Revision of the `Candidatus Phytoplasma' species description guidelines

Authors: BERTACCINI, ASSUNTA - University Of Bologna, Italy; AROCHA-ROSETE, YAIMA - Sporometrics, Inc; CONTALDO, NICOLETTA - University Of Bologna, Italy; DUDUK, BOJAN - Institute Of Pestiides And Environmental Protection; FIORE, NICOLA - University Of Chile; GUGLIELMI MONTANO, HELENA - Federal Rural University Of Rio De Janeiro; KUBE, MICHAEL - University Of Hohenheim; KUO, CHIH-HORNG - Academia Sinica; MARTINI, MARTA - University Of Udine; OSHIMA, KENRO - Hosei University; QUAGLINO, FABIO - University Of Milan; SCHNEIDER, BERND - Julius Kuhn Institute; Wei, Wei; ZAMORANO, ALAN - University Of Chile

Submitted to: International Journal of Systematic and Evolutionary Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/11/2022
Publication Date: 4/26/2022
Citation: Bertaccini, A., Arocha-Rosete, Y., Contaldo, N., Duduk, B., Fiore, N., Guglielmi Montano, H., Kube, M., Kuo, C., Martini, M., Oshima, K., Quaglino, F., Schneider, B., Wei, W., Zamorano, A. 2022. Revision of the `Candidatus Phytoplasma' species description guidelines. International Journal of Systematic and Evolutionary Microbiology. 72:005353. https://doi.org/10.1099/ijsem.0.005353.
DOI: https://doi.org/10.1099/ijsem.0.005353

Interpretive Summary: With the advancement of genome sequencing technology, whole genome sequence-based genotypic characterization becomes possible. The whole-genome average nucleotide identity (ANI) has emerged as a robust method for assessing species boundaries and estimating the genetic relatedness between two genomes. In bacteria, an ANI value of 95% to 96% has been generally accepted for circumscribing species. By comparing the sequence similarity values of 16S rRNA gene with whole genome ANI values, previous sequence similarity value of 16S rRNA gene for defining a new species, was evaluated to 98.65%. With the support of the International Committee on Systematics of Prokaryotes (ICSP) Subcommittee, an ARS scientist, in Beltsville Maryland, in collaboration with worldwide scientists revised the guideline for naming Candidatus phytoplasma species which was established in 2004. The new guidelines include: (1) The threshold for 16S rRNA gene sequence similarity for naming a new species is changed from 97.5% to 98.65. (2) The whole genome ANI 95-96% threshold is used to delineate a new species if the genome information is available.

Technical Abstract: The 'Candidatus Phytoplasma' genus was proposed to accommodate cell wall-less bacteria which are molecularly and biochemically incompletely characterized, and colonize plant phloem, and insect vector tissues. This provisional classification is highly relevant due to its application in epidemiological and ecological studies, mainly aimed at keeping the severe phytoplasma plant diseases under control worldwide. Given the increasing discovery of molecular diversity within the 'Ca. Phytoplasma' genus, the proposed guidelines were revised and clarified to accommodate those 'Ca. Phytoplasma' species strains sharing >98.65% sequence identity of their full or nearly full 16S rRNA gene sequences, obtained with at least 2-fold coverage of the sequence, compared with those of the reference strain of such species. Strains sharing <98.65% of sequence identity with the reference strain but >98.65% with other strain(s) within the same 'Ca. Phytoplasma' species should be considered related strains to that 'Ca. Phytoplasma' species. The guidelines herein keep the original published reference strains. However, to improve 'Ca. Phytoplasma' species assignment, complementary strains are suggested as an alternative to the reference strain. This will be implemented when only a partial 16S rRNA gene and/or a few other genes have been sequenced, or the strain is no longer available for further molecular characterization. Lists of 'Ca. Phytoplasma' species and alternative reference strains described are reported. For new 'Ca. Phytoplasma' species that will be assigned with identity =98.65% of their 16S rRNA gene sequences, a threshold of 95% genome-wide average nucleotide identity is suggested. When the whole genome sequences are unavailable, two among conserved housekeeping genes could be used. The officially published 'Candidatus Phytoplasma' species are 49 enclosing 'Ca. P. cocostanzaniae' and 'Ca. P. palmae' described in this manuscript.