week 6- genome evolution

Question 1

what is the 1C-value

Answer 1

the amount of DNA in the unreplicated gametic nucleus
usually reported in terms of mass in picograms or the number of base pairs in gigabsepairs
1 pg = 0.978 Gb

Question 2

what doe C in C value stand for

Answer 2

constant as this does not chnge between members of the species

Question 3

explain C-value paradox

Answer 3

across eukaryotes 65000 x range in genome size
-some unicellular porozoans larger genomes than multicellular mammals
-plants with fewer cell types can have larger genomes than animals
-and organisms similar in complexity can have different genome sizes

Question 4

what do people argue the c-value pradox arises from

Answer 4

varying amount of noncoding DNa such as repetitive DNA, introns in genes, regulartory elements of genes, pseudogenes etc.
now is suggested as a misundertanding of how evolution works

Question 5

what do most eukaryotes have

Answer 5

small genomes, giant genomes are rare

Question 6

what is variation in genome size driven by

Answer 6

the huge range in the amount of repetitive DNA, parasitic and “selfish” elements

Question 7

what is repetitive DNA

Answer 7

DNA sequence motifs that are repeated hundreds or thousands of times across the genome, including tandem repeats (e.g., DNA satellites) and dispersed repeats (e.g., DNA transposons and retroelements)

Question 8

what are 3 important evolutionary forces affecting genome size

Answer 8

-gene and genome duplications
-transposable elements
-deletions: some organisms are better at throwing out the trash

Question 9

what are 4 types of DNA duplication

Answer 9

partial gene duplication, gene duplication, segemntal duplication, polysomy

Question 10

what is homologous unequal crossing over

Answer 10

due to presence of highly similar sequences/repetitive elements

Question 11

what is nonhomologous crossing over

Answer 11

short sequences that have some similarity mainly by chance

Question 12

what do both types of crossing over result in

Answer 12

two chromosomal products, one that is longer (duplication) and one that is shorter than before (deletion)

Question 13

what is paralogy

Answer 13

sequence homology due to dyplication
paralogous genes are homologous genes within the same species (genome)

Question 14

what is orthology

Answer 14

sequence homology due to speciation
orthologous genes are homologous (corresponding) genes in different species

Question 15

what might happen to a paralogous gene following gene duplication

Answer 15

may undergo neofunctionalisation
in which case both gene copies are maintained in duplicate in perpetuity because the loss of either copy would be detrimental to the organism

Question 16

what is subfunctionalisation

Answer 16

expression divergence of the different copies
-different tissues
-different life stage
-different physiological conditions

Question 17

what is euploidy

Answer 17

multiples of haploid set of chromosome
e.g. haploids, diploids, triploids, tetraploids, pentaploids, hexaploids

Question 19

what are aneuploids

Answer 19

number of chromosomes is not exact multiple of haploid set

Question 20

What is polysomy

Answer 20

duplication of at least one cmplete chromosome (a type of aneuploidy)

Question 21

what is partial polysomy

Answer 21

duplication of a segment of a chromosome

Question 22

what does chromosomal duplication or deletion lead to

Answer 22

does not contribute to animal evolution
often lethal or leads to infertility

Question 23

in plants is polyploidy rare

Answer 23

It’s common, but permanent polysomy is hardly ever tolerated

Question 24

what does polyploidisation consist of

Answer 24

addition of a whole genome set
gametes of a tetraploid are diploid
unevem numbers of chromosomes are a problem in meiosis: no reproduction

Question 25

what is autopolyploidy

Answer 25

doubling of genome (single species of origin)

Question 26

what is allopolyploidy

Answer 26

combination of the two genomes of two species combination of unreduced gametes in hybridisation event

Question 27

example of autopolyploidy

Answer 27

potato solanum tuberosum -high levels of heterozygosity: max 4 alleles instead of 2 -higher fitness -higher Ne (effective population size); hence selection stronger effect -athough common: long evolutionary time not successful -genetic imbalances, problems in meiosis

Question 28

example of allopolyploidy

Answer 28

-results from interbreeding of different species -much more common: 80% land plant -present in various animal groups, but not common -basically all land plants and in particular angiosperms have had several rounds of polyploidisation -large proportion considered diploid

Question 29

evidence for genome duplication

Answer 29

80 grass species, log scale, peaks in multimodal distribution indicated

Question 30

allopolyploidy in agriculture

Answer 30

-domestiation over last 15000 years: most important crops often allopolyploidy -Bread wheat, triticum aestivum, is hexaploid -common ancestor 6.5 may -current macaroni and bread whear 8500 years old

Question 31

polyploids: diploidisation

Answer 31

many plant species that are diploid now were polyploid in the past and have undergone diploidisation

Question 32

why are polyploid genomes hard to maintain through meiosis

Answer 32

mechanismas lead to diploid-like chromosome pairing, resulting in polyploid genomes returning to an effectively diploid state

Question 33

what are transposable elements

Answer 33

mobile DNA sequences capable of replicating themselves within genomes independently of the host cell DNA 100-10000 bp long can be up to 85% of the genome multiple types of TE

Question 34

what is the selfish DNA hypothesis

Answer 34

Increased genome size is attributed to the proliferation of TE

Question 35

when do TE multiply until

Answer 35

They begin to affect (reduce) host fitness, thereby natural selection prevents their further proliferation

Question 36

are TE coding or not

Answer 36

they are coding, in the sense they code their machinery for proliferation

Question 37

what is the G-value paradox

Answer 37

-similar to the C paradox -the lack of correlation between organism complexity and te number of coding genes

Question 38

how can some complex organisms get away with having fewer genes

Answer 38

they do more with what they have via transcriptional controls, multifunctional proteins, more interaction with protein products, alternative splicing etc.

Question 39

is their correlation between number of chromosomes and genome size

Answer 39

no (negative) correlation several processes can change the number of chromosomes: fission and fusions

Question 40

example of synteny: conservation gene order

Answer 40

human vs mouse: little conservation of gene order except for X chromosomes 295 rearrangements huge difference between lineages in synteny conservation interchromosomal rearrangements 4x > intrachromosomal

Question 41

what does almost perfect correlation exist between

Answer 41

in both eubacteria and archaebacteria, between genome size and gene number

Question 42

what exhibits a large infraspecific variation in gene content

Answer 42

prokaryotes

Question 43

what is the pangenome

Answer 43

the full complement of genes in a species (all genes of all strains belonging to the species) consisting of core genome, accessory genome and unique genes

Question 44

what is core genome

Answer 44

all the genes found in all the strains

Question 45

what is the accessory genome

Answer 45

genes present in one or more strains

Question 46

what are unique genes

Answer 46

(strain specific genes) they are genes found in a single genome or a single strain

Question 47

what do prokaryotes have a tendency toward

Answer 47

genome miniaturization due to an inherent mutational bias towards deletions over insertions

Question 48

what happens at the genome level

Answer 48

a drastic reduction in genome size, invariably associated with loss of function

Question 49

what are parasitic and endosymbiotic modes of life affected by

Answer 49

genome miniaturisation

Question 50

what is the difference between prokaryotic genome evolution and eukaryotic

Answer 50

no G value paradox must consider the pangeonome vs core and accessory genomes have tendency towards genome miniaturisation