Textbook Question
You have just obtained 100 kb of genomic sequence from an as-yet-unsequenced mammalian genome. What are three methods you might use to identify potential genes in the 100 kb? What are the advantages and limitations of each method?
Ch. 16 - Genomics: Genetics from a Whole-Genome Perspective
Sanders3rd EditionGenetic Analysis: An Integrated ApproachISBN: 9780135564172
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Table of contents
- Ch. 1 - The Molecular Basis of Heredity, Variation, and Evolution64
- Ch. 2 - Transmission Genetics144
- Ch. 3 - Cell Division and Chromosome Heredity81
- Ch. 4 - Gene Interaction87
- Ch. 5 - Genetic Linkage and Mapping in Eukaryotes103
- Ch. 6 - Genetic Analysis and Mapping in Bacteria and Bacteriophages73
- Ch. 7 - DNA Structure and Replication71
- Ch. 8 - Molecular Biology of Transcription and RNA Processing79
- Ch. 9 - The Molecular Biology of Translation110
- Ch. 10 - Eukaryotic Chromosome Abnormalities and Molecular Organization100
- Ch. 11 - Gene Mutation, DNA Repair, and Homologous Recombination86
- Ch. 12 - Regulation of Gene Expression in Bacteria and Bacteriophage90
- Ch. 13 - Regulation of Gene Expression in Eukaryotes38
- Ch. 14 - Analysis of Gene Function via Forward Genetics and Reverse Genetics72
- Ch. 15 - Recombinant DNA Technology and Its Applications69
- Ch. 16 - Genomics: Genetics from a Whole-Genome Perspective49
- Ch. 17 - Organelle Inheritance and the Evolution of Organelle Genomes27
- Ch. 18 - Developmental Genetics43
- Ch. 19 - Genetic Analysis of Quantitative Traits66
- Ch. 20 - Population Genetics and Evolution at the Population, Species, and Molecular Levels105
Sanders3rd EditionGenetic Analysis: An Integrated ApproachISBN: 9780135564172Not the one you use?Change textbook
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Sanders 3rd EditionCh. 16 - Genomics: Genetics from a Whole-Genome PerspectiveProblem 11
Sanders 3rd EditionCh. 16 - Genomics: Genetics from a Whole-Genome PerspectiveProblem 11Chapter 16, Problem 11
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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Understand the concept of orthologous genes: Orthologous genes are genes in different species that evolved from a common ancestral gene through speciation. They typically retain similar functions across species.
Compare the sequences of the two genes: Use sequence alignment tools (e.g., BLAST) to compare the nucleotide or amino acid sequences of the genes. High sequence similarity is often indicative of orthology.
Analyze the phylogenetic relationship: Construct a phylogenetic tree using the sequences of the genes and their homologs from other species. Orthologous genes should cluster together based on their evolutionary history.
Consider synteny: Examine the genomic context of the genes (e.g., neighboring genes or conserved regions). Orthologous genes often reside in similar genomic locations across species.
Address pitfalls with incomplete genome sequencing: If one or both genomes are not fully sequenced, missing data can lead to incorrect identification of orthologs. Additionally, fragmented assemblies may obscure synteny or phylogenetic relationships, requiring careful interpretation and validation using additional data or methods.
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Key Concepts
Here are the essential concepts you must grasp in order to answer the question correctly.
Orthologous Genes
Orthologous genes are genes in different species that evolved from a common ancestral gene through speciation. They typically retain the same function across species, making them crucial for comparative genomics. Identifying orthologs helps in understanding evolutionary relationships and functional conservation.
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Mapping Genes
Genome Sequencing
Genome sequencing is the process of determining the complete DNA sequence of an organism's genome. Accurate sequencing is essential for identifying genes and their relationships. If one or both genomes are not sequenced, it can lead to incomplete data, making it difficult to accurately determine orthology.
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Pitfalls in Comparative Genomics
Pitfalls in comparative genomics include misidentifying orthologs due to incomplete or erroneous genome data. Factors such as gene duplication, horizontal gene transfer, and sequencing errors can complicate the analysis. These issues can lead to incorrect conclusions about evolutionary relationships and gene functions.
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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?
Textbook Question
What is a reference genome? How can it be used to survey genetic variation within a species?
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?
Textbook Question
Imagine yourself in the same position as Kristen Powers, faced with the decision of whether or not to undergo a genetic test that will discover if you have inherited Huntington disease. List five life decisions or choices that you think are likely to be affected by the results of the genetic test. Do you think you would make the same choice to test that Kristen made? Why or why not?