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Transposable elements in Melampsora larici-populina genome

Transposable elements in Melampsora larici-populina genome. Melampsora Genome Consortium 2008 Summer Workshop. Marie-Pierre Oudot-Le Secq. INRA-Nancy, August 20-21 2008. Outline. Transposable elements Main types characteristics Nomenclature TE annotation Annotation pipe-line

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Transposable elements in Melampsora larici-populina genome

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

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

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

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

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

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

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

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

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

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

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

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

  13. 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 MGC Summer Workshop INRA-Nancy, August 20-21 2008

  14. LTR Consensus 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...

  15. TIR Consensus 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%

  16. Mapping on genome

  17. example of nested elements

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