Huge plant genomes and polyploidy

Question 1

Variation in genome size of gymnosperms and angiosperms

Answer 1

Angiosperms
- Largest genomes + largest range in size
- Japanese canopy plant is largest -> 149 million base pairs

Gymnosperms
- Uniformly large genomes

Question 2

What leads to large genome size and variation?

Answer 2

Polyploidization (Allo/ auto)

Transposable elements (supression/ repair mechanisms?)

Question 3

Whole genome duplication

Answer 3

a) Polyploidisation (0.1-10mya)
- Allopolyploidy (hybridisation)
- Autopolyploidy (WGD)

b) Chromosome reshaping (5-200mya)
- Symetrical reciprocal translocation or assymetrical reciprocal translocation
- This defines architecture/ structure of chromosome

c) Extinction or fixation

WGD and reshaping allows innovation/ adaptation and accounts for much of the diversity in plant genome make-up

This means plants often have more than 2n chromosomes.

Example:
- strawberry is 8N
- Occurred in domesticated crops -> allow more control of grain shale, fruit shale, flowering time (e.g. wheat and cotton)

Can be both diploid and polyploid
- E.g. over 60% of fire weed populations have polyploid and diploid

Question 4

Types of polyploidisation

Answer 4

Autopolyploidy – multiple chromosomes derived from single taxon
- via no chromosome disjunction in meiosis
- or spontaneous, somatic genome doubling
- multiple homologous copies of each chromosomes

Allopolyploidy – chromosomes derived from 2+ diverged taxa brought together by hybridization
- two or more distinct sets of chromosomes (sun genomes)

Question 5

Example of allo-polyploidy in plants

Answer 5

Bread wheat
- Allohexaploid (AABBDD)
- Hybdrisation of different species has lead to allopolyplodation.
- AA + BB
- AABB + DD
- It has 3 homologous genomes with very little reshaping

• RNA sequencing in 3 homoleeous genes shows variation in trancript levels, tissue preference between chromosomes which is evidence of adapation and innovation.

Wheat quickly spread from Fertile Crescent due to accelerated genetic novelty through acquisition of new traits, new intergenic interactions, buffering of mutations

Example: cordgrass
- implications for the native species after hybridisation between native and invasive

Question 6

The fate of duplicated genes

Answer 6

Normally the duplicated gene loses it function.

But changes in function can occur…

Sub-functionalization: division of the function

Neo-functionalization: Changes in amino acid coding sequence of one of the copies leading to a new function completely

Example: 30% of wheat homolog triads showed non balanced expression. First steps towards neo or sub functionalisation

Example: sub function of taGW8 homologous. It is activator TF. Different haplotypes have different effects. Study’s have treated molecular markers for homologous so they can be bread into the same genome. One for grain weight, one for early maturity.

Gene duplication leads to the formation of genes with new functions therefore duplication can be favoured by natural selection.
(e.g. gene amplification of genes reprosible for smell and tase in plants -terpenes)

Question 7

Type I and II Transposable elements

Answer 7

Type 1 – Retrotransposon: A DNA sequence that is present on the chromosome is transcribed to RNA and then retro-transcribed back to DNA and then copies are inserted into the gene (copy + paste)

Type 2 – DNA transposon: A DNA sequence is removed from the strand and inserted elsewhere in the genome (cut and paste)

TE are activated by stress (e.g. drought/ pathogen)

LTR are used to date the age of translocation using moolecular clocks as the LTR degrade

Question 8

Retrotransposons examples

Answer 8

Gymnosperm-> conifers:
- RT comprise 60-85% of confer genome
- Conifers lack key repair mechanisms to remove LTR-RTs so have high % of them in their genomes

Angiosperm -> Monocots:
- RT comrise 30-70% of genome
-e.g. 65% maize

Question 9

Tracing duplicaiton events

Answer 9

Duplication events can be traced by looking at similarity in the genome
- Where: similiarty in genome
- When: degredation of the similarties

Question 10

Overview

Answer 10

Plant genomes are large and vary greately due to:

Polyploidy and reshaping
- Allpolyploidy: Results from hybridisation
- Autopolyploidy: Results from WGD (No chromosome reduction during meiosis)

Transposable elements
- DNA transposones
- Retro- transposones (most common in large genomes)

Repair mechanisms that remove RT also determine genome size

Natural selection can promote polypoidization as it allows the evolution of new genetic functions

Polyploidization can lead to rapid, short-term phenotypic change which may be beneifical (captured in crop domestication and developement)