TITLE:

Viral Dark Matter, and DNA Sequencing: identifying new functions and sequencing new genes at sea

DATE:

Friday, November 22nd, 2013

TIME:

3:30 PM

LOCATION:

GMCS 214

SPEAKER:

Dr. Robert Edwards. Department of Computer Science at San Diego State University

ABSTRACT:

Genomics and metagenomics have revolutionized our understanding of marine microbial ecology, and our view of the importance of microbes in global geochemical cycles. Sequencing DNA has become routine and straightforward. However, analyzing DNA sequences remains a challenge. Most of the DNA sequences in viral genomes are completely novel and unlike previously sequenced DNA. By combining high throughput methods with novel computational tools we have developed a pipeline to screen viral genes to identify new functions encoded by the proteins.

Even though sequencing is routine and straightforward, it still remains stuck in the laboratory confines, and DNA sequencing has always been an abstract extension of a research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we took a next generation DNA sequencer with us on board the ship, and successfully sequenced twenty two marine microbial genomes, and three marine microbial metagenomes using the Ion Torrent platform. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reefs of these islands and atolls, and to propose hypotheses and conduct experiments and further sampling based on the sequences generated.

By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.

HOST:

Dr. Jose Castillo

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