Using Core Genome Alignments To Assign Bacterial Species

Chung, Matthew; Munro, James B.; Tettelin, Hervé; Hotopp, Julie C. Dunning

doi:10.1128/msystems.00236-18

Cited by 70 publications

(57 citation statements)

References 83 publications

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“…Indeed, the digital DNA-DNA hybridization (DDH) [39] higher than 70 indicates that the two strains might belong to the same species (see Methods). The current analysis indicates only wOo with wOv and wMel with wCau having a dDDH higher than 70, representing the same Wolbachia species, as previously suggested [40].…”

Section: Multi-locus Phylogenies and Phylogenomicssupporting

confidence: 83%

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Pseudoscorpion Wolbachia symbionts: Diversity and Evidence for a New Supergroup S

Lefoulon

Clark

Borvető

et al. 2020

Preprint

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Abstract Background Wolbachia are the most widely spread endosymbiotic bacteria, present in a wide variety of insects and two families of nematodes, but so far, relatively little genomic data is available. The Wolbachia symbiont can be a parasite, as described for many arthropods, or an obligate mutualist, as in filarial nematodes. Although, the nature of these symbioses remains largely unknown, diverse Wolbachia genomic data will contribute to understanding their diverse symbiotic mechanisms. Results Our study focuses on Wolbachia infections in pseudoscorpion species collected in Montpellier (France) and indicates two distinct groups of Wolbachia : Geogarypus minor harbors Wolbachia ( w Gmin) and Chthonius ischnocheles harbors Wolbachia ( w Cisc), both related to supergroup H and Atemnus politus harbours Wolbachia ( w Apol), forming a novel divergent clade with Wolbachia from the pseudoscorpion Cordylochernes scorpioides . This later clade forms a new supergroup S, most closely related to Wolbachia supergroups C and F. Our data suggest multiple symbiont acquisition events within the evolutionary history of pseudoscorpions. Using target enrichment by hybridization with Wolbachia -specific biotinylated probes to capture large fragments of Wolbachia DNA, we produced a draft genome of w Apol characterized by a moderate Wolbachia size (1,445,964bp) containing a moderate number of transposable elements and WO bacteriophage insertions (total of 77,522 bp). Conclusions Our analyses indicate that w Apol forms a diverget clade. Annotation highlights complete biochemical pathways which are incomplete in many sequenced Wolbachia genomes, such as vitamin B and the cytochrome bd ubiquinol oxidase pathway. Further, the biotin operon appears to have been horizontally transferred multiple times along the Wolbachia evolutionary history.

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Section: Multi-locus Phylogenies and Phylogenomicssupporting

confidence: 83%

“…(which remains problematic for bacteria [40] Figure S9; Additional file 16, Figure S10). To avoid any confusion, we propose not to reuse the supergroup R [27] Figure 5).…”

Section: Discussionmentioning

confidence: 99%

Pseudoscorpion Wolbachia symbionts: Diversity and Evidence for a New Supergroup S

Lefoulon

Clark

Borvető

et al. 2020

Preprint

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“…3 and Additional file 4. Previous research has shown that the dDDH species cutoff (70%) is generally more stringent than the ANI species cutoff (95%~96%) [55]. Considering the intricacies of BCC taxonomy, we used the 70% dDDH (0.0361 for the recommended GGDC setting) and upper boundary 96% ANI (0.04 for the genome distance) thresholds to reclassify the BCC strains for species delineation, which divided 116 strains into 38 clusters and 36 clusters, respectively.…”

Section: Bcc Species Demarcation Based On Dddh and Animentioning

confidence: 99%

Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status

Yuan¹,

Zhou²,

Zhou³

et al. 2020

Biol Direct

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Background: Accurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research. The taxonomic status of BCC remains problematic and an improved knowledge about the classification of BCC is in particular needed. Methods: We compared phylogenetic trees of BCC based on 16S rRNA, recA, hisA and MLSA (multilocus sequence analysis). Using the available whole genome sequences of BCC, we inferred a species tree based on estimated single-copy orthologous genes and demarcated species of BCC using dDDH/ANI clustering. Results: We showed that 16S rRNA, recA, hisA and MLSA have limited resolutions in the taxonomic study of closely related bacteria such as BCC. Our estimated species tree and dDDH/ANI clustering clearly separated 116 BCC strains into 36 clusters. With the appropriate reclassification of misidentified strains, these clusters corresponded to 22 known species as well as 14 putative novel species. Conclusions: This is the first large-scale and systematic study of the taxonomic status of the BCC and could contribute to further insights into BCC taxonomy. Our study suggested that conjunctive use of core phylogeny based on single-copy orthologous genes, as well as pangenome-based dDDH/ANI clustering would provide a preferable framework for demarcating closely related species. Reviewer: This article was reviewed by Dr. Xianwen Ren.

