domestication, polyploidy and genomics of crops #pagxxv heslop-harrison
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Domestication, polyploidy and genomics of crops (and weeds)Pat Heslop-Harrison &Trude SchwarzacherLeicester, UK
phh@molcyt.com
www.molcyt.com
www.molcyt.org
Twitter Pathh1 .Crop Evolution Genomics & Future Agricultural Productivity PAGXXV 14 January 201720 min talk
Outputs
–Crops(Chemical energy)
– Food– Feed– Fuel– Fibre
– Flowers– Pharmaceuticals
– Fun2
Inputs
–Light
–Heat
–Water
–Gasses
–Nutrients
–Light
–Heat
–Water
–Gasses
–Nutrients
(Ecosystem services)
Outputs
–CROPS
– Chemical energy
Domestication, Polyploidy and Genomics of Crops
• CROPS: where one species controls the growth and reproduction of another
Domestication, Polyploidy and Genomics of Crops
• Most species domesticated 10,000 years ago (cereals, legumes/pulses, brassicas, fruits, cows/sheep/pigs, silkworm/bees)
• Few species more recently (rabbits, fish, trees, biofuel crops)
• A few dropped out of production
• First steps: productive, reproduce easily, disease-free, edible/tasty, harvestable …
• With critical technology of people: not obvious
Heslop-Harrison & Schwarzacher Domestication genomics in Arie Altman www.tinyurl.com/domest and review of rabbits www.tinyurl.com/rabdom
Pinus sylvestrisScots pine
Argemone mexicana
Japanese knotweed – invasive in EuropeFallopia (and Fallopia x Muehlenbeckia hybrids)
Larrea tridentaCreosote bush
Domestication, polyploidy and genomics of crops and weeds
• CROPS: where one species controls the growth and reproduction of another
• WEEDS
• Many animals collect food to see them through the winter, build nests in anticipation of reproduction
• A few plants kill off all others nearby
• Ants (Formicidae) farm plants, animals and fungi
• Humans only for 20% of their history – and still exploiting environment unsustainably!
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
Genomic Components: properties
• Tandem Repeats
• Simple Sequence Repeats
• Dispersed Repeats
• Functional Repeats
• Retroelements
• Genes
Typical Fraction
10%
5%
10%
15%
50%
10%
Domestication, polyploidy and genomics of crops and weeds
• Genome size
• Critical parameter for genome studies – first sequenced genomes chosen to be small ... Large genomes only tackled 25 years on
• But is it critical for species …
• No: you can’t ‘look’ at a species and make any suggestion about it’s genome size …
Nothing special about crop genomes?Crop Genome size 2n Ploidy Food
Rice 400 Mb 24 2 Triploid endosperm
Wheat 17,000 Mbp 42 6 Triploid endosperm
Maize 950 Mbp 10 4 (palaeo-tetraploid) Triploid endosperm
Rapeseed B.
napus
1125 Mbp 38 4 Cotyledon oil/protein
Sugar beet 758 Mbp 18 2 Modified root
Cassava 770 Mbp 36 2 Tuber
Soybean 1,100 Mbp 40 4 Seed cotyledon
Oil palm 3,400 Mbp 32 2 Fruit mesocarp
Banana 500 Mbp 33 3 Fruit mesocarp
Heslop-Harrison & Schwarzacher 2012. Tinyurl.com/domest
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.
#
TxS3 TxA978 TxO978
Repeat masker Genome % Repeat masker Genome % Repeat masker Genome %
1 Low complexity 1.60 Low complexity 0.965 Simple repeat 1.400
2 Low complexity 1.26 Low complexity 0.818 LTR.Gypsy 1.250
3 LTR.Gypsy 1.22 LTR.Gypsy 0.807 Simple repeat 1.200
4 LTR.Gypsy 1.17 Low complexity 0.796 Low complexity 0.963
5 Low_complexity 1.09 Low complexity 0.788 LTR.Gypsy 0.845
6 LTR.Copia 1.04 Low complexity 0.771 Low complexity 0.820
7 LTR.Gypsy 0.995 LTR.Gypsy 0.730 LTR.Gypsy 0.793
8 Low_complexity 0.982 Low complexity 0.713 Low complexity 0.781
9 LTR.Gypsy 0.940 LTR.Gypsy 0.682 LTR.Gypsy 0.741
10 LTR.Copia 0.841 Low complexity 0.671 Low complexity 0.724
S3
A978Petunia
Relative counts of various k-mers in three Taraxacummicrospecies
Rubar Salih et al. in prep
Dispersed on chromosomes in all microspecies: but differences
AA1_AK07_171D_45S B_010
AC1_O996_171 D_KsHC B_003AC11_S933_171 D_KsHC B_004
0.075%
Low complexity
Assembled to genome of:
A:
S:
O:
Sequence CL80 double-dots on 14 chromosomes (not 16 -not 2 genomes worth) - is it a centromeric repeat?
LTR.Copia (2hits, 0.103%)
Low complexity (5hits, 0.0895%)
Genome proportion = 0.2480%
Assembled to genome:
A =
S =
O =
AE (3)_A978_A dig_pta794_001
AE (4)_O976_A dig_pta794_002AE (2)_S3_A dig_Pta794 bio_002
Unknown or ChloroplastLow Complexity
Mixed RepeatLTR Degenerate
LTR GypsyLTR Copia
DNA TransposonsLINES
LTR CaulimovirusSimple Repeat
rRNATandem Repeat
Telomere
Gen
om
e p
rop
ort
ion
(%
)
Cluster (number)
I I I I I I I I1 50 100 150 200 250 300 351
Telomere
Tandem Repeat
rRNA
Simple Repeat
LTR Caulimovirus
LINES
DNA Transposons
LTR Copia
LTR Gypsy
LTR Degenerate
Mixed Repeat
Low Complexity
Unknown or Chloroplast
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
Homologue chromosome pairs Centromeres ZYP1
Early Zygotene
1 2 3
Subtelomeric synapsis Interstitial alignment Interstitial elongation
(a) Centromere, telomere and chromosome arm dynamics in meiotic prophase I.
Sepsi et al. Plant Journal 2016
• How do genomes evolve?–Gene mutation very rarely
• (human: 10−8/site/generation)
–Chromosome evolution
–Polyploidy and genome duplication
–Repetitive sequences: mobility & copy number• (10−4/generation in µsat)
–Recombination
–Epigenetic aspects: centromeres & expression
Repetitive sequences
• Many families and various types
• Abundant
• Rapidly evolving … or conserved
– Copy number and sequence
• May be near-genome specific, even chromosome-specific
• Various genome/chromosomal locations
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
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
Real? Passively Amplified DNA sequences: PADsOr: Transposable element derivatives (LTRs etc)?
Other genes
Transposable elements
Autonomous/ non-autonomous
Dispersed repeats that we don’t know about –
except each is significant proportion
of genome
Domestication, polyploidy and genomics of crops (and weeds)Pat Heslop-Harrison &Trude Schwarzacherand collaboratorsLeicester, UK
phh@molcyt.com
www.molcyt.com
www.molcyt.org
Twitter Pathh1 .
From Chromosome to Nucleus
Pat Heslop-Harrison phh4@le.ac.uk www.molcyt.com
• 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
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