W071 Transposable Elements and Their Evolution in Musa Date: Tuesday, January 13, 2015 Pat Heslop-Harrison, University of Leicester, United Kingdom Gerhard Menzel, Universität Dresden, Germany Tony Heitkam, Faisal Nouroz,Trude Schwarzacher, Thomas Schmidt Like other plant species, DNA transposable elements and retrotransposons represent a large fraction of the Musa genome. Mobile elements can be identified 1) by homology to known elements; 2) by characteristic sequence properties such are repeats and short duplications; and 3) by studying their mobility and insertions/deletions in comparisons of homologous or homoeologous chromosome sequences. We have used all three approaches in Musa and I will show results showing the nature of unselected mobile sequences in Musa accessions. Many of the active elements proved to belong to the hAT family of DNA transposons, where there has been limited information on their diversity, abundance and chromosomal localization in plants. Chromosomal in situ hybridization, in silico analysis of genomic sequences, Southern hybridization and biodiversity panels were used to show three major families of the elements in Musa, with some 70 complete autonomous elements, and abundant hAT-related MITEs (Miniature inverted tandem elements).MuhAT transposons and MuhMITEs were localized in subtelomeric, most likely gene-rich regions, of chromosomes. Variation between homologous chromosomes and transduplications of genomic sequences indicate activity of the transposons and suggest a role for the MITEs in modulation of genomic behaviour. Further details from www.molcyt.com; hAt element analysis: Chromosome Research 2015 DOI 10.1007/s10577-014-9445-5.

1. Transposable element evolution
and mobility in Musa genomes
Gerhard Menzel, Tony Heitkam,
Thomas Schmidt - Dresden Germany
Faisal Nouroz, Trude Schwarzacher
- Leicester UK
Pat Heslop-Harrison phh4@le.ac.uk
Pathh1:
www.molcyt.com UserID/PW ‘visitor’
.Slideshare.com pathh1

2. Heslop-Harrison & Schwarzacher T. 2007.
Domestication, genomics & future for banana.
Annals of Botany 100(5):1073-1084.

3. Sequence components of a genome
Tandem repeats
Telomeres Genes

4. Sequence components of a genome
Tandem repeats
Telomeres
Transposable
elements
Genes

5. Retrotransposons
Class I transposable
elements
RNA intermediate
DNA transposons
Class II transposable elements
Cut-and-paste
+
Transposable elements: Retrotransposons via RNA and DNA TEs

6. Transposable elements can be identified
- by studying their mobility and
insertions/deletions in comparisons of
homologous or homoeologous
chromosome sequences
- by characteristic sequence properties
such as repeats and short duplications
- by homology to known elements

7. Figure M1-1: Dot plot of homoeologous BAC clones Musa balbisiana ‘MBP_81C12’ (horizontal) against Musa acuminata ‘MA4_82I11’
(vertical). The comparison of the BACs showed large homologous region with several gap-insertion pairs. The gaps showed transposon insertions
present in one BAC and absent in others. Different TEs are encircled and named. Several small insertions are not highlighted here.
Musa balbisiana (MBP_81C12)
Musaacuminata(MA4_82I11)
Transposed MaN-hAT2
MaN-hAT1
MaN-hAT2
MbN-hAT4
MbMITE4
MbN-hAT3
MBT
MaMITE1
MAWA
Microsatellite
MaMUL1
Faisal Nouroz

8. Figure M1-1: Dot plot of homoeologous BAC clones Musa balbisiana ‘MBP_81C12’ (horizontal) against Musa acuminata ‘MA4_82I11’
(vertical). The comparison of the BACs showed large homologous region with several gap-insertion pairs. The gaps showed transposon insertions
present in one BAC and absent in others. Different TEs are encircled and named. Several small insertions are not highlighted here.
Transposed MaN-hAT2
MaN-hAT1
MaN-hAT2
MbN-hAT3
MBT
MaMITE1
MAWA
Microsatellite
hAT superfamily
8-bp TSD
Short variable TIRs of 5 to 27 bp
Single gene coding transposase with
TE class II-specific DDE amino acid motif

9. Alignment of two homologous Musa BACs shows in-dels
in B genome M. balbisiana and A genome M. acuminata
MA4_82I11
MBP_81C12
MuhAT
1
MuhAT2
a
XX TE (SINGLE)XX TE MITE
XX TE
(AGNABI)
MuhAT3 MuhAT4 MITE(MBIR
)
XX
TE
XX TE (MBT)
272 bp 102,190 bp
26, 410 bp 128,068 bp
DNA transposons hAT are particularly frequent
8 bp TSD, and short TIRs of 5–27 bp
transposase (sometimes degenerate) including a DDE site.
Non-autonomous (MITE) derivatives of hAT with deletion coding sequence

