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Domestication, polyploidy and genomics of crops (and weeds)Pat Heslop-Harrison &Trude SchwarzacherLeicester, UK
Domestication, polyploidy and genomics of crops and weeds
• Polyploidy is also critical part of genomes …
• No: you can’t ‘look’ at a species and make any suggestion about it’s ploidy …
D’Hont et al. Nature 2012
doi:10.1038/nature11241
D’Hont et al.
Nature 2012
doi:10.1038/na
ture11241
Whole-genome duplication events.
Domestication, polyploidy and genomics of crops and weeds
• Ancient polyploidy (detected by sequencing)
• Modern polyploidy (detected by cytogenetics)
• Advantages: more control, genes free to mutate, ?larger cells/organs
• Disadvantages: meiosis challenging, buffering of changes, more DNA to replicate
Repetitive DNA in dandelion3 microspecies 22, 12 & 12 Gb2n=3x=24 apomicticRubar Salih & Lubos Majesky
k-mer analysis
For a 16-mer length, there are 2 billion canonical 16-mers (416/2), and the average 16-mer occurs 10 times in the 22Gb of sequence data.
The overall distribution of these informs us about how repetitive the genome is, and the frequency of different repetitive elements.
k-mer analysisThe most abundant 16-mers in the 150bp genome reads:7bp telomere sequence (TTTAGGG/CCCTAAA) added ends of each chromosome
occurs a total of 7M times, much higher than the expectation of 140.
From 128-merGT10kbCoverage Depth = 7
AF(11)_S983_009Blue: DAPI fluorescence.Green: telomere primer HC_89bpRed: 5S rDNA
In asexual dandelion microspecies
Rubar M. Salih
Genome evolution and biodiversity
•Actively evolving repetitive sequences in the genome•Differences seen between microspecies in repeats•Structural and mobile components of genome identified•Chloroplast sequence gives phylogeny and robust markers for diversity (PLoS One in press Dec 2016)
So questions are
1) where is this sequence located in the genome? and 2) are there any differences between the microspecies in its abundance?
We can see this is a Ty1-Copia element because the retroelements coding domains are in the order
RNaseHReverse TranscriptaseIntegrase
LTRs divergentMore (solo LTRs)
RepeatExplorer: Graph-based clustering of related sequences, program/approach byNovák P, Neumann P, Pech J, Steinhaisl J, Macas J. RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics. 2013 Mar 15;29(6):792-3.
Widely dispersed
distribution of a copia
retroelementfamily over all chromosomes of Taraxacum
Retrotransposons in Taraxacum
2n=3x=24NOR sats shown
Distribution from RepeatExplorer
O978
the top 10 in terms of genome% and nature of sequence - for each of the three spp.
Retroelements and tandem repeats in Petunia Supplementary Ms 2. Bombarely et al. Petunia genome sequenceNature Plants 2: article number 16074.
Telomere
Tandem Repeat
rRNA
Simple Repeat
LTR Caulimovirus
LINES
DNA Transposons
LTR Copia
LTR Gypsy
LTR Degenerate
Mixed Repeat
Low Complexity
Unknown or Chloroplast
Organelle sequencesfrom chloroplasts or
mitochondria
Sequences from viruses
Transgenes introduced with molecular biology
methods
Genes, regulatory and non-coding low-copy sequences
Dispersed repeats
Repetitive DNA sequences
Nuclear Genome
Tandem repeatsSatellite sequences
DNA transposonsRetrotransposons
Centromericrepeats
Structural components of chromosomes
Telomericrepeats
Simple sequence repeats or
microsatellites
Repeated genes
Subtelomericrepeats
45S and 5S rRNA genes
Blocks of tandem repeats at discrete chromosomal loci
DNA sequence components of the nuclear genomeAfter Biscotti et al. Chromosome Research 2015
Other genes
Transposable elements
Autonomous/ non-autonomous
Dispersed repeats that we don’t know
about – except each is significant proportion
of genome
Japanese knotweed – invasive in watercourses in EuropeFallopia (and Fallopia x Muehlenbeckia hybrids)
Repeat Explorer analysis raw reads of F. japonica and M. australis. Top clusters represented 50% of the reads in F. japonica and 39.5% of reads in M. australis.F. japonica has a higher proportion of dispersed repeats than M. australis.
