Highlights

• Creation of the publically available AppIndels.com server.
• Uses unique molecular markers (conserved signature indels) to predict taxonomic affiliation of unknown strains.
  • CSIs are highly reliable markers, and rather than genetic similarity, are based on the presence of rare molecular synapomorphies for taxonomic predictions.
• Successfully predicted the taxonomic affiliation of >700 unclassified strains of Bacillus species, with phylogenomic trees confirming the predictions.

Abstract

Taxon-specific conserved signature indels (CSIs) in genes/proteins provide reliable molecular markers (synapomorphies) for unambiguous demarcation of taxa of different ranks in molecular terms and for genetic, biochemical and diagnostic studies. Because of their predictive abilities, the shared presence of known taxon-specific CSIs in genome sequences has proven useful for taxonomic purposes. However, the lack of a convenient method for identifying the presence of known CSIs in genome sequences has limited their utility for taxonomic and other studies.

We describe here a web-based tool/server (AppIndels.com) that identifies the presence of known and validated CSIs in genome sequences and uses this information for predicting taxonomic affiliation. The utility of this server was tested by using a database of 585 validated CSIs, which included 350 CSIs specific for ≈45 Bacillales genera, with the remaining CSIs being specific for members of the orders Neisseriales, Legionellales and Chlorobiales, family Borreliaceae, and some Pseudomonadaceae species/genera.

Using this server, genome sequences were analysed for 721 Bacillus strains of unknown taxonomic affiliation. Results obtained showed that 651 of these genomes contained significant numbers of CSIs specific for the following Bacillales genera/families: Alkalicoccus, ‘Alkalihalobacillaceae’, Alteribacter, Bacillus Cereus clade, Bacillus Subtilis clade, Caldalkalibacillus, Caldibacillus, Cytobacillus, Ferdinandcohnia, Gottfriedia, Heyndrickxia, Lederbergia, Litchfieldia, Margalitia, Mesobacillus, Metabacillus, Neobacillus, Niallia, Peribacillus, Priestia, Pseudalkalibacillus, Robertmurraya, Rossellomorea, Schinkia, Siminovitchia, Sporosarcina, Sutcliffiella, Weizmannia and Caryophanaceae.

Validity of the taxon assignment made by the server was examined by reconstructing phylogenomic trees. In these trees, all Bacillus strains for which taxonomic predictions were made correctly branched with the indicated taxa. The unassigned strains likely correspond to taxa for which CSIs are lacking in our database. Results presented here show that the AppIndels server provides a useful new tool for predicting taxonomic affiliation based on shared presence of the taxon-specific CSIs. Some caveats in using this server are discussed.

Updates

• 2025-03-28: At present, the server contains 1400+ validated CSIs for an even more diverse group of supported taxa. The list of supported taxa is dynamically updated and can be found here.

Recommended citation: Gupta, R. S., & Kanter-Eivin, D. A. (2023). AppIndels.com server: A web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its genera, 3(5). https://doi.org/10.1099/ijsem.0.005844
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