Lecture 6 - Establishing genomics platform for crop species Flashcards
Why is comparative genomics important?
- polyploid crops are related to species with simpler genomes
- polyploid crops are hard to work with - complex
- some species with small genomes have been developed as model systems
- lower genetic redundancy adis in the identification of genes
- model species are small and easy to grow
Give some examples of polyploid crops and their related diploid species
- Bead wheat - Brachypodium distachon (wild triticum species)
- Oilseed rape - arabidopsis thaliana (wild brassica species)
- potato (wild solanum species)
- cotton (wild gossypium species)
What are the elementary events of gene evolution?
- vertical descent (speciation) with modification
- gene duplication
- gene loss
- horizontal gene transfer
- fusion/fission/rearrangements
Define homologues
Genes sharing a common origin
Define orthologues
Genes originating from a single ancestoral gene in the last common ancestor of compared genomes
Doesn’t mean the functions are equivilent although they normally are
Deine paralogues
genes related by duplication
can exist in different genomes
What are homeologous genes?
orthologous genes in the same species as a result of recent polyploidy
Describe the genetics of bread wheat using nomenclature from the relationships of genes
Bread wheat has homologous genes inherited from ancestral genomes. Ancestoral species underwent speciation event to give rise to Aegilops and then a further speciation event to give rise to Aegilops speltoides and triticum uratu, then hybridised to form a polyploid Triticum turgidum (diploid) and Aegilops tauschii (monoploid) - these then hybridised to form bread wheat (triticum aestivum (3 genomes A,B,D,))
Describe the genetics of brassica using nomenclature from the relationships of genes
hybridisation of brassica rapa (2n=20) and Brassica oleracae (2n=18) formed Brassica napus (2n=38)
Formed polyploid from the hybridisation of two species and a doubling of chromosomes
A genome of B.rapa and C genome of B.oleracea hybridise to form AACC genome of B.napus (oilseed rape)
What is the range of plant genomes in size?
Arabidposis thaliana: 130 000 000 bp, 14% repetitive, 25 000 genes
Human: 3GB
Barley: 1/3 wheat genome
Hexaploid bread wheat: 17 GB (17 000 000 000bp) 80% repetitive (hard to assemble genomes by looking at which part of the genomes crossover with which - arises from transposon amplification), 90 000 genes (genes not a large component of the genome size, but does mean hard to target by genetic manipulation)
What is the history of plant genome sequencing in plants?
Earliest genome published (arabidopsis) 2000
relatively few genomes sequenced for many years due to the cost of sequencing and problems of assembling repetitive genomes
Big increase in genome sequences in recent years due to the improvements in next generation sequecing
Cost reduced and enabled sequening of more complex genomes
but mostly only of draft quality
Rice and arabidopsis well sequenced
What is the structure of the rice genome?
Oriza satica (spp. japonica cv. Nipponbare)
- 370 Mb finished sequence of around 440Mb
- 26% repetitive
- 37500 genes
- finished to a very high standard
How are the genomes of cereals mostly related?
Mostly colinear
however this isn’t normal
in most, polyploidy and genome rearrangment has occured increasing gene copy number and complicating colineararity studies
How is plant genome evolution shaped?
Cycles of polyploidy and diploidisation
Why is it particularly useful that the rice genome has been mostly sequenced?
Cereal crop genomes align very well when common markers are used that are present across multiple genomes (extensive marker colinearity)
Show a high degree of colinearisation of genomes in even distantly related genomes
- Triticeae, Maize, Sorghum, Sugar cane, Foxtail millet, rice