(05) Comparative Genomics

Question 1

What do comparative genetics and genomics examine?

Answer 1

• the similarities and differences in genome structure and function among species

Question 2

(Comparative Physical Mapping)

1. What is comparative physical mapping useful for?
2. In some species it is still difficult to distinguish certain chromosomes by ______ alone.
3. Chromosomes can be defined by their genetic content using what?

Answer 2

1. obtaining low resolution genome info for species which have less well-developed genome maps
2. banding patterns
3. FISH

Question 3

(Comparing Genome Structure)

1. How do you utilize the human genome for mapping an animals?
2. What type of mapping is this?
3. Look at figure - notice that some highly conserved/some highly rearranged - also notice how they are numbered - more rearrangements in cats
4. What is unique about cattle karyotype?

Answer 3

1. taking the whole chromosome from one species - then figuring out where it is in another species using the FISH technique

(Whole chromosome segments of one species can be used as hybridization/paint probes to locate the equivalent region on another species’ chromosome(s))

2. physical
3. all acrocentric except for sex chromosomes

Question 4

Answer 4

Question 5

What is special about the indian muntjak?

What has X fused to?

How does this explain the 6,7 thing?

Answer 5

• smallest amount of chromosomes of any mamal described (Females 6, males 7)
• chromosome 3
• because it has fused to X, males still need two of them around (but one doesn’t have the X and is called Y2) - so 1 Y extra makes 7 (males are XYY)

Question 6

(Comparing Genome Structure)

1. Zoo-FISH can define upwards of ____ conserved genomic segments between any two mammalian genomes
2. Large chromosomal segments have rearranged during speciation to form the current chromosomes of a given species. What 3 processes caused this to occur?
3. Genes close together on a chromosome of one species are typcially what on another species? Even when comparing what?

Answer 6

1. 50
2. translocation, fusion, inversion
3. also close together; highly divergent species

Question 7

(Comparative Genetic Mapping)

1. Are genetic maps using shared what?
2. What does this allow us to compare?
3. Is genetic mapping used all that much anymore? why not?

Answer 7

1. genetic markers
2. closely related species
3. not so much - genome sequencing is better - the ultimate genetic mapping technique in a sense

Question 8

1. How is using mapped clones better and worse than whole genome shotgun technique?
2. What is the general description of whole genome sequencing?

(look at this picture - it is on your ipad)

Answer 8

1. It is more thorough - but also much slower
2. Chopping up the genome into a million segments - shoving it through a computer - and letting the computer figure out how it all fits together

Question 9

1. Which chromosome in mammals has been “locked in” (not changed very much)?
2. Similarity in gene content across species at all levels of all resolution is what level?

Answer 9

1. the x chromosome (also 22)
2. extremely high similarity

Question 10

1. Is there conversion even at extreme evolutionary distances and in highly variable regions of the genome?
2. What is an example of this?

Answer 10

1. yes
2. Comparison of the Human MHC to that of the frog genome

Question 11

(Comparative Sequence Analysis)

1. Ordering of the same sets of genes in different species no their respective chromosomes by assembled sequences (and FISH) confirms what? What may still yield surprises?
2. The strucutre of all domestic animal genomes are now essentially referable to each other
3. If you know in which fhromosomal segment a gene for a trait of interest lies - what can be predicted - and what can you obtain?

Answer 11

1. the conservation of large chromosomal segments; the fine scale order of genes (with many small genomic rearrangements)
2. -
3. can predict the position on a chromosome; candidate genes for the trait can be obtained

Question 12

(Protein-encoding DNA sequences)

1. Basically mRNA can now be read in the same way that DNA is
2. Comparing the sequenced mRNA to the genomic DNA sequence allows for what?
3. Coding DNA sequences and the intron-exon boundaries from one species are very often at the same or different spot within the sequence of another species. They can be predicted from what?

Answer 12

2. identification of the intron-exon boundaries
3. the same; the whole genome sequence

Question 13

(Comparative Sequence Analysis)

1. Statistical comparison of cDNA and genomic DNA sequences across species is ongoing
2. How high can the nucleotide sequence conservation of the cDNA sequences between species be?
3. What is cDNA anyway?

Answer 13

2. quite high (> 90%)
3. In genetics, complementary DNA (cDNA) is DNA synthesized from a messenger RNA (mRNA) template

Question 14

(Emerging Comparative ANalyses)

1. Several genes that at one time coded for proteins in a species are present in other species, but are no longer what? What are some others?
2. Relatively small sequence differences in developmentally-regulated genes may lead to what?

Answer 14

1. no longer functional, others are absent

(RIG-1 (Retinoic acid-inducible gene 1 protein) is a pattern recognition receptor for RNA viruses. This gene is absent in the genome of domestic poultry, but present in the duck. One reason why the duck is a reservoir species for avian influenza.)

2. may lead to functional differences in proteins between closely related species