Comparison of the ribosomal RNA operon from Texas Phoenix decline and lethal yellowing phytoplasmas

Abstract

A comparison was made of the two palm yellows phytoplasmas affecting palms to determine if the entire ribosomal RNA operon portion of the phytoplasma genome, or portions thereof, could account for the observed palm host differences. Polymerase chain reaction (PCR) was used to amplify a 5.0 kb DNA fragment consisting of the entire ribosomal RNA operon from a subgroup 16SrIV-D phytoplasma that causes Texas Phoenix palm decline (TPD) in cabbage (Sabal palmetto) palm in west central Florida and from a subgroup 16SrIV-A phytoplasma that causes lethal yellowing (LY) in coconut (Cocos nucifera) palm in Jamaica. Before the PCR reaction, we sequenced by 454 sequencing a draft genome of the coconut LY phytoplasma, strain LYFL, that infects C. nucifera in Florida, and obtained from this draft sequence both copies of the entire ribosomal operon. Sequence analysis of the ribosomal RNA operons from both the LY and TPD phytoplasmas revealed the gene composition and orientation for the operons to be 5′16S rRNA-tRNAIle-23S rRNA-5S rRNA3′ and a tRNAVal3′ downstream of the 5S rRNA gene. Based on molecular comparisons using the sequences of the ribosomal RNA operon, the TPD (16SrIV-D) strain was 98 % similar to the LY (16SrIV-A) strains.