10. 8 bp TSDs - TCCCTGAG
30 bp TIRs - CAAGGTCTGcCATACCGtAcCGTACCGgCG
273 bp MaN-hAT1
TSD TIR TIR TSD
M. balbisiana MBP_81C12
M.acuminataMA4_82I11
874 bp MaN-hAT2
8 bp TSD - GTGcTAaC
15 bp TIR - CAGTGATTTaAAaAG
TSD TIR TIR TSD
M. balbisiana MBP_81C12
M.acuminataMA4_82I11

11. (n=38)
(n=20)
(n=6)
(n=6)
TIR
Terminal Inverted
Repeat
conservation
In Musa hATs

12. TSD TIR TIR TSD
8 bp TSDs - GTTGCAAC
15 bp TIRs - CAAGGTctGCaTACC
1292 bp MbN-hAT3
M. balbisiana MBP_81C12
M.acuminataMA4_82I11
8 bp TSDs - TTCAAATG
9 bp TIRs - CAAGGTtTG
524 bp MbN-hAT4
TSD TIR TIR TSD
M. balbisiana MBP_81C12
M.acuminataMA4_82I11

13. 100
100
100
97.4
9853.3
58.2
Hatvine-7
Hatvine-10
Hatvine-2
Tag1
Bg
Tip100
Tam3
Hatvine-9
Ac
Tag2
Hatvine-1
MuhAT III
MuhAT II
MuhAT I
Menzel et al. Dec 2014. The diversification and activity of hAT transposons
in Musagenomes. Chromosome Research 22: 559–571. see www.molcyt.org
HMM identifies three abundant
Musa hAT families

14. 100
100
100
97.4
9853.3
58.2
Hatvine-7
Hatvine-10
Hatvine-2
Tag1
Bg
Tip100
Tam3
Hatvine-9
Ac
Tag2
Hatvine-1
MuhAT III
MuhAT II
MuhAT I
Hidden Markov Model: 274 transposase sequences, 114 (shown) span
the five conserved hAT-specific amino acid blocks in the assembly (D’Hont et al. 2012)
61 + 47 +6 Complete and autonomous: 70 MuhAT I/II; no autonomous MuhAT III
HMM identifies three abundant
Musa hAT families

15. 15
Insertional polymorphisms of three Musa
hATs in 48 Musa/banana accessions by
PCR of flanking primers
HP-1 A1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 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 A48
HP-1 B1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 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 B48
-1 A1 2 3 4 5 6 7 8 HP-1 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 HP1 25 26 27 28 29 30 31 32 3 3 34 35 36 37 38 39 40 HP1 41 42 43 44 45 46 47 A48

16. Figure M1-11: Sequence specific insertion polymorphisms of Musa hATs. a-b) Agarose gel electrophoresis illustrating MbN-hAT3
insertion sites in various Musa accessions: Long bands (1441bp) showed the amplified element and short bands amplifying the pre-
insertion sites only. c-d) MbN-hAT4 amplification with degenerative primer pair MbNhAT4F and MbNhAT4R. Long bands (860-bp)
showed the amplified MbN-hAT4 element and short bands amplifying the flanking sequences only. Numbers across the base are
identifiers for individual specimens listed in table --- a and b.
0
HP1 A1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 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 A48
0
HP1 B1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 HP1 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 B48
0
HP1 A1 2 3 4 5 6 7 8 HP1 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 HP1 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 HP1 41 42 43 44 45 46 47 A48
)
HP1 B1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 HP1 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 HP1 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 B48
0

17. kb
0.5
1.0
2.0
3.0
10.0
6.0
kb
0.5
1.0
2.0
3.0
10.0
6.0
kb
0.5
1.0
2.0
3.0
10.0
6.0
1 2 3 4 5 6 7 8 9 10 11 12
Musa species (left 7 lanes) M. acuminata, M. balbisiana , Cavendish , M. obino l‘Ewai , M. textilis,#
M. velutina and M. ornata ; Zea mays (lane 8), Glycine max , Beta vulgaris, Arabidopsis thaliana and the gymosperm
Pinus elliottiii. DraI.digests
M. acuminata-specific dimerization
domain of the MuhAT I transposase
1 2 3 4 5 6 7 8 9 10 11 12
Full-length MuhMITE I
Probe
hAT abundance

18. v
n=159
n=140
autonomous (2206-6814 bp)
MITEs (646-1072 bp)
v
n=51
n=117
430-786 bp
116-286 bp
5‘-TSD5‘-TIR
MuhAT I: autonomous and derived MITES
transposase
5′- and 3′-
untranslated regions

