Genomics of ‘ca’ Phytoplasma Vitis ‘FD’ and Related Strains in Silico

Abstract

The current achievements and limitations of the genetics and genomics of ‘ca. Phytoplasma vitis Flavescence Dorée phytoplasma ‘FDp’ are reviewed and discussed here. The name originated from the Fr. flavescence (yellowing), and Fr. dorée (golden), the ‘ca.’ prefix stands for candidatus. The genetics of related Phytoplasma and Mycoplasma isolates are also discussed. Complete Phytoplasma genomes were compared in silico to follow the evolutionary scaled geneloss and genome reductions. DNA sequences of Prophages and PMUs (Potential Mobile Units) of Phytoplasma genomes were analyzed. The Phytoplasma GeneBank entries and the possible molecular cross reactions are discussed. Sequence parts of Phytoplasma strains were found to obviously show sequence similarities to bacteria and plant organelle genomes of cpDNA and mtDNA which have prokaryotic origins from α-ProteoBacteria. The continuous horizontal gene transfers (HGT; i.e., influx of organellar DNA to nuclear genome; cytonuclear interactions) from plant organelles cpDNA and mtDNA to nuclear genomes (2n), including genes of 16S rRNA, ftsH and all homolog (ortholog and paralog) and analog genes were suggested to provide multiplied sequence targets with putative cross reactions to Phytoplasma identification. TimeTree of Life analysis of two infected host plants of Vitis and Solanum attractive to ‘ca. Ph. vitis FD’ and ‘ca. Ph. solani BN’ showed ˃60 MY (Vitis) and >150 MY (Solanum) times in the history of evolution which indicated different time period exposed to Phytoplasma infections. The data presented here highlights the importance of the identification of further Phytoplasma secreted proteins, the need for new serological and plant symptoms analyses, the use of Microgenomics by single cell Laser MicroDissection (LMD) technology, single cell genomics (CSG), and the possibility of in vitro cultivation of ‘ca.’ Phytoplasma strains to elimination ‘ca.’ prefix.