Ch. 16 - Genomics: Genetics from a Whole-Genome Perspective

Sanders - Genetic Analysis: An Integrated Approach 3rd Edition

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Sanders 3rd Edition

Ch. 16 - Genomics: Genetics from a Whole-Genome Perspective

Problem 12

Chapter 16, Problem 12

What is a reference genome? How can it be used to survey genetic variation within a species?

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A reference genome is a digital nucleic acid sequence database, assembled as a representative example of a species' set of genes.

It serves as a standard or baseline for comparing the genomes of different individuals within the same species.

To survey genetic variation, researchers align the DNA sequences of individuals to the reference genome to identify differences, such as single nucleotide polymorphisms (SNPs), insertions, deletions, and structural variations.

These variations can be cataloged and analyzed to understand genetic diversity, evolutionary relationships, and associations with traits or diseases.

The reference genome is continually updated and refined as new sequencing technologies and data become available, improving its accuracy and utility in genetic research.

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Key Concepts

Here are the essential concepts you must grasp in order to answer the question correctly.

Reference Genome

A reference genome is a digital DNA sequence that serves as a representative example of a species' genetic makeup. It is constructed from the DNA of one or more individuals and provides a baseline for comparison in genomic studies. Researchers use reference genomes to identify genes, regulatory elements, and variations that may exist within a population.

Genetic Variation

Genetic variation refers to the differences in DNA sequences among individuals within a species. This variation can manifest as single nucleotide polymorphisms (SNPs), insertions, deletions, or structural changes. Understanding genetic variation is crucial for studying evolution, disease susceptibility, and traits within populations.

Genomic Survey Techniques

Genomic survey techniques involve methods such as whole-genome sequencing, genotyping, and comparative genomics to analyze genetic variation. These techniques allow researchers to compare individual genomes against the reference genome, identifying variations that contribute to phenotypic diversity and adaptation within a species.

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Related Practice

Textbook Question

The human genome contains a large number of pseudogenes. How would you distinguish whether a particular sequence encodes a gene or a pseudogene? How do pseudogenes arise?

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Textbook Question

Based on the tree of life in the following figure (Figure 16.12), would you expect human proteins to be more similar to fungal proteins or to plant proteins? Would you expect plant proteins to be more similar to fungal proteins or to human proteins?

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Textbook Question

When comparing genes from two sequenced genomes, how does one determine whether two genes are orthologous? What pitfalls arise when one or both of the genomes are not sequenced?

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Textbook Question

The two-hybrid method facilitates the discovery of protein–protein interactions. How does this technique work? Can you think of reasons for obtaining a false-positive result, that is, where the proteins encoded by two clones interact in the two-hybrid system but do not interact in the organism in which they naturally occur? Can you think of reasons you might obtain a false-negative result, in which the two proteins interact in vivo but fail to interact in the two-hybrid system?

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Textbook Question

Go to http://blast.ncbi.nlm.nih.gov/Blast.cgi and follow the links to nucleotide BLAST. Type in the sequence below; it is broken up into codons to make it easier to copy.

5' ATG TTC GTC AAT CAG CAC CTT TGT GGT TCT CAC CTC GTT GAA GCTTTG TAC CTT GTT TGC GGT GAA CGT GGT TTC TTC TAC ACT CCT AAG ACT TAA 3'

As you will note on the BLAST page, there are several options for tailoring your query to obtain the most relevant information. Some are related to which sequences to search in the database. For example, the search can be limited taxonomically (e.g., restricted to mammals) or by the type of sequences in the database (e.g., cDNA or genomic). For our search, we will use the broadest database, the 'Nucleotide collection (nr/nt).' This is the nonredundant (nr) database of all nucleotide data (nt) in GenBank and can be selected in the 'Database' dialogue box. Other parameters can also be adjusted to make the search more or less sensitive to mismatches or gaps. For our purposes, we will use the default setting, which is automatically presented. Press 'BLAST' to search. What can you say about the DNA sequence?

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Textbook Question

In the course of the Drosophila melanogaster genome project, the following genomic DNA sequences were obtained. Try to assemble the sequences into a single contig.

5' TTCCAGAACCGGCGAATGAAGCTGAAGAAG 3'

5' GAGCGGCAGATCAAGATCTGGTTCCAGAAC 3'

5' TGATCTGCCGCTCCGTCAGGCATAGCGCGT 3'

5' GGAGAATCGAGATGGCGCACGCGCTATGCC 3'

5' CCATCTCGATTCTCCGTCTGCGGGTCAGAT 3'

Go to the URL provided in Problem 14, and using the sequence you have just assembled, perform a blastn search in the 'Nucleotide collection (nr/nt)' database. Does the search produce sequences similar to your assembled sequence, and if so, what are they? Can you tell if your sequence is transcribed, and if it represents protein-coding sequence? Perform a tblastx search, first choosing the 'Nucleotide collection (nr/nt)' database and then limiting the search to human sequences by typing Homo sapiens in the organism box. Are homologous sequences found in the human genome? Annotate the assembled sequence.

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