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From sequences to species: Charting the phytoplasma classification and taxonomy in the era of taxogenomics

Authors :
Kiran Kirdat
Bhavesh Tiwarekar
Shivaji Sathe
Amit Yadav
Source :
Frontiers in Microbiology. 14
Publication Year :
2023
Publisher :
Frontiers Media SA, 2023.

Abstract

Phytoplasma taxonomy has been a topic of discussion for the last two and half decades. Since the Japanese scientists discovered the phytoplasma bodies in 1967, the phytoplasma taxonomy was limited to disease symptomology for a long time. The advances in DNA-based markers and sequencing improved phytoplasma classification. In 2004, the International Research Programme on Comparative Mycoplasmology (IRPCM)- Phytoplasma/Spiroplasma Working Team – Phytoplasma taxonomy group provided the description of the provisional genus ‘Candidatus Phytoplasma’ with guidelines to describe the new provisional phytoplasma species. The unintentional consequences of these guidelines led to the description of many phytoplasma species where species characterization was restricted to a partial sequence of the 16S rRNA gene alone. Additionally, the lack of a complete set of housekeeping gene sequences or genome sequences, as well as the heterogeneity among closely related phytoplasmas limited the development of a comprehensive Multi-Locus Sequence Typing (MLST) system. To address these issues, researchers tried deducing the definition of phytoplasma species using phytoplasmas genome sequences and the average nucleotide identity (ANI). In another attempts, a new phytoplasma species were described based on the Overall Genome relatedness Values (OGRI) values fetched from the genome sequences. These studies align with the attempts to standardize the classification and nomenclature of ‘Candidatus’ bacteria. With a brief historical account of phytoplasma taxonomy and recent developments, this review highlights the current issues and provides recommendations for a comprehensive system for phytoplasma taxonomy until phytoplasma retains ‘Candidatus’ status.

Details

ISSN :
1664302X
Volume :
14
Database :
OpenAIRE
Journal :
Frontiers in Microbiology
Accession number :
edsair.doi...........a20cf5b660fc2cbaa694412c5c055b37
Full Text :
https://doi.org/10.3389/fmicb.2023.1123783