Molecular Markers Specific for the Genera Provide Novel and Reliable Means for the Identification of Other Strains/spp. Related to These Genera

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2025 Feb 26

PMID 40004512

Authors

Bashudev Rudra

Radhey S Gupta

Affiliations

Soon will be listed here.

Abstract

Taxon-specific conserved signature indels (CSIs) exhibit a strong predictive ability of being found in other members of specific taxa/genera. Recently, multiple exclusively shared CSIs were identified for several newly described genera (viz. , , , , , , , , , , , and ). This study examines the potential applications of these CSIs for identifying other spp. (strains) related to these genera. This work utilized the AppIndels.com server, which uses information regarding the presence of known taxon-specific CSIs in a genome for predicting its taxonomic affiliation. For this purpose, sequence information for different CSIs specific for the species/genera were added to the server's database. The AppIndels server was used to predict the taxonomic affiliation of 1972 genomes of unclassified spp. (strains/isolates). Based upon finding a significant number of CSIs matching a specific taxon, the AppIndels server made positive predictions regarding the taxonomic affiliation of 299 examined genomes into the following clades/genera: clade (46), (64), (46), (32), (31), (22), (21), (17), (9), (4), (3), (2), and and (1 each). Phylogenetic studies confirmed that the taxonomic predictions by the server were 100% accurate. Our results demonstrate that the CSIs specific for species/genera, in conjunction with the AppIndels server, provides a novel and useful tool for identifying other species/strains affiliated with these species/genera. Phylogenetic studies suggest that many examined strains constitute novel species in the indicated genera.

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