genomes, as well as different implementations of these algorithms and most popular gene finding tools will be discussed.Genome analysis and gene function prediction depends on the comparison of sequences to the existing information stored in databases. They can either be simple repositories of nucleotide or protein sequence, or contain curated information related to the function of the genetic elements. Used in combination, bioinformatics databases constitute the most powerful method for gene function prediction. In this presentation, methods commonly used for functional annotation will be discussed.

     [Live Demo] – Rekha Seshadri

Microbial genome data analysis in IMG is set in the comparative context of multiple microbial genomes. IMG allows navigating the microbial genome data space along three key dimensions: genomes (organisms), functions (terms and pathways), and genes. In this section, ways in which users can interact with protein families, function assignments, and pathways in IMG will be presented.

The main differences between genomes and metagenomes in terms of data and analysis tools will be reviewed.

A snapshot of microbial community structure can be derived from analysis of metagenomic data. IMG/M methods and tools for establishing the taxonomic identity of community members will be presented along with tools for determining the fine population structure, genetic variation and genome dynamics of the dominant populations. Methods for assessing the diversity and abundance of microbial communities will be discussed.

Microorganisms exhibit complex metabolism and metabolic interactions with their environment, large parts of which remain unknown. Deficiencies in functional annotations of microbial genomes as well as incomplete knowledge of small molecule repertoires (metabolomes) of microorganisms limit the understanding of their metabolism. This talk will introduce mass spectrometry based metabolomics and approaches to link these to microbial genomics. This will include recent work connecting genes to the utilization of specific metabolites in bacteria by profiling metabolite utilization in libraries of mutant strains. Here, untargeted mass spectrometry-based metabolomics was used to identify metabolites utilized by soil microbes. Targeted high-throughput metabolite profiling of spent media of 8042 individual mutant strains was performed to link utilization to specific genes. Using this approach we identified genes of known function as well as those required for the metabolism of ‘novel’ metabolites.