Genome Evolution Chromosomes Heslop-Harrison ICC Prague

Chromosome and Genome
Evolution in Plants and
Animals
Pat Heslop-Harrison
Twitter: @PatHH1 #ICC22 Slideshare: PatHH1
www.molcyt.com phh@molcyt.com
International Chromosome Conference
Prague 2-5 September 2018

How do genomes evolve?
•Polyploidy / whole genome duplication
•Translocations / rearrangements
•Aneuploidy
•Recombination
•Repetitive DNA & genome size
•Cytoplasm-nuclear transfer

Wheat evolution and hybrids
Triticum uratu
2n=2x=14
AA
Einkorn
Triticum monococcum
2n=2x=14
AA
Bread wheat
Triticum
aestivum
2n=6x=42
AABBDD
Durum/Spaghetti
Triticum turgidum ssp durum
2n=4x=28
AABB
Triticum dicoccoides
2n=4x=28
AABB
Aegilops speltoides
relative
2n=2x=14
BB Triticum tauschii
(Aegilops squarrosa)
2n=2x=14
DD
Triticale
xTriticosecale
2n=6x=42
AABBRR
Rye
Secale cereale
2n=2x=14
RR

green plants
land plants
vascular plants
seed plants
flowering plants
diversification of angiosperms
ANA
ε Ginkgo
Taxus
Pinus
Cedrus
Sequoia
Welwitschia
Ephedra
Lycophytes
(ca. 1200 species)
Physcomitrium sp.
Chlorophytes
(ca. 4300 species)
0100200300400 Mya500
AGF
Charophytes
(ca. 12,000 species)
Sphagnum sp.
Physcomitrella
Monilophytes
(ca. 13,000 species)
Vitis (grapevine)
Solanum (tomato, potato)
Arabidopsis
Carica (papaya)
Populus (poplar)
Linum (flax)
Brassica (rapeseed)
Glycine (soybean)
Malus (apple)
Musa (banana)
Oryza (rice)
Triticum (wheat)
Zea (maize)
β α
γ
ρσ
τ
Nicotiana (tobacco)
Petunia
ζ
Bryophytes
(20,000 spp)
Gymnosperms
(1000 spp)
Green algae
‘Pteridophytes’
Angiosperms
(400,000 spp)
Eudicots
Monocots
Basal Angiosp.
Karine Alix, Schwarzacher, HH, Ann Bot 2017

4D T4DL*4Ai#2S
DAPI Afa Thin all
(blue) (green) (red)
rye
Th. intermedium
(Thin)
Heterochromatin
(hybridizes with
genomic rye and
Th. intermedium
DNA
pSc119.2/variabl
e between lines
5S rDNA
45S rDNA
dpTa1/Afa
T1BL*1RS
BP III
1B recombinant
BPI and BPII
Thin (red)
5S 45S 119.2
(green)
45S (red)
pSc119.2 (green)
Thin (red)
5S (green)
Thin (red)
119.2 (green)
1B
Th. intermedium DNA
pSc119.2/CS13
Ali N, PHH et al. Heredity 2016

NO2Y5149 Mace Tomahawk
Wheat Streak Mosaic Virus resistance
From Thinopyrum sp in wheat

Patokar C, PHH et al.
Chromosoma 2016

Recombination in alien fragments
Th. intermedium DNA-green
AfaThin-red NiazAli
Meiosis and chromosome pairing in
hexaploid wheat

Interphase Leptotene Early ZygoteneCENH3TRSDAPICENH3ASY1CENH3ASY1
Centromere dynamics and timing of chromosome synapsis (6x wheat)
Adel Sepsi, Higgins, HH, Schwarzacher. Dynamic progression through meiosis in hexaploid wheat. Plant Journal 2017
ImmunoFISH for insight into meiotic processes in nuclei of grasses
Adel Sepsi, HH, Schwarzacher et al. Frontiers in Plant Science 2018

Centromere dynamics and timing of chromosome synapsis (6x wheat)
Sepsi et al. Plant Journal 2017
0
5
10
15
20
25
30
35
40
Interphase Leptotene Early Mid-late Pachytene Diplotene
Zygotene Zygotene
2n=42
3 x 14
chromosomes
21 bivalents
3 x 7
pairs of
chromosomes

