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Chapter 21: Problem 4

Compare and contrast whole-genome shotgun sequencing to a map-based cloning approach.

Short Answer

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Question: Compare and contrast whole-genome shotgun sequencing and map-based cloning approach in terms of their steps, techniques, advantages, and drawbacks. Answer: Whole-genome shotgun sequencing involves randomly fragmenting DNA, sequencing the fragments, and computationally reassembling the sequences. It is faster and more accessible but may struggle with complex genomes or repetitive sequences. Map-based cloning approach requires constructing a chromosomal map and aligning sequenced fragments to it, making it more complex and time-consuming but providing better results for large and complex genomes.

Step by step solution

01

Define whole-genome shotgun sequencing

Whole-genome shotgun sequencing is an approach for sequencing entire genomes that involves randomly breaking up the DNA into smaller fragments and then sequencing these fragments. Once the individual pieces are sequenced, the raw DNA sequences are reassembled computationally to create an accurate representation of the original DNA molecule.
02

Define map-based cloning approach

Map-based cloning approach (also known as hierarchical or directed strategy) is another method of sequencing the genome. In this approach, the genome is first divided into larger fragments, which are then mapped to their specific chromosome locations. After mapping, each fragment is further subdivided and sequenced separately. The smaller sequences are then assembled into larger sequences, which are finally aligned to the chromosomal map to reconstruct the entire genome.
03

Compare the steps and techniques

In whole-genome shotgun sequencing, the entire genome is randomly fragmented, and the sequence is assembled without the need for any chromosomal mapping. In contrast, map-based cloning requires an initial chromosomal map, with the DNA fragments mapped to their respective locations before sequencing. This makes the map-based approach more complex and time-consuming, as it requires additional steps to create the map and align sequences.
04

Discuss the advantages of whole-genome shotgun sequencing

Whole-genome shotgun sequencing is faster, as it does not require chromosome mapping. It can also be applied to any organism, regardless of its genome size or complexity. This method is particularly useful for organisms with small and simple genomes or when the chromosome mapping information is not available or difficult to obtain.
05

Discuss the advantages of map-based cloning approach

The map-based cloning approach provides better results when dealing with large genomes, repetitive sequences, or complex regions of the genome. The chromosomal map allows researchers to focus on specific regions of interest and provides a framework for accurately aligning sequenced fragments. This approach reduces the chances of errors in the assembly process since it provides a reference for ordering the sequence fragments.
06

Compare the drawbacks

The main drawback of whole-genome shotgun sequencing is that it can struggle to accurately assemble repetitive sequences and complex regions, leading to errors in the final sequence assembly. On the other hand, map-based cloning can be more time-consuming and expensive due to the added steps of creating a chromosomal map and sequencing larger fragments. In conclusion, both whole-genome shotgun sequencing and map-based cloning have their merits and limitations. Whole-genome shotgun sequencing is faster and more accessible but may be less accurate for complex genomes. Map-based cloning requires more time and resources but can provide better results for large and complex genomes.

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Most popular questions from this chapter

Comparisons between human and chimpanzee genomes indicate that a gene that may function as a wild type or normal gene in one primate may function as a disease-causing gene in another (The Chimpanzee Sequence and Analysis Consortium, Nature, \(437: 69-87,2005\) ). For instance, the \(P P A R G\) locus (regulator of adipocyte differentiation) is associated with type 2 diabetes in humans but functions as a wild-type gene in chimps. What factors might cause this apparent contradiction? Would you consider such apparent contradictions to be rare or common? What impact might such findings have on the use of comparative genomics to identify and design therapies for disease-causing genes in humans?

What functional information about a genome can be determined through applications of chromatin immunoprecipitation (ChIP)?

In this chapter, we focused on the analysis of genomes, transcriptomes, and proteomes and considered important applications and findings from these endeavors. At the same time, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter, what answers would you propose to the following fundamental questions: (a) How do we know which contigs are part of the same chromosome? (b) How do we know if a genomic DNA sequence contains a protein-coding gene? (c) What evidence supports the concept that humans share substantial sequence similarities and gene functional similarities with model organisms? (d) How can proteomics identify differences between the number of protein- coding genes predicted for a genome and the number of proteins expressed by a genome? (e) What evidence indicates that gene families result from gene duplication events? (f) How have microarrays demonstrated that, although all cells of an organism have the same genome, some genes are expressed in almost all cells, whereas other genes show celland tissue-specific expression?

What is bioinformatics, and why is this discipline essential for studying genomes? Provide two examples of bioinformatics applications.

Systems biology models the complex networks of interacting genes, proteins, and other molecules that contribute to human genetic diseases, such as cancer, diabetes, and hypertension. These interactomes show the contribution of each piece towards the whole and where diseases overlap, and provide models for drug discovery and development. Describe some tions (Roy et al., 2008 ). In some cases, closely related homologs may engender completely different classes of proteins (enzymes). Consider the 3 D structure of two proteins with 60 percent homology with entirely different functions. Explain how different functions may evolve by discussing the position of the homologous amino acid track, its relation to nonhomologous tracks, and the role that chaperones (Chapter 14) may play in determining protein function. of the differences that might be seen in the interactomes of normal and cancerous cells taken from the same tissue, and explain how these differences could lead to drugs specifically targeted against cancer cells.
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