19. MuhAT transposases (top) and MuhMITEs I (lower): tending to be terminal on chromosomes

20. Retroelements
Sequences which amplify through an RNA intermediate
• 50% of all the DNA!

21. Retroelements
• Homologous BAC sequences from Calcutta 4
Homologous over the full length
• except for a 5kb insert
• a Ty1-copia retroelement

22. Diploid 2n=2x=22 Musa / banana metaphase probed red with retrotransposable element
Teo & Schwarzacher

23. A-genome specific MuhAT1 on ABB Musa
M. balbisiana (BB)
f)
Musa (ABB)

24. MuhAT transposases (top) and MuhMITEs I (lower): tending to be terminal on chromosomes

25. MuhAT transposons and MuhMITEs
Associated with genes – introns and exons
Family specificity
0
10
20
30
40
50
60
70
80
90
100
Portionofcopies[%]
Exon Intron ≤ 500 bp
≤ 1000 bp ≤ 1500 bp > 1500 bp
33 12 6 96 1512

26. hAT transposons and derived MITEs evolution in Musa
– Three major families
– Hundreds of copies of hATs
– Thousands of copies of MITEs
• Subtelomeric, gene-rich regions
• Species (A and B genome) -specific mobility of
MuhMITEs
• MuhMITE II showing transduplications of genomic
sequences
– active MuhAT transposons
– MuhMITEs as modulators of genome evolution
Gerhard Menzel, Thomas Schmidt, Faisal Nouroz
Pat Heslop-Harrison phh4@le.ac.uk
www.molcyt.com Twitter pathh1

27. http://molcyt.org/2014/11/10/the-
diversification-and-activity-of-hat-
transposons-in-musa-genomes/
• Menzel G, Heitkam T, Seibt KM, Nouroz F, Müller-Stoerme M, Heslop-Harrison JS, Schmidt T. 2014.
The diversification and activity of hAT transposons in Musagenomes. Chromosome Research 22:
559–571. DOI 10.1007/s10577-014-9445-5 and Pubmed link ID: 25377178And author print hATs in
Musa _2014_CR_MenzelEtAlAuthorVersion2014.
• Sequencing of plant genomes often identified the hAT superfamily as largest group of DNA
transposons. Nevertheless, detailed information on the diversity, abundance and chromosomal
localization of plant hAT families are rare. By in silico analyses of the reference genome assembly
and BAC sequences, respectively, we performed the classification and molecular characterization
of hAT transposon families in Musa acuminata. Musa hAT transposons are organized in three
families MuhAT I, MuhAT II and MuhAT III. In total, 70 complete autonomous elements of the
MuhAT I and MuhAT II families were detected, while no autonomous MuhAT III transposons were
found. Based on the terminal inverted repeat (TIR)-specific sequence information of the
autonomous transposons, 1722 MuhAT I- and MuhAT II-specific miniature inverted repeat
transposable elements (MuhMITEs) were identified. Autonomous MuhAT I and MuhAT II elements
are moderately abundant in the sections of the genus Musa, while the corresponding MITEs exhibit
an amplification in Musa genomes. By fluorescent in situhybridization, autonomous MuhAT
transposons as well as MuhMITEs were localized in subtelomeric, most likely gene-rich regions
of M. acuminata chromosomes. A comparison of homoeologous regions of M.
acuminata and Musa balbisiana BACs revealed the species-specific mobility of MuhMITEs. In
particular, the activity of MuhMITEs II showing transduplications of genomic sequences might
indicate the presence of active MuhAT transposons, thus suggesting a potential role of MuhMITEs
as modulators of genome evolution of Musa.
• Keywords Musa acuminata, Musa balbisiana, genome assembly, BAC, hATtransposons, FISH