Mid Zygotene Pachytene DiploteneEarly Zygotene
Dynamic of centromeres during meiosis
Sepsi A, Higgins JD, Heslop-Harrison JS and Schwarzacher T, 2017.
CENH3 morphogenesis reveals dynamic centromere associations during synaptonemal complex formation and the progression through
male meiosis in hexaploid wheat
Plant Journal 89: 235-249 doi: 10.1111/tpj.13379
CENH3 centromere
ASY1 associated with the lateral elements (unpaired)
ZYP1 central element of the synaptonemal complex (paired)

YouTube pathh1 – meiosis https://www.youtube.com/watch?v=8lBdErxq2Kk
Zygotene and Initiation of synapsis: short, linear paired SC (synaptonemal complex, purple,
anti-ZYP1) stretches at the telomere pole opposite to the centromeres (red, anti-CENH3):
ZYP1 polymerization starts from subtelomeric regions

Mid Zygotene Pachytene DiploteneEarly Zygotene
Dynamic of centromeres during meiosis

(a) (b) (c)
(d) (e) (f)
(g) (h) (i)
ASY1CENH3DAPI

(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 2017

B. nigra
BB
2n=2x=16
760Mbp
B. rapa
AA
2n=2x=20
564Mbp
B. juncea
AABB
2n=4x=36
1495Mbp
B. carinata
BBCC
2n=4x=34
1544Mbp
B. oleracea
CC
2n=2x=18
760Mbp
B. napus
AACC
2n=4x=38
1324Mbp

Genome Specificity of a CACTA
(En/Spm) Transposon – Karine Alix et al.
B. napus (AACC, 2n=4x=38) – hybridized with C-genome CACTA element red
B. oleracea (CC, 2n=2x=18) B. rapa (AA, 2n=2x=20)

Genome Specificity of a CACTA (En/Spm) Transposon
AJ 245479
AC 189496
AC 189446
AC 189655
AC 189480
Bot1-1
Bot1-2
Bot1-3
large insertion
specific of Bot1-1
Bo6L1-15
1010bp
large insertion in common between
Bot1-2 and Bot1-3
Rearrangement
specific of Bot1-3
B. napus
B. rapa
B. oleracea
AJ 245479
AC 189496
AC 189446AC 189446
AC 189655AC 189655
AC 189480AC 189480
Bot1-1Bot1-1
Bot1-2Bot1-2
Bot1-3Bot1-3
large insertion
specific of Bot1-1
Bo6L1-15
1010bp
large insertion in common between
Bot1-2 and Bot1-3
Rearrangement
specific of Bot1-3
B. napus
B. rapa
B. oleracea

Sequences of
chr A9 Brassica rapa
vs chr C8 Brassica oleracea

• FROM
• Feng Cheng, Jian Wu & Xiaowu
Wang. Genome triplication
drove the diversification of
Brassica plants
• Horticulture Research 1, Article
number: 14024 (2014)

Massive oligonucleotide pools –
>20,000 c. 50-mers =
>1,000,000 bp
• Designed along chromosome sequence, then
screened to remove sequences that have homology
to other sites or repetitive DNA

Probe pools to single-copy sequence, unique locations within 500kb
bands on selected A genome chromosomes.
Most (pie area is proportional to oligo numbers) mapped to bands on B
and C genome chromosomes.
Neha Agrawal

Oligo pool
Brassica rapa AA
2 pairs both ends
2 pairs one end
Neha Agrawal 2019

Illumina survey sequence of 5
animals
• Sarbast Mustafa
• In: Mitochondrial DNA part A
2018
Hamdani
Karadi

New mitochondrial assemblies compared with the nuclear chromosome assemblies
(Ovis aries Oar_v4.0)

16S rRNA
CYTB CDS (1036bp)Control region
ND1

Numts – nuclear-mitochondrial
sequences
De novo assembly of variant mitochondrial sequences
Blasting against NCBI
Assemblies of variant reads: homology to
mitochondria of Ovis canadensis, O. ammon, O.
vignei, genus Capra
A few regions reported as nuclear including to
O. canadensis chromosome 26, O. aries
chromosome X

How do genomes evolve?
•Polyploidy / whole genome
duplication
•Translocations / rearrangements
•Aneuploidy
•Recombination
•Repetitive DNA & genome size
•Cytoplasm-nuclear transfer

Organelle sequences
from 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 repeats
Satellite sequences
DNA transposonsRetrotransposons
Centromeric
repeats
Structural
components of
chromosomes
Telomeric
repeats
Simple sequence
repeats or
microsatellites
Repeated genes
Subtelomeric
repeats
45S and 5S
rRNA genes
Blocks of tandem
repeats at discrete
chromosomal loci
DNA sequence components of the nuclear genome
After Assunta Biscotti et al. Chromosome Research 2015
Other genes
Transposable elements
Autonomous/
non-autonomous
? PADS – Passively
amplified DNA
sequences ?

