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?

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Answer 1

Textbook Question

Chapter 16, Problem 1P

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?

Expert Solution & Answer

Summary Introduction

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.

Conclusion

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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Answer 2

Textbook Question

Chapter 16, Problem 1P

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?

Expert Solution & Answer

Summary Introduction

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.

Conclusion

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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Answer 3

Textbook Question

Chapter 16, Problem 1P

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?

Expert Solution & Answer

Summary Introduction

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.

Conclusion

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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Answer 4

Textbook Question

Chapter 16, Problem 1P

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?

Expert Solution & Answer

Summary Introduction

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.

Conclusion

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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Answer 5

Textbook Question

Answer 6

Textbook Question

Answer 7

Expert Solution & Answer

Summary Introduction

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.

Conclusion

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.

Answer 8

Expert Solution & Answer

Summary Introduction

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.

Conclusion

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.

Answer 9

Expert Solution & Answer

Answer 10

Expert Solution & Answer

Answer 11

Summary Introduction

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.

Answer 12

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.

Answer 13

Conclusion

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.

Answer 14

Ch. 16 - You have discovered a new species of Archaea from...Ch. 16 - 16.2 Repetitive DNA poses problems for genome...Ch. 16 - 16.3 When the whole-genome shotgun sequence of the...Ch. 16 - How do cDNA sequences facilitate gene annotation?...Ch. 16 - 16.5 How do comparisons between genomes of related...Ch. 16 - 16.6 You are designing algorithms for the...Ch. 16 - 16.7 You have sequenced a region of the Bacillus...Ch. 16 - You have just obtained 100-kb of genomic sequence...Ch. 16 - 16.9 The human genome contains a large number of...Ch. 16 - Based on the tree of life in Figure 16.12, would...

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?

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