Plant genome

Question 1

whole genome duplication

Answer 1

• occurred repeatedly during plant evolution and diversification
• provides genetic layers for morphological innovation

Question 2

types of DNA duplications

Answer 2

• partial gene duplication
• gene duplication
• segmental duplication
• polysomy

Question 3

duplication mechanisms

Answer 3

• unequal crossing over
• homologous, non-homologous or both

Question 4

homologous unequal crossing over

Answer 4

• due to presence of highly similar sequences

Question 5

non homologous unequal crossing over

Answer 5

• short sequences have some similarities
• mainly by chance

Question 6

both homologous sand non homologous unequal crossing over

Answer 6

• result in 2 chromosomal products: one is longer (duplication), other is shorter (deletion)
• size of duplicated region = very short -> very long
• accelerated if multiple copies of a gene sequence close together

Question 7

orthologous genes

Answer 7

• homologous genes in a diff. species

Question 8

paralogous genes

Answer 8

homologous genes w/in the same species

Question 9

prevalence of gene duplication

Answer 9

• high rates
• small fraction retained
• 40% human and drosophila genes arose through duplication
• some become pseudogenes

Question 10

specialisation of isozymes

Answer 10

• essentially duplications
• mammalian lactate dehydrogenase = 6 genes in humans
• A subunits = high affinity for NADH
• B subunits = high affinity for NAD+

Question 11

polysomy

Answer 11

• duplication of complete chromosome

Question 12

euploidy

Answer 12

• multiples of haploid sets of chromosomes
• haploids, diploids, triploids etc.

Question 13

aneuploidy

Answer 13

• no. of chromosomes is not exact multiple of haploid set

Question 14

partial polysomy

Answer 14

• duplication of a segment of a chromosome

Question 15

polyploidisation

Answer 15

• addition of a whole genome set
• gametes of tetraploid are diploids
• uneven no. of chromosomes are made a problem in meiosis

Question 16

autoploidy

Answer 16

• doubling of a genome
• can double the size of plants
• used in agriculture

Question 17

allopolyploidy

Answer 17

• combination of the two genomes of two species
• results in interbreeding of diff. species
• much more common than auto
• present in various animal groups

Question 18

consequences of polyploidy

Answer 18

• some species show no effect of phenotype
• often cell vol = larger
• unstable genomes

Question 19

diploidisation

Answer 19

• to make polyploids like diploids in meiosis
• switch from quadrivalent to bivalents in meiotic pairing
• tetratomic inheritance becomes disomic inheritance
• genes that get lost = non-housekeeping genes

Question 20

genome bloating

Answer 20

• probably a limit to genome size
• evolutionary costs to having a large genome

Question 21

G-value paradox

Answer 21

• hard to determine exact no. of proteins (often inflated)
• relationship between no. of protein coding genes and organismal complexity
  more functions due to:
• gene regulation
• alternative splicing
• multifunctional proteins
• simpler ways for functions to exist

Question 22

methodologies for studying gene repertoire evolution

Answer 22

• first gen
• second gen
• third gen

Question 23

first gen gene repertoire evolution method

Answer 23

• infer nucleotide identity using dNTPs
• visualise w/ electrophoresis
• 500-1000 bp fragments

Question 24

second gen gene repertoire evolution method

Answer 24

• high throughput from parallelisation of sequencing reactions
• ~ 50-500 bp fragments

Question 25

third gen gene repertoire evolution method

Answer 25

- sequence native DNA in real time w/ single-molecule resolution - tens of kb fragments