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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 TCDVd parfait 16/16 PSTVd parfait 242/248 1mismatch 3/248 (AJ007489, EF459697, AY937480) 2 mismatches 1/248 (EU273604) 2 insertions 1/248 (EU879925, EU879926) PMTVd/MPVd parfait 14/14 PCFVd 4 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 TCDVd parfait 15/16 1 mismatchnt 6 (DQ859013) PSTVd parfait 221/230 1 mismatch nt 4 (HQ454924)->OK 1 mismatchnt 14 (HQ454931)->peut poser problème 1 insertion entre nt 13-14 (HQ454925)->peu poser problème 1 mismatch nt 14 (FJ797614)->contrôler la signification de R 1 mismatchnt 3 (AY372398)->devrait fonctionner 2 mismatches nt 2 et 3 (AY372394)->devrait fonctionner (séquence de mauvaise qualité?) 1 mismatch nt10 (FM998551)->OK 2 mismatches nt 2 et 3 (DQ308555)->devrait fonctionner (séquence de mauvaise qualité?) 1 déletion nt 13 (E00278)-> potentiellement problématique PMTVd/MPVd parfait 14/14 CLVd 1 mismatch en 5’ pour 79/79 PCFVd parfait 37/38 1 mismatch nt 4 (JF446886)->OK CSVd parfait 74/77 1 mismatch nt1 (FN673554)->OK 1 mismatch nt 1 (FN673553)->OK 4 mismatches nt 2,7,8,9 et 1 insertion nt10 (FN646407)->Pas reconnu (séquence de mauvaise qualité?) MPVd et TPMVd parfait 14/14 CEVd parfait 209/222 1 mismatch nt 5 (HQ452417)->OK 1 insertion entre nt 5-6 (AY372391)->devrait fonctionner 2 mismatches nt3,6 et 4 deletions nt 7 (AY372390)->Pas reconnu (séquence de mauvaise qualité?) 2 insertions nt 11 (EU877744)->problème d’hybridation (séquence de mauvaise qualité?) 2 insertions nt 11 (EU877745)->problème d’hybridation (séquence de mauvaise qualité?) 1 mismatch nt4 (DQ431992)->OK 1 mismatch nt 4 (DQ431993)->OK 2 mismatches nt10,11 (DQ431991)->OK 2 insertions nt 11 (DQ400342)->problème d’hybridation 1 insertion nt 11 (AY523584)->problème d’hybridation 3 mismatches nt 1,4,6 (AY517494)->problème d’hybridation 2 mismatchesnt 1,4 (AF434678)->problème d’hybridation 1 mismatch nt 7 (K00965)->OK TASVdparfait 22/23 1 deletion nt 13 (AY062121)->OK IrVd parfait 5/5

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