Pat Heslop-Harrisonphh4@le.ac.ukwww.molcyt.com pw/user: ‘visitor’

Social media: #ICC18 andPathh1 on TwitterReports: AoBBlog.com and Storify.com/pathh1

Arachis hypogaea – 2n=4x=40In situ hybridization of two BACs including repeatsContrasting distribution of their major repeat familie

audia Guerra Araujo et al in prep 2011, EMBRAPA, Brazil

Darwin 1859The only figure in “The origin of species”

Patel, Badakshi, HH, Davey et al 2011 Annals of Botany in press

Cell fusion hybrid of two tetraploid tobacco species

Resistance to Peronosporainherited in cell fusion hybrid (right) from one parent

Brassica rapa (AA)

Brassica nigra (BB)

Brassicajuncea (AABB)

Brassica napus (AACC)

Brassicacarinata (BBCC)

Brassica oleracea (CC)2n=20

2n=362n=34

2n=16

2n=382n=18

8

The Brassica genus is monophyletic, from single common ancestor.What has changed in the DNA sequences?

B. napus (AACC, 2n=4x=38) – hybridized with C-genome CACTA element redB. oleracea (CC, 2n=2x=18) B. rapa (AA, 2n=2x=20)

Alix et al. The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferation. Plant Journal

AJ 245479

AC 189496

AC 189446

AC 189655

AC 189480

B ot1-1

B ot1-2

B ot1-3

large insertion specific of Bot1-1

Bo6L1-151010bp

large insertion in common between Bot1-2 and Bot1-3

Rearrangementspecific of Bot1-3

B. napus

B. rapa

B. oleracea

AJ 245479

AC 189496

AC 189446AC 189446

AC 189655AC 189655

AC 189480AC 189480

B ot1-1B ot1-1

B ot1-2B ot1-2

B ot1-3B ot1-3

large insertion specific of Bot1-1

Bo6L1-151010bp

large insertion in common between Bot1-2 and Bot1-3

Rearrangementspecific of Bot1-3

B. napus

B. rapa

B. oleracea

…

Dotplot comparisons at scale of 10,000s bpTwo Musa chromosomes are >95% homologous with gapsFaisal Nouroz 2012

2011/09/01 12

Dotter plot of Brassica oleracea var. alboglabra clone BoB028L01 x Brassica rapa subsp. pekinensis clone KBrB073F16 with transposable elements.

Brassica oleracea (C genome) sequence

Bra

ssic

a ra

pa (A

gen

ome)

seq

uenc

eDot-plots of genomic sequence from homoeologous pairs of BACs

An inversion

Region of low homology

Region of high homology between A and C sequence

Transposed (moved) sequence

500bp Insertion-gap pair: present in A

4kb Insertion-gap pair: present in C genome

gi 195970379 vs. gi 199580153

Microsatellitekb

Sequence level at scale of 100s to 1000s of bp – analysis by dotplot

9-bp TSD (TATCCTATT)6-bp TIR and 66-bp imperfect sub-TIR

551-bp BART1 TE

TSD TIR TIR TSD

2011/09/01 14

TATCCTATTGCGCAATTGTCAATAATAGCACTTTTTGAAGTTTATGTCTCAAAATAGCACTAGAAGGAGAAAGTCACAAAAATGATATTCATTAAAGGGTAAAATATCTCTTATATCCTTGGTTTAAAATTAAATAAACAAACAAAAATAAATAAAAATAAATAAAAAAAATGAAAAAAAAGAAATTTTTTTTATAGTTTCAGATTATATGTTTTCAGATTCGATTTTTTTTTTATTTTTTTATTTTTTTCGAAATTTTTTTTTTATTTTTTTTCAAATTTTCTTTTTATAATTTAAAAATACTTTTTGAAACTGTTTTTTTAATTTTTATTTTTTATTTTAGTATTTATTTTTTATAAAATTTTAAACCCTAATTCCTAAACCCCCACCCCTTAACTCTAAACCCTAAGGTTTGGATTAATTAACCCAATGGATATAAGTGTATATTTACCTCTTTAATGAAACCTATTTTTGTGACTTTGAATCTTGAGTGCTACTTTGGGAACAAAAACTTGGTTTGGTGCTATCCTAGTCTTTTTCTCTATCCTATT

