1 Sequencing Workshop Koln, October 15, 2008 Toni Granell My apologies for not being here Thanks Joyce Chr9 sequencing update Spain

2 Sequencing Workshop Koln, October 15, 2008 SourceSeed BACs selected Cornell University : overgo hybridation (HindIII) 15 Asociación computacional marcador-BE 9 Syngenta 2 Cornell University : overgo hybridation (MboI) 2 Total 28 SourceSeed BACs selected Cornell University : overgo hybridation (MboI) 0 1 Total 8 Syngenta Info PCRs pools IBMCP EXPEN-2000 Syngenta TES Number of Seed BACs available for Chr9 rapidly becoming exhausted Computational Association TES-BE * 5 seed BACs nuevos incorporados en agosto. Situación por determinar. En análisis. 2 Chr9 sequencing update

3 Sequencing Workshop Koln, October 15, 2008 Resumen 66 BACs completed 34 Seed BACs 32 Extension 14 Clones Seq analysis 2 Seed BACs 12 Extension: 9 BACs 3 Fosmids Verification Average insert size : 102 kb (<117 kb) Total pb secuenced*: 6.5 Mb (40%) 96 Clones 42 seed BACs 54 clones de extensión Seed BACs: FPC Syngenta ILs Italy X TES markers search for seed BACs 16 Clones in progress (August) 6 Seed BACs 10 Extension: 5 BACs 5 Fosmids * Last 30 clones not included 19 Clones Finishing (analisis) 4 Clones sequencing pipeline 7 Clones at the library stage Chr9 sequencing update

4 Sequencing Workshop Koln, October 15, 2008 cLEI-10-F11 cM 2 cLET-7-O3 cM 32 Brix9-2-5 cM 37,5 cLET-3-C15 cM 34 C2_At2g37500 cM 37,7 cTOB-1-K3 cM 44 C2_At5g43940 cM 45,7 BACs completed BACs in progress No further extension clones Possibility of extension clones Fosmids in verification Fosmids in progress BACs in verification Estado actual de la secuenciación del Chr9 Number of contigs Number BACs/F forming the contig 42 (1 seed) 83 (1 seed, 1 con 2 seeds) 34 (1 seed, 1 con 2) 25 (1 y 2 seed) (2 y 3 seed) 28 (2 y 3 seed) How are they distributed? cLPT-4-C24 cM 0 9 B T0758 cM 11 TG18 cM 14 TG9 cM 23 CT143 cM 28 T0532 cM 30 Sy cM 37,4 9 9 T0565 cM 52 T1212 cM 48 T1177 cM 46 Sy 16 cM 56,9 At2g29210 cM 55,6 T1416 cM 57T1421 cM 60T1407 cM 61 TG35 cM 63 TES0840 cM 82,2 At3g23400 cM 85 TG424 cM 86 T1519 cM 90 C2_At3g24050 cM 97 CT220 cM 112 TG591 cM 107 T0486 cM 109 Chr9 sequencing update

5 Sequencing Workshop Koln, October 15, 2008 Discrepancy with the progress shown at SGN due to bioinformaticians shortage in our side. Will be fixed in two weeks Seed BACs: all resources basically exhausted. All possible useful markers for euchromatic regions or nearby,have already been screened by in Silico and by PCR on BAC pools 29 dead ends defined as those where in silico or PCR screening on BAC pools failed to find suitable extension BACs or Fosmids 18 possible extension points (10 from BACs, 8 from Fosmids). We dont know yet how useful Fosmids will be (i.e. to extend further with extension BACs). Current effort: too slow and costly. For how long? Other strategies needed Chr9 sequencing update

6 Sequencing Workshop Koln, October 15, 2008 Vicky Fernandez Sheila Zuñiga Fancisco Camara Roderic Guigó Sonia Osorio Clara Pons Amparo Micó Antonio Granell Chr9 sequencing update