The Joint Genome Institute Production Genomics Facility (PGF) has produced over 2.75 billion bases of draft paired-end sequencing since January 1, 2001. Our sequencing methodologies incorporate two types of DNA template generation: inoculation/SPRI purification and Rolling Circle Amplification (RCA). In order to manage the flow of samples through these processes, a robust database tracking system was developed using ORACLE. Data input and reporting for the workflow has been produced using a combination of commercial database development software and in-house programs. These include ORACLE s WebDB and CGI Perl programming. By leveraging the rapid report and form development cycle using WebDB and augmenting this with the flexibility of in-house programming, we have efficiently deployed a critical laboratory information management system for our data tracking.

Here, we report the draft genome sequences of two Butyrivibrio-type strains isolated from rumen fluid. The genome sequence of Butyrivibrio hungatei DSM 14810 was 3.3 Mb with 3,093 predicted genes, while the Butyrivibrio fibrisolvens DSM 3071 genome sequence was 4.8 Mb with 4,132 predicted genes.

In this poster we will provide an overview of the Joint Genome Institute's Microbial Sequencing projects with an emphasis on recent efforts to improve data quality by performing various quality control operations during sequencing and prior to beginning finishing. Some of these methods have been applied tooled projects in an attempt to correct obvious data problems and, therefore, provide a minimum standard of quality satisfied by all projects. We will describe a rapid and automated protocol which removes low quality and likely contamination from our projects. Application of this protocol typically removes between 5 and 30 percent of the reads in a project without negatively affecting the number of major contigs in draft assemblies.

JGI Microbial process has undergone through major changes in the last year. The implementation of the new sequencing technologies, Roche 454 and Illumina, have been the key factor in migrating the microbial draft sequencing from the older Sanger pipeline to the new 454 and Illumina pipelines. This poster will present the current sequencing process for the microbial genomes at the PGF, Walnut Creek facility. Scope of Work for microbial projects will be discussed as well as the production workflow process steps from the DNA receipt to finishing. A brief summary of each process step will be provided as well as important statistics for the area. Scheduling will be addressed to show how the two separate pipelines are managed for project scheduling and synched in order to produce a complete dataset at the end. The poster will also provide information on the current number of microbes in process and the PMO forecast for the year.

Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.

Granulicella tundricola strain MP5ACTX9(T) is a novel species of the genus Granulicella in subdivision 1 Acidobacteria. G. tundricola is a predominant member of soil bacterial communities, active at low temperatures and nutrient limiting conditions in Arctic alpine tundra. The organism is a cold-adapted acidophile and a versatile heterotroph that hydrolyzes a suite of sugars and complex polysaccharides. Genome analysis revealed metabolic versatility with genes involved in metabolism and transport of carbohydrates, including gene modules encoding for the carbohydrate-active enzyme (CAZy) families for the breakdown, utilization and biosynthesis of diverse structural and storage polysaccharides such as plant based carbon polymers. The genome of G. tundricola strain MP5ACTX9(T) consists of 4,309,151 bp of a circular chromosome and five mega plasmids with a total genome content of 5,503,984 bp. The genome comprises 4,705 protein-coding genes and 52 RNA genes.

Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations. Both DSE possess an expanded number of carbohydrate active enzymes (CAZymes), including plant cell wall degrading enzymes (PCWDEs). Those were similar in three other DSE, and contributed a signal for the separation of root endophytes in principal component analyses of CAZymes, indicating shared genomic traits of DSE fungi. Number of secreted proteases and lipases, aquaporins, and genes linked to melanin synthesis were also relatively high in our fungi. In spite of certain similarities between our two DSE, we observed low levels of convergence in their gene family evolution. This suggests that, despite originating from the same habitat, these two fungi evolved along different evolutionary trajectories and display considerable functional differences within the endophytic lifestyle.

The Opitutaceae bacterium strain TAV5, a member of the phylum Verrucomicrobia, was isolated from the wood-feeding termite hindgut. We report here its complete genome sequence, which contains a chromosome and a plasmid of 7,317,842 bp and 99,831 bp, respectively. The genomic analysis reveals genes for methylotrophy, lignocellulose degradation, and ammonia and sulfate assimilation.