TACCACCCTTCTTTGTTCAATACTTTTTACAGTTTTTGGAAAGGACATGTTTCTTCTATCATCACTTAATGGTTATATATGTATGAGAAGTTTGAAAGAGATTACACTGTTTTGGAATATTAAAAAAAAAAGATATTACAAGATCTGATTTTGTTTGTATTTTAAAATTCTACCAAATCTCTCCTCAAAATCTTGGTCAAAGTCCAAAAATCCAAATATCTCAGTTAAATTCCACCAAATATGAAATCCTAAAACTTTTCCAAAATAGTTCAATAAGCCCTTAGTGTTTGGTG

AAGTGAATGGATGCTCGCATTAGTTACTATGAGCCGATTCTCGCTCTTGCGAAAGCTAAAGAGGAAAAGGCCTTCGCATTGCAGAAGAGCTGGCTGCCAGCGAGCAAGAGGTTTTCAATATTGGCTTGTGGAAAATTTGTTGCCACTTTTGCTTTACTAAGGAATGAAATAATACTTGTTTTTTTTTTTCATGGTTAATATTAGAAGATATAATTTCCTTTGAAGTTAGATTACGTTTCTTTATGTCGACGAAGTGAAGAAATATTGTCTTGTTTATGGTTCCTTCTAGTCCCAACCTTTTTTCAAGAAGGTACAGTACGTGTCAGGATTTATATGGATATACACA

Brassica rapa with inserted 542bp sequence not present in B. oleracea. 9bp TSD (red letters and arroand TIR (blue). Flanking primers used in PCR (next slide) as blue arrows on sequenceFaisal Nouroz 2011

………………..……………….

1 246 TSD TIR 542-bp TE TIR TSD 790 1000

Rapa185F Rapa177RRapa8002Rapa141F

B. rapa (47186-48200)B. oleracea (66,350-66750)

B. rapa (AA) B. juncea (AABB)

………………..……………….

B. napus (AACC)

………………..……………….

………………..……………….

………………..……………….=A =T =C =G

B. nigra (BB)

B. oleracea (CC)

B. carinata (BBCC)

B. oleracea (GK97361)

Hexaploid Brassica (carinata x rapa)

Schematic representation of insertion in Brassica rapa and other Brassica genomes. Green, red, blue and

black boxes showing DNA motifs.

700 bp hAT

Microsatellite

715 bp hAT

1016 bp in LINE

258 MITE

402 bp hAT

237 bp Mariner Like

Inversion

914 bp LINE

2781 bp MuDR Like

505 bp Unknown

1655 bp in B.rapa

380 in B.rapa

670 bp hAT

819 bp Unknown

524 bp SINE

216 bp SINE

1189 bp Mariner Like

3869 bp TE

1080 bp LINE

242, 644 & 274 bp SINEs

Brassica oleracea (C genome; EU642504.1)

Bra

ssic

a ra

pa(A

gen

ome;

A

C18

9298

.1)

TEs in B. oleracea

1284 bp Unknown

ancestral

Low-copy number High-copy number Low-copy number High-copy number

Low-copy number High-copy number

High copy spp: homogenized, amplification from a limited number of master copies

Low copy spp: much variation

S.vav42!248

0.1

Afacer1T.mono106/42!133pt1T.mono106/42!155pt1

Ae.umb106/208!1911Ae.umb106/208!1810Ae.umb106/208!2012

S.vav147!259pt1Pet w 25/208!088Pet w 25/208!077

S.vav106/208!215pt1S.vav106/208!204pt2

S.vav106/208!215pt2S.vav25/208!182

S.mon42!136Pet 22594 25/42!3324

Pet 22594 25/42!3425CS/325/208!1820

S.vav25/208!193T.tau25/147!2524pt2

CS/325/147!2322pt2L.moll25/42!156

Pet w25/147!123CS/325/208!1719

CS/325/147!2120Pet w25/147!3231

Ae.umb25/147!124Ae.umb25/208!168

L.moll25/42!167119Repeat2

Pet w 25/208!099S.mon147!1811

S.vav106/208!204pt1119Repeat3

S.vav147!2711pt1S.mon25/147!081

T.mono25/208!1212

S.vav42!237pt1S.vav42!237pt2

T.tau25/147!2625T.tau25/147!2726

Ae.umb25/208!157T.tau25/208!1517

T.tau106/42!177Ae.umb25/42!091

L.moll25/42!189CS/325/208!1618

T.tau25/147!2524pt1CS/325/147!2322pt1

Pet 22594 25/208!2325Pet 22594 25/147!1918

Pet 22594 25/208!2426T.tau25/208!1315

T.tau25/208!1416Ae.umb25/147!135

Ae.umb25/147!146Ae.umb25/208!179

7491000

996

1000

725

985

564

1000

580

646

942

616882

998

981

623

537915

578

120bp repeat unit family

in Triticum, Aegilops and

Secale species

119Repeat1

Homology between sequences

70-100% in Triticum/Aegilopsand Secale species

Pet 2259425!315

Colour blockrepresents species

High copy,

High diversity

T.tauschii (D genome)

