Chimera alert! The threat of chimeric sequences causing inaccurate taxonomic classification of phytoplasma strains

Abstract

AbstractThe 16S rRNA gene is a primary marker used to study bacterial taxonomy, particularly for bacteria with ‘Candidatus’ status, where it serves as a primary reference sequence for identification. Despite its usefulness, ensuring the authenticity of publicly available sequences has always posed a challenge. To address this issue, multiple tools and databases with curated collections of reference 16S rRNA gene sequences were established. However, even with these efforts, many sequence chimeras still exist. These chimeric gene sequences are formed by the fusion of sequence parts from multiple organisms and can arise from errors during PCR amplification or sequencing. The objective of this study was to identify chimeric sequences from a dataset of over 4500 phytoplasma 16S rRNA gene sequences using multiple tools. The tools ChimeraSlayer and UCHIME identified 12 and 11 chimeric sequences, respectively. Notably, these sequences included the reference 16S rRNA gene sequence of ‘Ca. Phytoplasma wodyetiae’ strain Bangi-2 (KC844879) and ‘Ca. Phytoplasma allocasuarinae’ (AY135523). The study’s outcomes indicated the existence of chimeric 16S rRNA gene sequences, emphasizing the threat posed by such sequences in correctly assigning taxonomic status to phytoplasma strains. These findings underscore the importance of rigorously verifying the authenticity of 16S rRNA gene sequences to ensure their accuracy in identifying and classifying bacterial species.