Fallopia x Muehlenbeckia hybrid : Differential probes identified by k-mer and RepeatExplorerGreen is Fallopia-specific; Red is equal in both genomesDesjardins, Bailey, Wang, Schwarzacher, Heslop-Harrison. 2017 in prep
Desjardins, Bailey, Wang, Schwarzacher, Heslop-Harrison. 2017 in prep.
Panicum sensu stricto c. 100 species; x=9Evolution of Panicum miliaceum Proso millet
P. miliaceum 2n=4x=36
P. capillare2n=2x=18
P. repens2n=4x=36
also 2n=18 to 54
P. sumatrense2n=2x=18 or 4x=36
Global North-temperate
Low genetic diverstiy
Weedy forms
P. virgatum2n=4x=36 or 2x=18
? ? ? ? ??
• Hunt , HH et al. 2014. Reticulate evolution in Panicum (Poaceae): the origin of tetraploid broomcorn millet, P. miliaceum. J Exp Bot. 2014
Chromosome and genome engineering
Cell fusionhybrid of two4x tetraploidtobaccospecies
Patel, Badakshi, HH, Davey et al 2011 Annals of Botany
Nicotianahybrid4x + 4x
cell fusions
Each of 4chromosome
sets hasdistinctiverepetitiveDNA when
probed withgenomic DNA
Patel et alAnn Bot 2011
Cell fusionhybrid of two4x tetraploidtobaccospecies
Four genomesdifferentiallylabelled
Patel, Badakshi, HH, Davey et al 2011 Annals Botany
Wheat evolution and hybridsTriticum uratu
2n=2x=14AA
EinkornTriticum monococcum
2n=2x=14AA
Bread wheatTriticumaestivum2n=6x=42AABBDD
Durum/SpaghettiTriticum turgidum ssp durum
2n=4x=28AABB
Triticum dicoccoides2n=4x=28AABB
Aegilops speltoidesrelative
2n=2x=14BB Triticum tauschii
(Aegilops squarrosa)2n=2x=14
DD
TriticalexTriticosecale
2n=6x=42AABBRR
RyeSecale cereale
2n=2x=14RR
Centromere dynamics and timing of chromosome synapsis (6x wheat)Adel Sepsi, Higgins, Heslop‐Harrison, Schwarzacher. CENH3 morphogenesis reveals dynamic centromere
associations during synaptonemal complex formation and the progression through male meiosis in hexaploid wheat. Plant Journal. 2016 Sep 1.
Sepsi et al. Plant Journal 2016
(b) Centromere depolarisation and SC formation during Zygotene
Interphase Leptotene Zygotene Late ZygoteneTelomere bouquet
• About half of all higher plant species are recognizable as polyploids, a major feature of genome architecture where there are more than two sets of chromosomes. Advantages include multiple copies of each gene with different regulation, so essentially fixing heterosis; larger cell size; and the opportunity for mutation without lethality. Disadvantages include twice as much DNA to replicate; incorrect control of multiple gene copies in interacting genomes; chromosome instability at mitosis; and the challenges of ensuring chromosome pairing and regular meiotic segregation in seed crops, in breeding hybrid materials, or else combining sterility with parthenocarpy in fruit crops. Given these substantial contrasts, it is perhaps surprising that the top three cereal crops are wheat (a modern hexaploid 2n=6x=42), rice (diploid, 2n=2x=14), and maize (palaeotetraploid, 2n= 2 or 4 x =20), suggesting neither advantages nor disadvantages are overwhelming. I will consider the balance of positives and negatives over evolutionary and crop-breeding timescales. In the second part of my talk, I will consider how knowledge of polyploid behaviour and knowledge of ancestors can be exploited, discussing our work with polyploids, both well-known (wheat, Brassica, banana) and less known (proso millet, ornamentals and saffron crocus). Further details and references will be at www.molcyt.com. Email phh(a)molcyt.com