S. cereale (R genome)

Triticum aestivum 2n=6x=42

DAPI pSc119.2 dpTa1

High copy number – low diversity in each of 3 genomes

Correlation between genetic relationships and similarity of dpTa1

hybridization

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1

Coefficient of parentage

Prop

orti

on o

f ch

rom

osom

e ar

ms

with

id

enti

cal i

n si

tu s

igna

l

Chromosomal

location of

DBC-150

repeats

Micro- or dot chromosomes

Kuhn (Belo Horizonte, Brazil) et al. Chromosome Research

Interspersion of pBuM and DBC-150

pBuM DBC-150

High interspersion

Low interspersion

Non-homologous repeats

D. gouveai D. antoneita D. seriema

ancestral

A B C D

High-copy number High-copy number High-copy number High-copy number

E F

Low-copy number Low-copy number

New species-specific variants

From species level to populations …

High copy numberlong and continuous homogeneous arrays

Low copy number interspersed and discontinuous arrays

Total = 119 repeats

NJ tree

High copy species

Low copy species

Alpha/beta repeat variation

Kuhn et al. 2011 in press Mol Biol Evol

A

B

C

A’

B’

C’

XL1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

CEN

26 27 29 30 31

C

3228 33 34

3L61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 82 83 84 85 86 87 89 90 91 92 93 94 95 96 97 98 99

3R81 88 100

47 48 50 5249 51 53 54 55 56 57 58

2L21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

2R

35 36 37 38 39 4041 42 43 44 45 46

CEN

CEN

C

C

XL

XR

XR

2L 2R

3L 3R

?

1.688 tandem repeats in Drosophila melanogaster

Large arrays n heterochromatin of chromosomes 2, 3 and XShort arrays are found in the euchromatin

Het (2)Het (3)Het (X)Eu (2)Eu (3)Eu (X)

30F

2RHet25A-B

22A-C

2L-Het

21D

21E-F

25C-D

59D 59C-D57A26D-F

27C

25D-E

24D

96A9

6C

D

96F

98B

3L-H

et

(B2)

3L-H

et

(B1)

XL-Het12E-F

2B (B1)

2B (B2)

12D-E 12B-C

12B-C 13E

8E

3C

12F-13A

12F-13A

Homogenization of arrays: differential for hetero- and eu-chromatin

Proportion of 1.688 arrays in three genomic landscape classeseuchromatic arrays are close to, genes or within intronsArray size could be selectively constrained by a role as gene regulators

0%10%20%30%40%50%60%70%80%90%

100%

Chr. 2 (16) Chr. 3 (7) Chr. X (29)

Transcription

Flanked by genes

Desert

Kuhn et al. 2011 in press Mol Biol Evol

Kim, HH, Cho et al. 2011 Science Signaling

Circadian Clock regulationafter Leloup & Goldbeter

cf Andrew Millarin Arabidopsis

X X

Y

Y

Z

Z

Many of the repetitive sequences are retrotransposons and DNA transposonsSome are microsatellite motifsSome are satellites – including the most rapidly evolving sequences

rapid evolution in copy number, location and sequence, with diverse turnover mechanisms

often mark the major differences between closely related species

it is hard to analyse by next generation or whole-genome sequencing methods

Th. intermedium Anti 5meC

Th. intermedium DNA Anti 5meC

Niaz Ali, Trude Schwarzacher – Poster 59

Wsm-1: only highly effective source of resistance to WSMV

Greybosch et al. 2009

0

0.5

1

1.5

2

2.5

3

3.5

4

1961 1970 1980 1990 2000 2007

Maize Rice

Wheat Human

Area

United Nations Millennium Development Goals- MDGs

• Goal 1 – Eradicate extreme poverty and hunger

•Goal 2 – Achieve universal primary education

• Goal 3 – Promote gender equity and empower women

• Goal 4 – Reduce child mortality

• Goal 5 – Improve maternal health

• Goal 6- Combat HIV/AIDS, malaria and other diseases

• Goal 7 - Ensure environmental sustainability

• Goal 8 - Develop a global partnership for development

Pat Heslop-Harrisonphh4@le.ac.ukwww.molcyt.com pw/user: ‘visitor’

Social media: #ICC18 andPathh1 on TwitterReports: AoBBlog.com and Storify.com/pathh1