1. Transposable elements in Melampsora larici-populina genome Marie-Pierre Oudot-Le Secq Melampsora Genome Consortium 2008 Summer Workshop Melampsora Genome Consortium 2008 Summer Workshop INRA-Nancy, August 20-21 2008

2. MGC Summer Workshop INRA-Nancy, August 20-21 2008 Outline 1.Transposable elements 1.Main types characteristics 2.Nomenclature 2.TE annotation 1.Annotation pipe-line 2.Manual curation

3. MGC Summer Workshop INRA-Nancy, August 20-21 2008 « mobile DNA segments in the genome » Eubacteria - Archaebacteria - Eukaryotes Impact on the host genome 1.Transposable elements

4. MGC Summer Workshop INRA-Nancy, August 20-21 2008 2 classes Transposition 1. Transposable elements 1.1. Main types characteristics RNA: Class I « Retrotransposons » Reverse Transcriptase Copy-and-paste DNA: Class II « DNA transposons » Transposase Cut-and-paste

5. Nature reviews Genetics Wicker et al. December 2007 1. Transposable elements 1.2. Nomenclature

6. MGC Summer Workshop INRA-Nancy, August 20-21 2008 1. Transposable elements 1.2. Nomenclature

7. MGC Summer Workshop INRA-Nancy, August 20-21 2008 1. Transposable elements 1.2. Nomenclature

8. MGC Summer Workshop INRA-Nancy, August 20-21 2008 2.TE annotation Starting point: TE annotation pipe-line result Ran on the previous assembly of Melampsora larici- populina genome Timothé Flutre, Elodie Duprat and Hadi Quesneville

9. MGC Summer Workshop INRA-Nancy, August 20-21 2008 Grouper Connected HSPs Matcher Gathering of repeated sequences and making consensus out of them Gathering of repeated sequences and making consensus out of them Consensus Lucy Groups of repeated sequences RECON PILER RECON PILER Pairwise alignments Blaster Set of sequences Multiple alignments Multiple alignments 2. TE annotation 2.1. TE pipe-line Timothé Flutre, Elodie Duprat and Hadi Quesneville

10. MGC Summer Workshop INRA-Nancy, August 20-21 2008 Structural annotation RepBaseUpdate proteins RepBaseUpdate proteins Functional annotation Consensus TIR, LTR Poly A tail SSR Putative ORFs Consensus characterization Known TE associated ORFs 2. TE annotation 2.1. TE pipe-line Timothé Flutre, Elodie Duprat and Hadi Quesneville RepBaseUpdate nucleotides RepBaseUpdate nucleotides Characterized consensus Characterized consensus

11. MGC Summer Workshop INRA-Nancy, August 20-21 2008 2.1. TE pipe-line 2. TE annotation

12. MGC Summer Workshop INRA-Nancy, August 20-21 2008 2.2. Manual curation Checking the consensus Blasts of consensus on genomic sequence Checking of the result on Artemis: refining elements detection and fine annotation of nested elements 2. TE annotation Annotation of elements

13. MGC Summer Workshop INRA-Nancy, August 20-21 2008 Number of consensus in Melampsora Number of LTRcomp: 13 Number of LTRuncomp: 0 Number of LARD: 17 Number of LINEcomp: 32 Number of LINEuncomp: 0 Number of SINE: 536 Number of TIRcomp: 180 Number of TIRuncomp: 117 Number of MITE: 212 (+ 107) Number of Helitron: 0 Number of Polinton: 0 Number of confused: 1372 Number of NoCat: 4616

14. Fine checking and annotation of scaffold_1: other full elements found => 2 rounds of blast/annotation At the moment: 2660 (full and partial) covering 7.855.502 bp => 7.77% From original consensus: Order LTR:6 Copia 7 Gypsy Order DIRS... LTR Consensus

15. Original consensus: 12 Tc1/Mariner 28 hAT 3 Mutator 15 harbinger 19 undefined 107 without blast hits or caracteristic ORF=> « MITE » Raw mapping: 4159 (full and partial) covering 12.046.646 bp => 11.92% TIR Consensus

16. Mapping on genome

17. example of nested elements