6. Plant genomes Flashcards
What current day industries use plants in which their genomes are worth studying?
- food: breeding favours genetic diversity
- bioproducts: >25% of drugs are derived from plants
- conservation: specific species can / can’t cope with biotic/abiotic stresses due to their genomes
Do plants have diverse genomes on average?
Yes, plants have very diverse genomes + ‘rules’ are broken in plant genomes
How many genomes does a plant have?
3 genomes:
- chloroplast genome
- mitochondrial genome
- nuclear genome
Explain how chloroplast genomes in plants differ from other genomes
cp genomes are different inn GC content vs coverage
Explain what is intergenomic transfer?
Transfer of gene between genomes - in plants between the three genomes within a cell - cp / mt / n - without evolutionary impact - just g=change a gene’s location
Does cpDNA contribute a lot to the entire plant DNA content?
Not too much ~ 10%
What are the common features of cp genomes?
cp genomes:
- highly conserved
- maternally inherited
- haploid - all identical within an individual
Do cp genomes vary in size between plant species?
Yes - major influence - level of parasitism - the more parasitic - the lower cpDNA content - less photosynthesis - nutrients stolen from the host - gene reduction: if not used -> reduced
What are the levels of parasitism in plants?
- Autotrophs - non-parasitic free living - chloroplasts fully functional
- Facultative - can use chloroplasts - but also can parasitise a host depending on host availability
- Obligate - parasitic - needs a host to survive
- Holoparasite - completely lost capacity to photosynthesise - chloroplasts lost
How does photosynthetic function change in autotrophs / facultative / obligate / holoparasitism?
Photosyntheiss steep decline in obligate parasites - host required to lose cp fucntion
Explain what is heteroplasmy
Heteroplasmy - situation in which 2+ cpDNA / mtDNA variants exist within the same cell
How are chloroplasts inherited in plants?
Biparental inheritence of cp but later reduced only to maternal cp in development via heteroplasmic sorting??? research more
Explain what is heteroplasmic sorting of chloroplasts
Heteroplasmic sorting - removal of chloroplast variants in heteroplasmy: Developing plant from shoot apical meristems - can contain ~80 copies of chloroplast DNA -
Do plants show variation in mt genome sizes?
Yes - plants show great variation in mt genomes - but have similar gene contents as animals even though larger mt genomes
Is all mtDNA circular in plants?
No - mtDNA genome can be:
- branched structure
- circular
- linear
Are all parasitic plants’ mt genomes smaller?
No - unlike cpDNA - mtDNA genomes are similar size - except few species - ex mistletoe (parasitic) - lost 11 core genomes needed for respiration - mtDNA downsizing lineage specific - but mtDNA downsizing not common to all parasitic plants
Plant mt and cp genome summary
Why are plant genomes so variable?
Plant genomes are large because of:
- high proportions of transposons
- polyploidy
What is the term used to determine large plant genomes?
Genomic obesity
Do plants exhibit large genomic variation between species?
Yes - large genomic size variation
What are the types of transposons?
Class I - retrotransposons - copy and paste
Class II - DNA transposons - cut and paste
Which class of transposons is more likely to contribute to genome expansion?
Retrotransposons - copy and paste - increase in copy numbers - increased genome sizes
Is transposon frequency similar or different between plant species?
Different transposon contents between plant spiecies
Why does transposon repeat content decrease over time?
Individual transposons gain mutations - no longer detected as repeats - contribute to genome dark-matter present in large genomes
Describe transposon distribution in plant genomes
Transposons accummulate in gene poor regions of the genome - form clusters
What increase maize vs sorghum genome size?
Bursts of transposition in past 5 mil years in maize genome
How can transposition events be traced?
End ot transposon regions change over time - mutate - can be identified
What is the influence of TEs in plant genomes?
TEs usually are deleterious - insert inside a gene - deactivate it - sometime selected for in plant domestication - ex: blood oranges
Explain how TEs contributes to blood orange phenotype?
TE inserted into upstream region of ruby gene - codes for TF only if exposed to cold -> ruby TF upregulates anthocyanin expression - gives dark colour => blood roanges grow only in specific geographical locations - ex Sicily
What is the role of TEs in plant genome evolution?
TEs - identical repeats - allow alignment -> duplication / deletion / inversion of genomic elements - genomic re-arrangements -> genome evolution
Explain what is polyploidy?
Polyploidy - presence of more than two sets of genes (chromosomes with homologous genes)
Plant nuclear genome + TE summary
In which plants polyploidy is mots common and why?
In flowering plants - because of unreduced gametes (2n) or multiple fertilisation by several sperm
What are the types of polyploidy?
- Autopolyploidy: unreduced gametes - within a species
- Allopolyploidy: hybridization of different species - between species
What is crop polyploidy history?
Explain what is diploidisation
Diploidisation - creation of another chromosome through duplication -> mutation
Explain what functions can the new chromosome gain in diploidisatino?
Subfunctionalization: one function divided between two chrom - ex colour of petal + colour of pistil
Neofunctionalization: gain of new function - ex new smell
What is the historic polyploidy of grapevine?
What events contribute to genome reduction?
Genome reduction:
- gene loss ex HR via TEs pairing
- genome re-arrangement
Explain polyploidisation of Utricularia
Explain what is genome fractionation
Genome fractionation - DNA loss after duplication
