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Specificity analysis Pospiviroid detection method

Specificity analysis Pospiviroid detection method. Amorce PLCV4f. Logo sequence based on all CLVd sequences available in Genbank at 2012-04-18 Conclusion: problem at the 3’ end. Primer should be shortened by 3 nucleotides.

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Specificity analysis Pospiviroid detection method

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  1. SpecificityanalysisPospiviroiddetectionmethod

  2. Amorce PLCV4f Logo sequencebased on all CLVdsequencesavailable in Genbankat 2012-04-18 Conclusion: problemat the 3’ end. Primer shouldbeshortened by 3 nucleotides. New primer proposed. 100% similaritywith all publiclyavailableCLVdsequences

  3. Amorce Pospi1Deg-FW One mismatchat the 5’ end nucleotidebetween the primer Pospi1Deg-Fw and the 78 CLVdsequencespubliclyavailableat 2012-04-18 Consensus sequence of 358 sequencesof pospiviroidsotherthanCLVd publiclyavailableat 2012-04-18 5’-GGGAKCCCCGGGGMAAC-3’ Pospi1Deg-FW primer sequence: K= G or T; M= A or C

  4. Pospi-RE AGCTTCAGTTGTWTCCACCGGGT TCDVdparfait 16/16 PSTVdparfait 242/248 1mismatch 3/248 (AJ007489, EF459697, AY937480) 2 mismatches1/248 (EU273604) 2 insertions 1/248 (EU879925, EU879926) PMTVd/MPVdparfait 14/14 PCFVd4 mismatches en 5’ 37/37 (publi montre que ça marche?) CSVd parfait 76/76 MPVd et TPMVd parfait 14/14 CEVd parfait 113/222 1 mismatch en 3’ (HQ284024, EF488068, DQ471994) 1 mismatch en 5’ (EF488055, DQ846884) 2 mismatches centre (Y00328) 5 mismatches (AJ490825) TASVd parfait 23/23 IrVd parfait 5/6 1 mismatch en 5’ (DQ846886)

  5. Pospi1Deg-FW GGGAKCCCCGGGGMAAC TCDVdparfait 16/16 PSTVdparfait 242/248 1mismatch 3/248 (AJ007489, EF459697, AY937480) 2 mismatches1/248 (EU273604) 2 insertions 1/248 (EU879925, EU879926) PMTVd/MPVdparfait 14/14 PCFVd4 mismatches en 5’ 37/37 (publi montre que ça marche?) CSVd parfait 76/76 MPVd et TPMVd parfait 14/14 CEVd parfait 113/222 1 mismatch en 3’ (HQ284024, EF488068, DQ471994) 1 mismatch en 5’ (EF488055, DQ846884) 2 mismatches centre (Y00328) 5 mismatches (AJ490825) TASVd parfait 23/23 IrVd parfait 5/6 1 mismatch en 5’ (DQ846886)

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