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Chr9 Sequencing Update in Spain: Limited Resources and Need for New Strategies

This update provides information on the progress of Chr9 sequencing in Spain, including the exhaustion of available seed BACs, PCR pools, and computational analysis. The update also highlights the need for new strategies to overcome challenges and improve the efficiency of the sequencing process.

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Chr9 Sequencing Update in Spain: Limited Resources and Need for New Strategies

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  1. Chr9 sequencing update Spain • Toni Granell • My apologies for not being here • Thanks Joyce

  2. 2007 2008 Chr9 sequencing update Number of Seed BACs available for Chr9 rapidly becoming exhausted Syngenta Info 3 PCRs pools IBMCP EXPEN-2000 Syngenta TES 2 0 2 Computational Association TES-BE * 5 seed BACs nuevos incorporados en agosto. Situación por determinar. En análisis.

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

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

  5. Chr9 sequencing update • 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

  6. Chr9 sequencing update • Vicky Fernandez • Sheila Zuñiga • Fancisco Camara • Roderic Guigó • Sonia Osorio • Clara Pons • Amparo Micó • Antonio Granell

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