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Chapter 20: Problem 27

The presence \((+)\) or absence \((-)\) of six sequences in each of five bacterial artificial chromosome (BAC) clones (A-E) is indicated in the following table. Using these markers, put the BAC clones in their correct order, and indicate the locations of the numbered sequences within them. $$ \begin{array}{ccccccc}&&&\text{Sequences} \\ \hline \text { BAC clone } & \mathbf{1} & \mathbf{2} & \mathbf{3} & \mathbf{4} & \mathbf{5} & \mathbf{6} \\ \hline \text { A } & \+ & \- & \- & \- & \+ & \- \\ \hline \text { B } & \- & \- & \- & \+ & \- & \+ \\ \hline \text { C } & \- & \+ & \+ & \- & \- & \- \\ \hline \text { D } & \- & \- & \+ & \- & \+ & \- \\ \hline \text { E } & \+ & \- & \- & \+ & \- & - \end{array} $$

Short Answer

Expert verified
The BAC clones are ordered as: E, B, D, C, A, based on overlapping sequences.

Step by step solution

01

Understand the Problem

We need to arrange BAC clones in a sequence based on the presence "+" or absence "-" of certain sequences. The sequences in each BAC clone tell us about their overlaps, which help us determine their order and coverage.
02

Identify Overlapping Markers

Look for overlapping markers in the BAC clones. For example, Sequence 3 in Clone C and D overlaps, sequence 4 overlaps in Clone B and E, and so on. Notice where sequences are shared across BAC clones and use this to infer adjacency.
03

Determine the First BAC Clone

Clone E has sequences 1 and 4, which overlaps with Clone A and B, indicating it is likely at the start because it introduces Sequence 1 which isn't shown by any other BAC to the right.
04

Order Subsequent BAC Clones

Order the BAC clones to connect overlapping sequences. After E (1,4), Clone B connects with Sequence 4 (4,6). Clone D follows since it shares Sequence 5 with A. C is next due to sharing Sequence 3 with D, connecting finally to A due to Sequence 5.
05

Validate the Order

Cross-verify the order with all possible combinations and align sequences to validate: **E-B-D-C-A** forms a consistent order using overlaps: E (1, 4), B (4, 6), D (5), C (2, 3), A (1, 5), indicating a consistent sequence.

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Key Concepts

These are the key concepts you need to understand to accurately answer the question.

Genetic Sequencing
Genetic sequencing is a fundamental process in the field of genetics that involves determining the order of nucleotides in DNA or RNA. This sequence carries the genetic information needed for the organism's development and functioning.
Sequencing has become an essential tool for researching genetic variation, mapping genomes, and studying biological systems.

Modern sequencing technologies allow for rapid and cost-effective sequence determination, aiding significantly in biomedical research.
  • Sanger Sequencing: This is one of the oldest and most reliable methods for sequencing, which utilizes selective incorporation of chain-terminating dideoxynucleotides.
  • Next-Generation Sequencing (NGS): A more recent advancement, NGS allows for massive parallel sequencing, enabling researchers to sequence thousands to millions of molecules simultaneously.
In the context of BAC clone mapping, genetic sequencing enables the identification of a specific order of sequences across different BAC clones.
This plays a crucial role in determining the overlap and the arrangement of these clones, facilitating the mapping of entire genomes.
Molecular Markers
Molecular markers are sequences of DNA that are used as reference points for genetic mapping. They help in the identification of specific sequences or the determination of genetic diversity within a population.
Molecular markers are indispensable in the study of heredity and genetic variability.
  • Benefits of Molecular Markers:
    • *Non-invasive and highly specific* - they target the specific regions in genomes with great accuracy.
    • *Highly reproducible* - provide consistent results across different experiments.
In the BAC clone mapping exercise, the presence "+" or absence "-" of molecular markers helps determine the overlaps between clones.
These overlaps are used to elucidate the sequence of BAC clones accurately, providing a roadmap for genomic arrangements.
Bacterial Artificial Chromosome
A Bacterial Artificial Chromosome (BAC) is a large DNA construct used for transforming and cloning in bacteria鈥攕pecifically, E. coli. It is considered one of the key tools in genomic research.
  • Function:
    • BACs are employed to clone large fragments of DNA (up to 350,000 base pairs), making them ideal for constructing complex genomes.
    • They replicate like bacterial chromosomes and are stable within their host.
BACs play a crucial role in genome projects, as they allow scientists to piece together the entire genome by mapping these large DNA sequences.
In terms of BAC clone mapping, BACs help to identify how various sequences are laid out in relation to each other, often utilized together with molecular markers and genetic sequencing.
This way, they assist in determining the correct order and position of genetic sequences within a genome.

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Most popular questions from this chapter

What is genomics, and how does structural genomics differ from functional genomics? What is comparative genomics?

Genome size varies considerably among multicellular organisms. Is this variation closely related to the number of genes and the complexity of the organism? If not, what accounts for some of this variation?

A linear piece of DNA that is \(14 \mathrm{~kb}\) long is cut first by EcoRI alone, then by SmaI alone, and finally by both EcoRI and SmaI together. The following results are obtained: $$ \begin{array}{lll} \text { Digestion by } & \text { Digestion by } & \text { Digestion by both EcoRI } \\ \text { EcoRI alone } & \text { Smal alone } & \text { and Smal } \\ \text { 3-kb fragment } & 7-\mathrm{kb} \text { fragment } & 2-\mathrm{kb} \text { fragment }\\\ \text { 5-kb fragment } & \text{7-kb fragment }& \text{3-kb fragment}\\\ \text{6-kb fragment}&& \text{4-kb fragment}\\\ && \text{5-kb fragment} \end{array} $$ Draw a map of the EcoRI and SmaI restriction sites on this \(14-\mathrm{kb}\) piece of DNA, indicating the relative positions of the restriction sites and the distances between them.

Ribosomal RNAs are the most abundant RNAs in the cell. In experiments looking at levels of gene expression in different cell types, rRNAs are generally removed before carrying out RNA sequencing. Why might this be a useful step in these experiments? Why are researchers often less interested in rRNA than in other types of RNA?

What is linkage disequilibrium? How does it result in haplotypes?
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