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Frédéric CHOULET A pseudomolecule of 774 Mb: the 3B experience INRA GDEC – Clermont-Ferrand, France.

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Presentation on theme: "Frédéric CHOULET A pseudomolecule of 774 Mb: the 3B experience INRA GDEC – Clermont-Ferrand, France."— Presentation transcript:

1 Frédéric CHOULET A pseudomolecule of 774 Mb: the 3B experience INRA GDEC – Clermont-Ferrand, France

2 3B Sequenced physical map  #MTP BACs 8452  3B MTP-BAC sequencing  #BAC pools 922  #Roche 8 kb MP lib. 922  bp coverage (Roche/454) 36x  BAC-ends (Sanger) 42,551  Whole Genome Prof. tags 327,282  Whole 3B shotgun (Illumina) 82x

3  #BACs  #BAC-contigs Physical map 132,000 (19x) 1282  #MTP-BACs B 900 Mb 3B physical map

4 ACGTAGACTACA 3B  Assembly and scaffolding 3B-v1 16,136 scaff 1,040 Mb

5 o Curation of the scaffolding V. Barbe, S. Mangenot (Genoscope)  Assembly and scaffolding  Integration of BAC-end match positions  Parsing of MP read positions scaff00001scaff00013 scaff00024scaff00008 scaff00011 scaff00007 scaff B-v1 16,136 scaff 1,040 Mb 18% Ns 3B-v3 4,999 scaff 992 Mb 13% Ns

6 o Curation of the scaffolding V. Barbe, S. Mangenot (Genoscope)  Assembly and scaffolding 3B-v3 4,999 scaff 992 Mb 13% Ns 3B-v1 16,136 scaff 1,040 Mb o Gap filling o Seq. error corrections JM. Aury, A. Couloux (Genoscope) Illumina reads Whole 3B Shotgun  109,914 gaps filled  126,290 bases corrected (error rate: 0.1%) 18% Ns 3B-v % Ns

7 o Curation of the scaffolding V. Barbe, S. Mangenot (Genoscope)  Assembly and scaffolding 3B-v1 16,136 scaff 1,040 Mb o Gap filling o Seq. error corrections JM. Aury, A. Couloux (Genoscope) o Redundancy removal and scaffold merging S. Theil (INRA GDEC) Pool_A Pool_B ctg1 ctg2 2,808 scaff 833 Mb 3B-v443 scaffAssembler.pl 3B-v4 4,999 scaff 992 Mb redundancy: 160 Mb

8 Search for shared TE-junctions

9  Ordering scaffolds 2,808 scaff 833 Mb 3B-v443 o SNP discovery Bait TE DNA captured from 10 genotypes gene  52,265 baits isbpProbeDesign.pl  39,077 SNPs SureSelect® seq. capture (E. Paux, N. Cubizolles, E. Rey)

10  Ordering scaffolds o SNP discovery  Genetic mapping (P. Sourdille) + Neighbor map: 3865 markers  LD mapping (F. Balfourier) Anchor map: 384 indiv Cs x Renan o Genotyping mapping pop  3,075 SNPs 367 lines from a core-collection

11 3B  Ordering scaffolds genetic map 44.8 cM 152 scaffolds LD map 19 LD blocks 366 bins 0 cM133 cM 554 bins

12 64 markers at the same genetic position Linkage Disequilibrium

13  Ordering scaffolds pseudomolBuilder.pl 1358 scaff 774 Mb pseudomolecule unlocalized 1450 scaff 59 Mb 93% 7% NNNNNNNN o SNP discovery o Genotyping mapping pop o Integration of phys. map info

14 3cM ABCDE o orientation unknown: 48% of the seq. o micro-order unknown: 554 bins / 1358 scaff ?? o RH map o Optical map o Long reads  Future Improvements ?

15 7264 protein coding genes TRIANNOT 234,606 TEs CLARI-TE 774 Mb  Annotation

16  Bioinformatics  Scaffolding/pseudomolecule construction  scaffAssembler.pl  Annotation  gapCloser  ssrFinishing  triAnnot (new modules: filtering, pseudogenes, transfer annotation)  clari-TE & clari-TE-lib  Data management  gowDB (Bio::DB::seqFeatureStore)  URGI  pseudomolBuilder.pl  isbpProbeDesign.pl  Assembly  Newbler

17 3B-MTP 3B-CSS  Pseudomolecule vs GenomeZipper

18 Sébastien Theil Natasha Glover Josquin Daron Lise Pingault Pierre Sourdille Etienne Paux Philippe Leroy Jacques Le Gouis Nicolas Guilhot Aurélien Bernard Nelly Cubizolles Catherine Feuillet François Balfourier M. Alaux L. Couderc V. Jamilloux H. Quenesville URGI H. Berges A. Bellec CNRGV BIA A. Alberti V. Barbe J. Poulain C. Durand S. Mangenot JM. Aury A. Couloux P. Wincker Genoscope J. Dolezel J. Safar IEB K. Vandepoele K. Mayer et al. P. Schnable S. Rounsley D. Ware C. Gaspin SAB VIB MIPS Acknowledgments Hélène Rimbert TGAC J. Rogers, M. Caccamo et al. J. Rogers K. Eversole


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