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Lowering Costs for Genome Assembly
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The time requirement and cost of sequencing genomes has decreased exponentially in recent years. The human genome project, in which the entire human genome was sequenced, took 13 years and three billion dollars. Now, an entire human genome can be sequenced within a few days. While human genome sequencing is viewed as a way to provide individualized medicine and screen individuals for susceptibility to certain genetic conditions, sequencing the genomes of other organisms is viewed as a way to gain information about different species. Genome sequencing is becoming an important tool in scientific research, to help identify species and find important DNA sequences and proteins. Genome sequencing helps researchers group together similar organisms to find both beneficial as well as detrimental properties of the organisms. Many organisms have had their genomes sequenced, including humans, monkeys, apes, plants, mice, and a myriad of bacteria, to name just a few. By sequencing the genomes of so many different organisms, researchers can determine evolutionary relationships between different species, important genes for pathogenesis in disease causing microbes, and proteins that can be utilized for human benefit from plants, fungi, and bacteria.

The Department of Energy Joint Genome Institute is interested in sequencing microbial genomes in order to determine which microbes might be useful for production of biological energy sources. They are studying microbes that could potentially have effects on carbon processing, energy production, and environmental concerns. In fact, the DOE Joint Genome Institute is currently involved with or funding approximately twenty percent of the whole genome sequencing studies that are underway around the world. The potential benefits of microbes for solving environmental issues are numerous, and could help researchers at the DOE Joint Genome Institute find methods to curb the production of greenhouse gases and other pollutants.

Whole genome sequencing usually is done using what is called the “shotgun method”, which involves sequencing many tiny, overlapping fragments of DNA, then putting the pieces together in the correct order. While the sequencing itself is relatively easy and straightforward, putting the segments back together can be more difficult. The small fragments are ordered by using overlaps that occur within the sequences, which is a very time consuming process. The current preferred method for genome sequencing is called the Sanger method. Using the Sanger method, nucleotide sequences of less than a thousand bases are sequenced and then ordered together. This requires the production of multiple libraries of the genome, in order to get sufficient overlap of the nucleotides to aid in restructuring.

Along with Pacific Biosciences and the University of Washington, the DOE Joint Genome Institute worked to develop a more efficient, fully automated system to help put the segments back together in the correct order. By making the process of restructuring the genome faster and more efficient, the cost of reconstructing genomes will also decrease rapidly.

The technique for genome assembly is called the hierarchical genome assembly process. The technique uses a single molecule, real time DNA sequencing system, which is a system developed by Pacific Biosciences. This allows the sequencing of long pieces of DNA, up to tens of thousands of nucleotides long. A single library of nucleotide sequences is produced, composed of these very large fragments of DNA. The longer stretches of nucleotides being sequenced and the reduction from multiple genomic libraries to only one library means that there are fewer nucleotide sequences to combine together, which makes the genome restructuring process faster.

To test the hierarchical genome assembly process technique, the genomes from three separate microbes were sequenced. All of these microbes had previously had their genomes sequenced by the DOE Joint Genome Institute using conventional methods. The sequences obtained using the hierarchical genome assembly process techniqure were then compared to previously obtained data. The sequences matched up, indicating that the hierarchical genome assembly process is accurate as well as fast. The next step that the researchers at Pacific Bioscienecs plan to take is expanding the ability of the hierarchical genome assembly process to help reconstruct and sequence genomes from larger, more complex organisms. Improvements in genome sequencing such as those provided by the hierarchical genome assembly process will help make whole genome sequencing an even more accessible and important tool for many areas of biological research.


References:

http://www.sciencedaily.com/releases/201...145933.htm
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