15. Genomes and Genomics

Sequencing the Genome

Open Question
Repetitive DNA poses problems for genome sequencing.Why is this so?
Multiple Choice
Restriction enzymes are proteins responsible for what?
Multiple Choice
What is the name of a short sequenced DNA fragment?
Multiple Choice
The purpose of a sequence assembly is to what?
Multiple Choice
Which of the following sequence techniques requires the use of vectors?
Multiple Choice
Dideoxy nucleotides (ddNTPs) are used in Sanger sequencing because they have what function?
Open Question
You have discovered a new species of archaea from a hot spring in Yellowstone National Park.How would your strategy change if you were unable to grow the strain in culture?
Open Question
You have discovered a new species of archaea from a hot spring in Yellowstone National Park.After growing a pure culture of this organism, what strategy might you employ to sequence its genome?
Open Question
In this chapter, we focused on a number of interesting applications of genetic engineering, genomics, and biotechnology. 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?How can we correlate the genome with RNA expression data in a tissue or a single cell?
Open Question
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?

How do we know which contigs are part of the same chromosome?
Open Question
Repetitive DNA poses problems for genome sequencing.What strategies can be employed to overcome these problems?
Open Question
Repetitive DNA poses problems for genome sequencing.What types of repetitive DNA are most problematic?
Open Question
When the whole-genome shotgun sequence of the Drosophila genome was assembled, it comprised 134 scaffolds made up of 1636 contigs.How can physical gaps be closed?
Open Question
When the whole-genome shotgun sequence of the Drosophila genome was assembled, it comprised 134 scaffolds made up of 1636 contigs.What is the difference between physical and sequence gaps?
Open Question
When the whole-genome shotgun sequence of the Drosophila genome was assembled, it comprised 134 scaffolds made up of 1636 contigs.Why were there so many more contigs than scaffolds?