noise or symphony: how to address transposable elements? · 25/10/11 marie-anne van sluys...
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25/10/11
Marie-Anne Van Sluysmavsluys@usp.brBotânica – IBUSP
Noise or Symphony: how to address transposable elements?
25/10/11
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?
25/10/11
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?
25/10/11
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
25/10/11
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
%
25/10/11
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?
25/10/11
SUCESTGenes
ADRESSING THE SUGARCANE GENOME
Markers
Allelic variation for breeding
TE COMPONENT
25/10/11
Evolutive considerations on Poaceae
Kellog E (2000) Ann. Rev.Ecol Syst
(4) ~60 MY(8) ~25 MY (C4)(9) ~32-15 My
25/10/11
Evolutive considerations on Poaceae
de Setta Metcalfe, Cruz, Ochoa & Van Sluys, TCG reviews
(4) ~60 MY(8) ~25 MY (C4)(9) ~32-15 My
Click to edit Master subtitle style
25/10/11
50 labs 200 researchers
238000 ESTs43000 Transcripts
The SUCEST EST Sequencing Project
26 libraries - 13 cultivars - Over 90% of sugarcane genes tagged
25/10/11
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
Click to edit Master subtitle style
25/10/11
Current Opinion in Biotechnology; 2011.
Panel of varieties in the current breeding programs is limited.
25/10/11
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
25/10/11 Fabio Nogueira, Renato Vicentini & Guilherme Cruz
Mapping small RNA population onto TE unit
Leaf tissue
25/10/11
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
25/10/11
SUCESTGenes
ADRESSING THE SUGARCANE GENOME
Markers
Allelic variation for breeding
TE COMPONENT
• 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
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