PCR products should be sequenced either directly or by first cloning them into a PCR cloning vector.
Sequence data can be analysed using the Basic Local Alignment Search Tool, BLASTN, available at the
National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). If the sequence shares less
than 97.5% identity with its closest relative, the phytoplasma is considered to be a new ‘Candidatus
Phytoplasma’ species. In this case, the entire 16S rRNA gene should be sequenced and phylogenetic
analysis performed. Sequencing a separate region of the genome such as the 16S/23S rRNA spacer
region, secY gene, ribosomal protein genes or the tuf gene is also desirable.