Comparative genome analysis of different strains of phytoplasma

Abstract

Candidatus Phytoplasma Mali (Project ID: 25335, at Federal Biological Research Center for Agriculture and Forestry), and Onion yellows phytoplasma OY-M (Project ID: 13750, at The University of Tokyo) genomes were retrieved from NCBI Genome database (http://www. ncbi. nlm. nih. gov/). The protein coding potential of genomes were determined using web online software GeneMark-hmm-p by using species specific parameters of the Markov models of coding and non-coding regions (7). This approach allows delineating local variations of coding potential. A graph also is available which shows details of the protein-coding potential distribution along a sequence. The Open Reading Frames (ORFs) predicted by GeneMark were compared with ORF Finder software in NCBI server. Molligen 2.0, a complete bacterial genome analysis server with genome data and tools, is used for phytoplasma genome annotation (6). Pairwise genome alignment and protein homologous analysis were done using different tools in the same server. ClustalX, a standalone multiple sequence alignment (MSA) software is used to find closely related proteins from multiple homology and these proteins were identified by ClustalX tool TreeView. Uneven distribution (skew) of GC content were determined followed by origin of replication site prediction is done using GenSkew software in MIPS server (http://mips. helmholtzmuenchen. de/services/analysis/genskew).