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• W2950197287 abstract "With the exponential increase in the number of bacterial taxa with genome sequence data, a new standardized method to assign species designations is needed that is consistent with classically obtained taxonomic analyses. This is particularly acute for unculturable, obligate intracellular bacteria with which classically defined methods, like DNA-DNA hybridization, cannot be used, such as those in the Rickettsiales. In this study, we generated nucleotide-based core genome alignments for a wide range of genera with classically defined species, as well as those within the Rickettsiales. We created a workflow that uses the length, sequence identity, and phylogenetic relationships inferred from core genome alignments to assign genus and species designations that recapitulate classically obtained results. Using this method, most classically defined bacterial genera have a core genome alignment that is ≥10% of the average input genome length. Both Anaplasma and Neorickettsia fail to meet this criterion, indicating that the taxonomy of these genera should be reexamined. Consistently, genomes from organisms with the same species epithet have ≥96.8% identity of their core genome alignments. Additionally, these core genome alignments can be used to generate phylogenomic trees to identify monophyletic clades that define species and neighbor-network trees to assess recombination across different taxa. By these criteria, Wolbachia organisms are delineated into species different from the currently used supergroup designations, while Rickettsia organisms are delineated into 9 distinct species, compared to the current 27 species. By using core genome alignments to assign taxonomic designations, we aim to provide a high-resolution, robust method to guide bacterial nomenclature that is aligned with classically obtained results. IMPORTANCE With the increasing availability of genome sequences, we sought to develop and apply a robust, portable, and high-resolution method for the assignment of genera and species designations that can recapitulate classically defined taxonomic designations. Using cutoffs derived from the lengths and sequence identities of core genome alignments along with phylogenetic analyses, we sought to evaluate or reevaluate genus- and species-level designations for diverse taxa, with an emphasis on the order Rickettsiales, where species designations have been applied inconsistently. Our results indicate that the Rickettsia genus has an overabundance of species designations, that the current Anaplasma and Neorickettsia genus designations are both too broad and need to be divided, and that there are clear demarcations of Wolbachia species that do not align precisely with the existing supergroup designations." @default.
• W2950197287 created "2019-06-27" @default.
• W2950197287 creator A5024171828 @default.
• W2950197287 creator A5039491087 @default.
• W2950197287 creator A5075044494 @default.
• W2950197287 creator A5084925508 @default.
• W2950197287 date "2018-10-30" @default.
• W2950197287 modified "2023-10-13" @default.
• W2950197287 title "Using Core Genome Alignments To Assign Bacterial Species" @default.
• W2950197287 cites W1135492795 @default.
• W2950197287 cites W1569904835 @default.
• W2950197287 cites W1600857725 @default.
• W2950197287 cites W1977301455 @default.
• W2950197287 cites W1977558436 @default.
• W2950197287 cites W1983412522 @default.
• W2950197287 cites W1991330646 @default.
• W2950197287 cites W2008856488 @default.
• W2950197287 cites W2020284185 @default.
• W2950197287 cites W2027558100 @default.
• W2950197287 cites W2030964004 @default.
• W2950197287 cites W2034285706 @default.
• W2950197287 cites W2038357425 @default.
• W2950197287 cites W2039400507 @default.
• W2950197287 cites W2039805990 @default.
• W2950197287 cites W2041564020 @default.
• W2950197287 cites W2044055478 @default.
• W2950197287 cites W2044074704 @default.
• W2950197287 cites W2050158427 @default.
• W2950197287 cites W2061880687 @default.
• W2950197287 cites W2064641442 @default.
• W2950197287 cites W2078096656 @default.
• W2950197287 cites W2087076382 @default.
• W2950197287 cites W2096404721 @default.
• W2950197287 cites W2097477547 @default.
• W2950197287 cites W2101305165 @default.
• W2950197287 cites W2107282968 @default.
• W2950197287 cites W2108093581 @default.
• W2950197287 cites W2108718991 @default.
• W2950197287 cites W2111647009 @default.
• W2950197287 cites W2116206245 @default.
• W2950197287 cites W2116913446 @default.
• W2950197287 cites W2117040787 @default.
• W2950197287 cites W2117043113 @default.
• W2950197287 cites W2117801354 @default.
• W2950197287 cites W2118442768 @default.
• W2950197287 cites W2123735523 @default.
• W2950197287 cites W2123799144 @default.
• W2950197287 cites W2124351063 @default.
• W2950197287 cites W2126006180 @default.
• W2950197287 cites W2126161931 @default.
• W2950197287 cites W2127036970 @default.
• W2950197287 cites W2127303481 @default.
• W2950197287 cites W2127774996 @default.
• W2950197287 cites W2128784468 @default.
• W2950197287 cites W2129637857 @default.
• W2950197287 cites W2130706420 @default.
• W2950197287 cites W2130706942 @default.
• W2950197287 cites W2131184698 @default.
• W2950197287 cites W2134650310 @default.
• W2950197287 cites W2141047744 @default.
• W2950197287 cites W2142503351 @default.
• W2950197287 cites W2142678478 @default.
• W2950197287 cites W2143420371 @default.
• W2950197287 cites W2150550043 @default.
• W2950197287 cites W2151409320 @default.
• W2950197287 cites W2154026962 @default.
• W2950197287 cites W2156273926 @default.
• W2950197287 cites W2159008215 @default.
• W2950197287 cites W2164786886 @default.
• W2950197287 cites W2166659140 @default.
• W2950197287 cites W2169895835 @default.
• W2950197287 cites W2291091413 @default.
• W2950197287 cites W2321224938 @default.
• W2950197287 cites W2336330109 @default.
• W2950197287 cites W2344940607 @default.
• W2950197287 cites W2555257828 @default.
• W2950197287 cites W2582104246 @default.
• W2950197287 cites W2588775853 @default.
• W2950197287 cites W2598646915 @default.
• W2950197287 cites W2614081736 @default.
• W2950197287 cites W2771107535 @default.
• W2950197287 cites W2781065955 @default.
• W2950197287 cites W2781763834 @default.
• W2950197287 cites W2889019390 @default.
• W2950197287 cites W2951464304 @default.
• W2950197287 cites W4242729757 @default.
• W2950197287 cites W4249747683 @default.
• W2950197287 cites W626926365 @default.
• W2950197287 cites W67428209 @default.
• W2950197287 doi "https://doi.org/10.1128/msystems.00236-18" @default.
• W2950197287 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/6280431" @default.
• W2950197287 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/30534598" @default.
• W2950197287 hasPublicationYear "2018" @default.
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