noise or symphony: how to address transposable elements? · 25/10/11 marie-anne van sluys...

25/10/11

Marie-Anne Van [email protected]ânica – IBUSP

Noise or Symphony: how to address transposable elements?

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

Pallen & Wren; Nature 2007

HorizontalGene

Transfer

Pseudogenes

Recombination &

Rearrengement

• Can transposable elements play a role in speciation?

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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. …”

Controlling elements of the gene?

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In the 80`s... Selfish gene or Junk DNA

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Genome size & Complexicity

25,000 genes or 50,000 genes?

(26,000 genes)

(6,000 genes) (13,000 genes)

(18,000 genes)

From: Plant Biochemistry & Molecular Biology Ed: Buchanan 1998

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Transposable elements

> Belong to the repetitive sequences category > Ubiquitous> Constitute significant portions of the eukaryotic genome> Transposon and Retrotransposons are not equally distributed

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.

Species

Con

tribu

ição

rela

tiva

%

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TEcontent

Genomic Islands

Gene Evolution

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Addressing the

Solanaceae GENOME and the

association of Tnt1

superfamily

Func

tion

?

BMC Evolutionary Biology 2007, 7:34 doi:10.1186

Horizon tal gen e tran sfer?

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SUCESTGenes

ADRESSING THE SUGARCANE GENOME

Markers

Allelic variation for breeding

TE COMPONENT

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Evolutive considerations on Poaceae

Kellog E (2000) Ann. Rev.Ecol Syst

(4) ~60 MY(8) ~25 MY (C4)(9) ~32-15 My

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Evolutive considerations on Poaceae

de Setta Metcalfe, Cruz, Ochoa & Van Sluys, TCG reviews

(4) ~60 MY(8) ~25 MY (C4)(9) ~32-15 My

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S. officinarum S. spontaneum Modern sugarcane

D´Hont 2005

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Split between Rice and Sorghum is predicted to be 60 MYA

Click to edit Master subtitle style

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50 labs 200 researchers

238000 ESTs43000 Transcripts

The SUCEST EST Sequencing Project

26 libraries - 13 cultivars - Over 90% of sugarcane genes tagged

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recombinantsS. spontaneum

S. officinarum

2C=10 000 Mb17 000 cM

Main objectives in BIOEN

2n=ca 115

Sugarcane = complex polyploid

•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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Current Opinion in Biotechnology; 2011.

Panel of varieties in the current breeding programs is limited.

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Genetic Similarity (GS) using AFLP and EST-SSRs and coefficient of parentage

2009; Genome (52)191.

25/10/11 Domingues et al, submitted

Mutator lineage

Rossi et al, MGG; 2004Saccaro-Jr et al, Gene; 2007

LTR-RT lineages

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100 BAC sample

0

10

20

30

40

50

60

70

80

90

100

TEs Classification

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25/10/11 Fabio Nogueira, Renato Vicentini & Guilherme Cruz

Mapping small RNA population onto TE unit

Leaf tissue


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hAT-like elements

•Clade I > similar to domesticated element described in Arabidopsis (DAYSLEEPER)…only two copies in

rice genome

•Clade II > Transposon

(Jesus et al, MGG in press)

S > SolanumC > CatasetumA > AnanasO > OryzaZ > ZeaSsSoScSc

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SUCESTGenes


Markers

Allelic variation for breeding

TE COMPONENT

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TE Diversity

Markers

• 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• UFRN: Katia Scortecci (Adilson S Trindade, Amanda Medeiros)• IIEP-Albert Einstein: JP Kitajima

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)

• International Collaborators

> SUGARCANE • EUA:

• Paul Moore, Robin Buell, Ray Ming, Andy Paterson

• France:• Helene Bergers, Angelique

D`Hont• South Africa:

• Bernard Poitier• Australia:

• Rosanne Casu, Kate Aitken, Robert Henry

Acknowledgments > Xanthomonas• EUA:

• Jan E Leach, Adam Bogdanove• France:

• Valerie Verdier• UK:

• Max Dow

> Solanaceae. EUA:

Pal Maliga. France:

MA Grandbastien, Françoise Simon Platz

. UK: Andrew Leitch

noise or symphony: how to address transposable elements? · 25/10/11 marie-anne van sluys...

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