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“…In fact, almost every Wolbachia 16S amplicon and sequence attributed to A. gambiae is unique, and their diversity spans at least two Wolbachia supergroups (genetic lineages roughly equivalent to species in other bacterial genera, Fig. 3) (40). In combination, we interpret the very low titers and the conflicting phylogenetic affiliations of the sequenced strains as incompatible with the notion of a stable, intraovarially-transmitted Wolbachia symbiont in A. gambiae .…”

Section: Molecular Evidence For Natural Wolbachia In Anopheles Gambiaementioning

confidence: 99%

Is Anopheles gambiae a natural host of Wolbachia?

Chrostek

Gerth

2018

Preprint

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8Wolbachia (Alphaproteobacteria, Rickettsiales) is an intraovarially-transmitted symbiont of 9 insects able to exert striking phenotypes, including reproductive manipulations and pathogen 10 blocking. These phenotypes make Wolbachia a promising tool to combat mosquito-borne diseases. 11Although Wolbachia is present in the majority of terrestrial arthropods, including many disease 12 vectors, it was considered absent from Anopheles gambiae mosquitos, the main vectors of malaria 13 in sub-Saharan Africa. In 2014, Wolbachia sequences were detected in A. gambiae samples 14 collected in Burkina Faso. Subsequently, similar evidence came from collections all over Africa, 15 revealing a high Wolbachia 16S sequence diversity, low abundance, and a lack of congruence 16 between host and symbiont phylogenies. Here, we reanalyze and discuss recent evidence on the 17 presence of Wolbachia sequences in A. gambiae. We find that although detected at increasing 18 frequencies, the unusual properties of these Wolbachia sequences render them insufficient to 19 diagnose natural infections in A. gambiae. Future studies should focus on uncovering the origin of 20 Wolbachia sequence variants in Anopheles and seeking sequence-independent evidence for this 21 new symbiosis. Understanding the ecology of Anopheles mosquitos and their interactions with 22Wolbachia will be key in designing successful, integrative approaches to limit malaria spread. 23 2Although the prospect of using Wolbachia to fight malaria is intriguing, the newly discovered 24 strains do not bring it closer to realization. 25 26 Significance 27 Anopheles gambiae mosquitos are the main vectors of malaria, threatening around half of the 28 world's population. The bacterial symbiont Wolbachia can interfere with disease transmission by 29 other important insect vectors, but until recently it was thought to be absent from natural A. 30 gambiae populations. Here, we critically analyze the genomic, metagenomic, PCR, imaging and 31 phenotypic data presented in support of the presence of natural Wolbachia infections in A.32gambiae. We find that they are insufficient to diagnose Wolbachia infections and argue for the 33 need of obtaining robust data confirming basic Wolbachia characteristics in this system. 34Determining Wolbachia infection status of Anopheles is critical due to its potential to influence 35 Anopheles population structure and Plasmodium transmission. 36 37 42 manipulations, where maternally inherited symbionts favor survival and reproduction of 43 transmitting females over non-infected females and non-transmitting males (2). One of the 44 reproductive manipulations, cytoplasmic incompatibility (CI) (3), has been proposed as a tool to 45 suppress mosquito populations and decrease arbovirus burden on humans (4, 5). Bidirectional CI 46 -the inability of females to produce offspring with males harboring a different Wolbachia strain -47 3 has been successful in eliminating the filariasis vector, Culex pipiens fatigans from Okpo, 48 Myanmar in 1967 (5), and suppres...

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Using Core Genome Alignments To Assign Bacterial Species

Cited by 70 publications

References 83 publications

Pseudoscorpion Wolbachia symbionts: Diversity and Evidence for a New Supergroup S

Pseudoscorpion Wolbachia symbionts: Diversity and Evidence for a New Supergroup S

Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status

Is Anopheles gambiae a natural host of Wolbachia?

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