L19 Gene Mapping

Question 1

Shotgun sequencing

Answer 1

does not define a genome, requires assembly and annotation

Question 2

Genome sequence

Answer 2

does not provide all the information

- chromatin information, epigenetic states are important too

Question 3

Single reference genome does not represent the whole species

Answer 3

variation via:

1. mutation
2. migration
3. selection
4. drift

Question 4

Genetic markers used as landmarks

Answer 4

• to assess genetic diversity

- to gain positional information about genetic basis of traits

Question 5

Genetic markers predate genome information

Answer 5

first genetic markers: phenotypic markers in drosophila e.g. eye colour

first molecular markers: isozymes

molecular markers often require combining technologies

Question 6

Genome information

Answer 6

highly valuable at defining a species and gaining information on the structures and function of the organism

Question 7

Sequencing a genome

Answer 7

see onenote

• Shotgun sequencing e.g. Illumina

Fragments:

• single reads
• paired-end reads
• mate-pair libraries

Question 8

Assembling a genome

Answer 8

see onenote

1. build contigs based on sequence overlap represented in a de Bruijin graph
2. scaffold contigs using large inserts/long read technology

Question 9

Integrating scaffolds into maps

Answer 9

Physical maps = BAC
Genetic maps = linkage maps

Genetic and physical mapsillustrate the arrangement ofgenes andDNA markers on a chromosome. The relative distances between positions on agenetic mapare calculated using recombination frequencies, whereas aphysical mapis based on the actual number of nucleotide pairs between loci.

Question 10

Annotating a genome

Answer 10

see onenote

1. gene prediction models
2. expression data
3. homologous protein identification
4. final model combining multiple sources of evidence

confronting obtained annotation gene set against a biological expectation

Question 11

Coupling chemical or enzymatic treatment with sequencing

Answer 11

1. bisulfite conversion
2. chromatin immuno-precipitation
3. assay for transposase accessible chromatin
4. high throughput chromosome conformation capture

Question 12

Coupling chemical or enzymatic treatment with sequencing

Answer 12

1. bisulfite conversion
2. chromatin immuno-precipitation
3. assay for transposase accessible chromatin
4. high throughput chromosome conformation capture

Question 13

Genetic markers for population genetics

Answer 13

• simpler genetic landmarks used as a proxy for more complex and less accessible causal source of variation
• explicitly relies on linkage disequilibrium

Question 14

A good marker is

Answer 14

• polymorphic and abundant
• unambiguous/repeatable
• neutral (not causal) + co-dominant

Question 15

SNP as the reference marker

Answer 15

• most abundant
• easy to genotype either using microarray or direct sequence
• neutral?

Question 16

Coverage: depth vs breadth

Answer 16

coverage = completeness
depth = accuracy 

genome sizes and complexities for non-model species often limit whole-genome sequencing approaches, forcing the use of reduced representation, targeted or not

Question 17

Absence of prior knowledge

Answer 17

For population level information: use of restriction-assisted DNA sequencing

• increase depth of coverage for a set of neutral markers
• accurate estimate of frequencies
• random coverage of genome (no linkage with specific loci)

Question 18

With good prior knowledge

Answer 18

For individual genotype level information targeting specific loci