Terminology

Question 1

Single nucleotide polymorphism (SNP)

Answer 1

Single base variations between genomes.

Question 2

Haplotype

Answer 2

A local combination of genetic polymorphisms that tend to be inherited together.

Question 3

Recombination

Answer 3

Exchange of genetic material between homologous chromosomes, separating or bring together alleles of different chromosomes.

Question 4

Sequence assembly

Answer 4

Inference of the complete sequence of a region, from the data on individual fragments from the region, by piecing together overlaps.

Question 5

Coverage

Answer 5

The ratio of the total number of sequenced bases over the genome length.

Question 6

Contig

Answer 6

A partial assembly of data by overlapping fragments into a contiguous region of sequences.

Question 7

Single-end read

Answer 7

A technique in which sequence is reported from only one end of a fragment.

Question 8

Paired-end read

Answer 8

A technique in which sequence is reported from both ends of a fragment. (with a number of undetermined bases between the reads that are known only approximately).

Question 9

Read length

Answer 9

The number of bases reported on a single fragment from a single experiment.

Question 10

Linkage

Answer 10

Absence or reduction of independent assortment of parental genes, which are usually transmitted together because they lie on the same chromosome and entail the distribution of loci among chromosomes.

Question 11

Linkage disequilibrium

Answer 11

The non-random association between two genetic markers or loci, and entail the distribution of allelic patterns in populations. The deviation of the genotype distribution in the population from the ultimate 1:2:1 ratio.

Question 12

Retrotransposons (class I)

Answer 12

Replicate via an RNA intermediate, meaning, there will ultimately be two copies of the same element at two different locations. As a result, they use a ‘copy-and-paste’ mode.

Question 13

Transposons (class II)

Answer 13

They produce DNA copies without an intermediate RNA stage; encode transposase, which recognizes sequences within the transposon itself, cuts it out, and inserts it elsewhere, thus, using a ‘cut-and-paste’ mode

Question 14

Restriction fragment

Answer 14

A fragment of a DNA molecule that has been cleaved by a restriction enzyme.

Question 15

Restriction map

Answer 15

The reconstruction of restriction fragments into an entire sequence.

Question 16

C-value

Answer 16

refers to the constancy of the amount of DNA per haploid cell in a species

Question 17

Neo-functionalization

Answer 17

Following duplication, one copy may acquire a novel, beneficial function and become preserved by natural selection, while the other copy retains the original function

Question 18

Sub-functionalization

Answer 18

Following duplication, both copies may become partially compromised by mutation accumulation to the point at which their total capacity is reduced to the level of the single-copy ancestral gene

Question 19

Non-functionalization

Answer 19

Following duplication, one copy may simply become silenced by degenerative/deleterious mutations, while the other copy retains the original function

Question 20

Ka/Ks ≈ 1 neutral evolution

Answer 20

silent and substitution mutations have occurred to approximately equal extents

Question 21

Ka/Ks > 1 positive (adaptive) selection

Answer 21

substitution mutations are more prevalent than silent mutations, implying that selective pressures are active and the substitutions are advantageous

Question 22

Ka/Ks < 1 purifying (negative) selection

Answer 22

substitution mutations are underrepresented, implying that the sequence is optimized fairly rigidly, with relatively little tolerance for mutation

Question 23

Polyploid

Answer 23

An organism that contains multiple sets of entire chromosomes

Question 24

Autopolyploid

Answer 24

An organism that contains multiple copies of genomes from the same parent

Question 25

Allopolyploid

Answer 25

An organism that contains multiple copies of genomes from different parents.