28. https://pag.confex.com/pag/xxiii/web
program/Paper14993.html
• W071Transposable Elements and Their Evolution in Musa
• Date: Tuesday, January 13, 2015
Time: 11:10 AM
• Room: Pacific Salon 6-7 (2nd Floor)
• Pat Heslop-Harrison , University of Leicester, Leicester, Leic, United Kingdom
• Gerhard Menzel , Institute of Botany, Technische Universität Dresden, Dresden, Germany
• Tony Heitkam , Institute of Botany, Technische Universität Dresden, Dresden, Germany
• Faisal Nouroz , University of Leicester, Leicester, United Kingdom
• Trude Schwarzacher , University of Leicester, Leicester, United Kingdom
• Thomas Schmidt , Dresden University of Technology, Dresden, Germany
• Like other plant species, DNA transposable elements and retrotransposons represent a large fraction of the Musa
genome. Mobile elements can be identified 1) by homology to known elements; 2) by characteristic sequence
properties such are repeats and short duplications; and 3) by studying their mobility and insertions/deletions in
comparisons of homologous or homoeologous chromsome sequences. We have used all three approaches in
Musa and I will show results showing the nature of unselected mobile sequences in Musa accessions. Many of the
active elements proved to belong to the hAT family of DNA transposons, where there has been limited information
on their diversity, abundance and chromosomal localization in plants. Chromosomal in situ hybridization, in silico
analysis of genomic sequences, Southern hybridization and biodiversity panels were used to show three major
families of the elements in Musa, with some 70 complete autonomous elements, and abundant hAT-related MITEs
(Miniature inverted tandem elements).MuhAT transposons and MuhMITEs were localized in subtelomeric, most
likely gene-rich regions, of chromosomes. Variation between homologous chromosomes and transduplications of
genomic sequences indicate activity of the transposons and suggest a role for the MITEs in modulation of genomic
behaviour.Further details fromwww.molcyt.com; hAt element analysis: Chromosome Research 2015
DOI10.1007/s10577-014-9445-5.

29. Some Musa / banana papers from
Pat Heslop-Harrison and www.molcyt.com
• 311. Menzel G, Heitkam T, Seibt KM, Nouroz F, Müller-Stoerme M, Heslop-Harrison JS, Schmidt T. 2014.
The diversification and activity of hAT transposons in Musagenomes. Chromosome Research 22: 559–
571. DOI 10.1007/s10577-014-9445-5 and Pubmed link ID: 25377178And author print hATs in Musa
_2014_CR_MenzelEtAlAuthorVersion2014.
• 300. D’Hont A, … Heslop-Harrison P, … Wincker P. 2012. The banana (Musa acuminata) genome and the
evolution of monocotyledonous plants. Nature 488 (7410), 213-217.
DOI: http://dx.doi.org/10.1038/nature11241
• 303. Nair AS, Heslop-Harrison P, Schwarzacher T. 2013. Production of haploid tissues and SNP analysis of
the genome in Musa acuminata cv.‘Matti’ (AA). Plant Mutation Reports 3(1): 18-24. PMR Vol3 No1
• 250. Heslop-Harrison JS, Schwarzacher T. 2007. Domestication, genomics and the future for
banana. Annals of Botany 100(5):1073-1084.doi:10.1093/aob/mcm191
• 238. Nair AS, Teo CH, Schwarzacher T, Heslop-Harrison JS. 2005 Genome classification of banana cultivars
from South India using IRAP markers.Euphytica 144: 285-290. DOI: 10.1007/s10681-005-7321-2
• 237. Teo CH, Tan SH, Ho CL, Faridah QZ, Othman YR, Heslop-Harrison JS , Kalendar R , Schulman AH.
2005. Genome constitution and classification using retrotransposon-based markers in the orphan crop
banana. Journal of Plant Biology 48(1): 96-105
• 184. Harper G, Osuji JO, Heslop-Harrison JS, Hull R. 1999. Integration of banana streak badnavirus into
the Musa genome: molecular and cytogenetic evidence. Virology 255: 207-
213. doi:10.1006/viro.1998.9581
• 168. Osuji JO, Harrison G, Crouch J, Heslop-Harrison JS. 1997. Identification of the genomic constitution
of Musa L. lines (bananas, plantains and hybrids) using molecular cytogenetics. Annals of Botany 80: 787-
793.

30. From Chromosome to Nucleus
Pat Heslop-Harrison phh4@le.ac.uk www.molcyt.com

31. MuMITE I-8
81,400 81,800 82,200 82,600 83,000 83,400
(B) AC226051
MuMITE II-24
MuMITE I-9
MuMITE II-8 MuMITE II-7 MuMITE II-9 MuMITE II-13 MuMITE II-12 MuMITE II-11 MuMITE II-10
2000 3000 4000 5000 6000 7000 8000 9000 10,000 11,000 12,000 13,000 14,000 15,000 16,000 17,000 18,000 19,000
(A) AC226036

32. Genome evolution
How do genomes evolve?
– Gene mutation very rarely (human: 10−8
/site/generation)
– Chromosome evolution
– Polyploidy and genome duplication (ancient and modern)
– Repetitive sequences: mobility & copy number (10−4
/gen.in µsat)
– Recombination
– Epigenetic aspects – centromeres & expression
How can we exploit knowledge of genome evolution?
– Biodiversity
– Chromosome and genome engineering
– Breeding
– Markers