Concept explainers
You have discovered a new species of Archaea from a hot spring in Yellowstone National Park.
After growing a pure culture of this prokaryote, what strategy might you employ to sequence its genome?
How would your strategy change if you were unable to grow the strain in culture?
To analyze:
Considering a new species of Archaea from a hot spring in Yellowstone National Park, answer the following –
The strategy that might be employed to sequence its genome, after growing a pure culture of this prokaryote.
The change in strategy if the strain is unable to grow in culture.
Introduction:
In prokaryotes, genome consists of a single DNA molecule. These genomes are much longer than the genome lengths that can be sequenced using a traditional single dideoxy sequencing reaction. An efficient way of sequencing DNA molecule involves breaking the whole DNA into smaller fragments and sequencing the fragments in parallel.
Explanation of Solution
The DNA sequence of the newly discovered organism can be obtained using whole-genome shotgun (WGS) sequencing. WGS sequences genomic DNA by the shotgun method which does not require prior construction of a physical map. Therefore, WGS can be applied to any genome. The entire DNA of an organism can be sequenced using this approach. As it is possible to grow a pure culture of newly discovered archaea, the entire DNA (large quantity) can be obtained for sequencing (this is not possible for unculturable microorganisms). In WGS, DNA representing the entire genome is fragmented into smaller pieces and a large number of fragments are randomly chosen to sequence.
If it is assumed that the strain cannot be cultured, conventional WGS sequencing cannot be used for sequencing. Metagenomics studies the genetic sequences of groups of organisms whose member species is difficult to culture. In this approach, environmental samples where targeted organisms are present are collected and filtered. The genomes of organisms in the sample are isolated and are cloned into vectors. Sequencing of clones is performed randomly to reconstruct consensus sequence.
The newly discovered archaea can be sequenced using whole genome shotgun sequencing approach if it is cultivable. If the organism is assumed to not be cultivable, metagenomics approach can be used for sequencing the genome.
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