Revealing new information from existing genomic data for pepper mild mottle virus pathotype determination

Abstract

Primary goals of 21st century science involve eco-friendly solutions for detection, control and suppression of plant viruses. Even though we are accumulating knowledge and data on plant viruses' nucleotide sequences, we are still using a minimum of information available from the collected data. Applying bioinformatics tools and data mining approach to viral sequences is extremely useful in revealing the hidden knowledge, giving guidelines for further biological/bioinformatics studies and developing novel environmental-friendly virus specific defense strategies in crop protection. In this paper we tested to what extent modern bioinformatics methods are able to reveal new information that would bring us closer to our primary goals. On the date of the search (March 2015) we extracted all available PMMoV entries from publically available databases, represented by heterogeneous data set containing 231 nucleotide sequences covering different parts of the PMMoV genome, that were of different geographical origin, related to different time periods, associated with different pathotypes, and were not previously compared to each other. Results revealed that nucleotide content at genomic positions 552, 565, 639, 666, 708, 5921, 5975 and 6002 can be used to discern three distinct PMMoV genotype variants and their association to one of two virus pathotypes, P-1,P-2 or P-1,P-2,P-3. These sites have never been reported as informative before, probably because by being silent mutations they escaped usual research scrutiny of looking for pathotype determinants among nonsense, missense mutations and indels. Our model was further tested in predicting pathotype of ten newly deposited PMMoV sequences and the successful outcome of the test supported the model as an useful asset for discrimination among pathotypes P-1,P-2 and P-1,P-2,P-3 according to distinct nucleotide content in replicase and coat protein encoding genes. Based on the presented results, we also suggested new tests for fast and cost-effective screening of PMMoV pathotypes and eventually for inducing plant resistance against pepper mild mottle virus.