Noise or Symphony: how to address
transposable elements?
Marie-Anne Van Sluys
[email protected]
Botânica – IBUSP
25/10/11
Biodiversity
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How can biodiversity be generated?
•
Cellular organisms (Eukarya - Bacteria – Archea)
•
Similar trends
–
Gene gain
–
Gene loss
–
Gene change
•
Whole genome duplication
•
Sex & Recombination
•
Horizontal
Gene
Transfer
Pseudogenes
Recombination
&
Rearrengement
Can transposable elements play a role in speciation?
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Pallen & Wren; Nature 2007
Transposable elements...
“… I believe we are again
experiencing such a revolution.
It is altering our concepts of
the GENOME: its component
parts, their organization,
mobilities and their mode of
operation. …”
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Controlling elements of the gene?
In the 80`s... Selfish gene or Junk DNA
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Genome size & Complexicity
(26,000 genes)
(6,000 genes)
(18,000 genes)
(13,000 genes)
25,000 genes or 50,000 genes?
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From: Plant Biochemistry & Molecular Biology Ed: Buchanan 1998
Transposable elements
Belong to the repetitive sequences category
Ubiquitous
Constitute significant portions of the eukaryotic genome
Transposon and Retrotransposons are not equally distributed
Contribuição relativa %
>
>
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Species
Sc: Saccharomyces cerevisiae; Sp: Schizosaccharomyces pombe; Hs: Homo sapiens; Mm: Mus musculus; Os: Oryza sativa; Ce: Caenorhabditis elegans; Dm:
Drosophila melanogaster; Ag: Anopheles gambiae, malaria mosquito; Aa: Aedes aegypti, yellow fever mosquito; Eh: Entamoeba histolytica; Ei: Entamoeba invadens; Tv:
Trichomonas vaginalis.
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Gene Evolution
Genomic
Islands
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TE
content
Horizontal gene transfer?
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Addressing
the
Solanaceae
GENOME
and the
association
of Tnt1
superfamily
Function?
BMC Evolutionary Biology 2007, 7:34 doi:10.1186
ADRESSING THE SUGARCANE GENOME
Allelic variation for
breeding
Markers
SUCEST
Genes
TE COMPONENT
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Evolutive considerations on Poaceae
(4) ~60 MY
(8) ~25 MY (C4)
(9) ~32-15 My
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Kellog E (2000) Ann. Rev.Ecol Syst
Evolutive considerations on Poaceae
(4) ~60 MY
(8) ~25 MY (C4)
(9) ~32-15 My
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de Setta Metcalfe, Cruz, Ochoa & Van Sluys, TCG reviews
S. officinarum
S. spontaneum
D´Hont 2005
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Modern sugarcane
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Split between
Rice and Sorghum
is predicted to be
60 MYA
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The SUCEST EST Sequencing Project
Click to edit Master subtitle style
50 labs
238000 ESTs
200 researchers
43000 Transcripts
26 libraries - 13 cultivars - Over 90% of sugarcane genes tagged
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Main objectives in BIOEN
2C=10 000 Mb
17 000 cM
S. spontaneum
S. officinarum
recombinants
Sequence 1000 BACs of selected
regions
•
300 from R570 ✔
•
700 from SP80-3280
•
1x shotgun coverage of SP80-3280
(PI G Souza)
•
Alellic variation & Gene content
•
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Sugarcane = complex polyploid
2n=ca 115
Current Opinion in Biotechnology; 2011.
Panel of varieties in the
current breeding programs is
limited.
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2009; Genome (52)191.
Genetic Similarity (GS) using AFLP and EST-SSRs and coefficient of parentage
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LTR-RT lineages
Mutator lineage
Rossi et al, MGG; 2004
Saccaro-Jr et al, Gene; 2007
Domingues et al, submitted
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100 BAC sample
TEs Classification
100
90
80
70
60
50
40
30
20
10
0
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Mapping small RNA population onto TE unit
Leaf tissue
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Fabio Nogueira, Renato Vicentini & Guilherme Cruz
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Click to edit Master subtitle style
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hAT-like elements
S > Solanum
C > Catasetum
A > Ananas
O > Oryza
Z > Zea
Ss
So
Sc
Sc
Clade I > similar to domesticated
element described in Arabidopsis
(DAYSLEEPER)…only two copies in
rice genome
•
Clade II > Transposon
•
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(Jesus et al, MGG in press)
ADRESSING THE SUGARCANE GENOME
Allelic variation for
breeding
Markers
SUCEST
Genes
TE COMPONENT
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ADRESSING THE SUGARCANE GENOME
Markers
TE Diversity
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Acknowledgments
(Nathalia de Setta, Cushla Mercalfe, Robson F de Souza, Eduardo
Arantes, Guilherme MQ Cruz, E Andres O Cruz, Andreia Prata, Mayra
Kuroki, Jonas Gaiarsa, Erika de Jesus, Danielle Quintanilha)
•
•
USP:
•
IQ > Glaucia Souza (Carlos Hotta, Roberta Campos, Paloma, Carolina, Milton)
•
ESALQ > Claudia M Vitorello; AA Garcia; ML Carneiro (Alessandra Alves)
UNICAMP:
•
Michel Vincentz (Mariane Vilela, LE Delben)
•
Renato Vicentini
•
Anete P de Souza
•
UNESP: Fabio T Nogueira (Cristiane s Alves)
•
UFSCAR: Monalisa Sampaio
•
IAC: Silvana Crestes
Acknowledgments
•
International Collaborators
> Xanthomonas
•
EUA:
•
> SUGARCANE
•
EUA:
•
Paul Moore, Robin Buell, Ray
Ming, Andy Paterson
•
Helene Bergers, Angelique
D`Hont
South Africa:
•
•
France:
•
•
Bernard Poitier
Australia:
•
Rosanne Casu, Kate Aitken,
Robert Henry
Valerie Verdier
UK:
•
France:
•
•
•
Jan E Leach, Adam Bogdanove
Max Dow
> Solanaceae
. EUA:
Pal Maliga
. France:
MA Grandbastien, Françoise
Simon Platz
. UK:
Andrew Leitch