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Specificity analysis Pospiviroid detection method

This study presents a refined detection method for pospiviroids, focusing on the CLVd sequences available in GenBank as of April 2012. Our analysis reveals that the 3' end of the original primer should be shortened by three nucleotides to improve specificity. A new primer, Pospi1Deg-FW, showing 100% similarity with all publicly available CLVd sequences is proposed. The consensus sequence of 358 other pospiviroids is also examined, highlighting the efficacy of the new primer in enhancing detection accuracy, even amidst variations such as mismatches and insertions.

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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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