Plant Genome Structure Flashcards
How do genes become tandemly duplicated?
Normal genetic recombination between sister chromatids during meiosis relies upon the two chromatids lining up together.
This normally has no effect on gene order or number
because the 2 recombination sites are identical on each chromatid.
Double strand break induced in one of the strands.
Need identical sequence to form a double stranded homolog.
But the genes on REAL chromosomes are embedded in repeated ‘junk’ sequences.
These repeats can confuse the recombination machinery
- leading to cross-overs between different positions on the two chromatids- gene duplication and gene deletion.
Recombine- still have homology, but everything has moved.
Duplication and deletion go together.
Arrangements subjected to selection- if the new combos are an advantage/ not a disadvantage, they will persist.
Why do genes become tandemly duplicated?
Gene duplication produces 2 identical copies of a gene - these copies can then diverge by mutation over evolutionary timescales.
Two copies can diverge and produce a new functionality that wasn’t present in the original organism.
Gene divergence can result in the ‘death’ of a gene, producing a non-functional pseudogene. Gene can accumulate mutations and degrade- become a dead gene.
What is a pseudogene?
A gene that no longer functions- a dead gene.
Describe aluminium tolerance and duplication of transporter genes in rye.
The element Aluminium (Al) is toxic to plants when soil conditions are acidic, leading to high concentrations of Al3+. The Alt4 locus specifying aluminium tolerance in rye maps to 7RS, encoding an acid transporter protein that pumps Al3+ out of roots. An aluminium-tolerant haplotype M39A-1-6 has 5 non-identical copies of the gene at the locus and a susceptible haplotype has 2 non-identical copies. 2 of the ‘tolerant’ genes and 1 of the ‘susceptible’ genes are highly expressed when Al3+ is present. Recombinants between these haplotypes show that both the 39-1 gene and a chimeric gene resulting from the recombination event are necessary and sufficient to confer aluminium tolerance.
Knocked out main ones (39-1 and 4)- combination of 77-1 and 39-2 is now conferring resistance.
Conclusion: Gene duplication does not always imply ‘gain of function’. Subsequent divergence of the sequences of the duplicates can complicate the picture.
Describe the NBS-LRR genes in Arabidopsis?
NBS-LRR genes encode resistance proteins against pathogens.
Genome sequencing has revealed hundreds of these genes in plant genomes.
Genetic and bioinformatic analysis has shown that many of these genes are found in tandemly repeated clusters.
Function- to recognise secretions from pathogens and alert cell that it has been invaded. Apoptosis at site. Keep invasion localised.
Describe purindoline genes and grain hardness in Triticeae cereals.
Grain hardness is a defining character of wheat - ‘bread’ wheat Triticum aestivum has a soft endosperm and is suitable for bread making while durum wheat Triticum durum has a hard endosperm and is suitable for pasta making.
Soft texture is additively dominant over hard texture and is associated with the amount of ‘friabilin’ protein in the endosperm that binds to starch, preventing its adhesion to the protein matrix. Friabilin protein preparations can be resolved int 3 proteins - purindoles A and B (PINA & PINB), plus small amounts of Grain Softness Protein 1 (GSP-1)
All three proteins are encoded by genes at a single grain hardness locus of wheat. The locus contains one, two or all three genes depending upon the wheat genome.
Genes here distinguish between bread wheat and pasta wheat.
Bread wheat grain has extra protein group that gives it softness. Pasta wheat grain is more brittle.
What causes gene copy number variation and presence/absence variation in Maize?
Many presence/absence variations in maize are due to insertional polymorphism of a special transposable element class called helitrons which capture gene segments and transpose them around the genome.
What are the two main classes of transposable elements?
Class I TEs= retrotransposons.
ClassII TEs= DNA TEs.
What are features of retrotransposons?
Ubiquitous in plants.
Very diverse in their sequences. Huge variation within and between classes.
Occupy large proportions of plant genomes.
What are LINEs?
Subclass of retrotransposons. Long interspersed nuclear repeats. There are three major groups of retrotransposonsEach group contains many different retrotransposon typesAll transpose replicatively (“copy & paste”) They occur in large clusters in many large genomes (and not just plants!)
LINEs are ancestors.
Descendants separated by order of genes.
Have long terminal repeats at each end, which have the same sequence.
4,000-10,000 bases.
What are LARDs and TRIMs?
LArge Retrotransposon Derivative (LARD) elements . 20-30,000 bases. Full of non-coding DNA.
Terminal Repeat retrotransposons In Miniature (TRIM elements)- deletion that removed all middle genes, just repeats and a tiny bit of LINE.
All LARD and TRIMs and almost all particular copies of every other TE class cannot encode the enzymes needed for their retrotransposition – they are defective. The actual transposition machinery is encoded by non-defective (full length) transposons somewhere else in the genome – and these are typically very rare. Both of these groups don’t have any genes, but can move anyway.
What are SINEs?
Short interspersed nuclear repeats.
Another subclass of retrotransposon.
Few hundred bases.
All are pseudogenes of small RNA genes.
Quite rare in plant genomes, but common in animals.
Transposition-defective (can’t move), but can transpose to new genomic locations if there are helper LINE retrotransposons.
How do LTR retrotransposons transpose?
RNA is translated into many proteins that form a particle.
This particle contains enzymes and structural proteins.
Two RNA particles are inserted.
Reverse transcriptase in the particle converts RNA back into DNA. Double stranded DNA that is formed has an almost identical sequence to the original DNA.
Integrase in the particle catalyses the insertion of new DNA into the genome.
TRIM elements just need identical ends that are recognised by integrase to be put in genome.
No change in original donor copy, only been transcribed.
Copy and paste mechanism.