Repeats and diversity in sheep - 2n=54
Major tandemly
repeated
sequences SatI
and SatII at
many centromeres
Sex chromosomes
are different to
autosomes
X
Y Chromosome Research:
special issue on repetitive
DNA December 2015
Cover Sarbast Mustafa et al.

Repeats in sequence reads
•SatI: 816bp monomer, 6% of
genome
•SatII: 702bp monomer, c. 1.6% of
genomeSatellite I Satellite II

Satellite I
SCP1
Satellite II
Clusters at
centromeres
Schwarzacher et al. 2019

SCP1 Telo SatI
SCP1 Sat I SatII OAR2
DOMESTIC SHEEP
OVIS ARIES (OAR, 2n=54)

METACENTRIC GC- rich
centromeric
heterochromatin
• Mc1-Al: present in all metacentric
chromosomes (SSC1 – SSC12 and X )
• Mc1-Av: present only in SSC1
• Mc1-Pv: present on SSC10, 11 and
12
ACROCENTRIC AT-rich
centromeric
heterochromatin
• Ac2-3.4: present in all acrocentric
chromosomes (SSC13-18);
• Ac2-3.5: present in all acrocentrics
(SSC13-SSC18)
KARYOTYPE OF THE DOMESTIC PIG
SUS SCROFA DOMESTICA
(SSC; 2n = 38)
Michael Jantsch, Vienna

(Schwarzacher et al., 1984; Jantsch et al., 1990).
METACENTRIC GC- rich
centromeric
heterochromatin
• Mc1-Al: present in all metacentric
chromosomes (SSC1 – SSC12 and X )
• Mc1-Av: present only in SSC1
• Mc1-Pv: present on SSC10, 11 and
12
ACROCENTRIC AT-rich
centromeric
heterochromatin
• Ac2-3.4: present in all acrocentric
chromosomes (SSC13-18);
• Ac2-3.5: present in all acrocentrics
(SSC13-SSC18)
Michael Jantsch, Vienna
KARYOTYPE OF THE DOMESTIC PIG
SUS SCROFA DOMESTICA

XY
Sus scrofa domestica
Immuno-Staining and FISH
SSC1
SSC1
SCP1 Mc1-Av
Ac2-3.5
Mc1-Av
Dafria. Tekiner, Schwarzacher

SSC1
Ac
Ac
Ac
Ac
Ac
Ac
SCP1 Ac2-3.5
SCP1 telomere
The acrocentric heterochromatin forms a
tight DAPI positive chromocentre at
pachytene .
The repetitive sequences of the six
acrocentric bivalents join together into one
or sometimes two large areas .
The SCs are however not associated
themselves or directly via their telomeres
Pachytene
Conventional
spread
DAPI staining
SC
Schwarzacher, Dafria and Akdeniz

X
X
Mc1-Al Ac2-3.4
SCP3 Ac2-3.5 Mc2-Al
Acrocentric
heterochromatin
associates
Metacentric
heterochromatin
is dispersed
Schwarzacher and Akdeniz

Fundamental properties of a genome
• DNA sequence (example: GTGTCACT…)
• Genome size (eg 2,000 Mbp)
• Chromosome number (eg 2n = 24)
• Ploidy (eg 2n = 8x)
• Chromosome morphology
• Repetitive DNA nature and content
BUT …
does it matter? can they be exploited or used?

Nothing special about crop genomes?
Crop Genome size 2n Ploidy Food
Rice 400 Mb 24 2 3x endosperm
Wheat 17,000 Mbp 42 6 3x endosperm
Maize 950 Mbp 10 4
(palaeo-
tetraploi
d)
3x endosperm
Rapeseed
Brassica napus
1125 Mbp 38 4 Cotyledon oil/protein
B. oleracea
Cabbage etc
488 Mbp 18 2 Leaf/flower/bud/root
Cassava 770 Mbp 36 2 Tuber
Soybean 1,100 Mbp 40 4 Seed cotyledon
Oil palm 1,800 Mbp 32 2 Fruit mesocarp
Banana 540 Mbp (x) 33 3 Fruit mesocarp
Heslop-Harrison & Schwarzacher 2012. Genetics and genomics of crop domestication. In Altman
& Hasegawa Plant Biotech & Agriculture. Tinyurl.com/domest
… and crops are ‘random’ subset of all genomes

Genome Evolution Chromosomes Heslop-Harrison ICC Prague

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