scholarly journals Using Core Genome Alignments To Assign Bacterial Species

mSystems ◽  
2018 ◽  
Vol 3 (6) ◽  
Author(s):  
Matthew Chung ◽  
James B. Munro ◽  
Hervé Tettelin ◽  
Julie C. Dunning Hotopp
Keyword(s):  
High Resolution ◽  
Core Genome ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Distinct Species ◽  
Obligate Intracellular ◽  
Wide Range ◽  
Obligate Intracellular Bacteria ◽  
Neighbor Network

ABSTRACTWith 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 theRickettsiales. 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 theRickettsiales. 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. BothAnaplasmaandNeorickettsiafail 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,Wolbachiaorganisms are delineated into species different from the currently used supergroup designations, whileRickettsiaorganisms 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.IMPORTANCEWith 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 orderRickettsiales, where species designations have been applied inconsistently. Our results indicate that theRickettsiagenus has an overabundance of species designations, that the currentAnaplasmaandNeorickettsiagenus designations are both too broad and need to be divided, and that there are clear demarcations ofWolbachiaspecies that do not align precisely with the existing supergroup designations.

scholarly journals Using Core Genome Alignments to Assign Bacterial Species

2018 ◽  
Author(s):  
Matthew Chung ◽  
James B. Munro ◽  
Julie C. Dunning Hotopp
Keyword(s):  
Dna Hybridization ◽  
Core Genome ◽  
Sequence Data ◽  
Bacterial Species ◽  
Intracellular Bacteria ◽  
Obligate Intracellular ◽  
Exponential Increase ◽  
Wide Range ◽  
Obligate Intracellular Bacteria ◽  
The Relationship

ABSTRACTWith the exponential increase in the number of bacterial taxa with genome sequence data, a new standardized method is needed to assign bacterial species designations using genomic data that is consistent with the classically-obtained taxonomy. This is particularly acute for unculturable obligate intracellular bacteria like those in the Rickettsiales, where classical methods like DNA-DNA hybridization cannot be used to define species. Within the Rickettsiales, species designations have been applied inconsistently, often obfuscating the relationship between organisms and the context for experimental results. In this study, we generated core genome alignments for a wide range of genera with classically defined species, includingArcobacter,Caulobacter,Erwinia,Neisseria,Polaribacter,Ralstonia,Thermus, as well as genera within the Rickettsiales includingRickettsia,Orientia,Ehrlichia,Neoehrlichia,Anaplasma,eorickettsia, andWolbachia. A core genome alignment sequence identity (CGASI) threshold of 96.8% was found to maximize the prediction of classically-defined species. Using the CGASI cutoff, theWolbachiagenus can be delineated into species that differ from the currently used supergroup designations, while theRickettsiagenus is delineated into nine species, as opposed to the current 27 species. Additionally, we find that core genome alignments cannot be constructed between genomes belonging to different genera, establishing a bacterial genus cutoff that suggests the need to create new genera from theAnaplasmaandNeorickettsia. By using core genome alignments to assign taxonomic designations, we aim to provide a high-resolution, robust method for bacterial nomenclature that is aligned with classically-obtained results.

Phaeosphaeria chinensis sp. nov. (Phaeosphaeriaceae) with an asexual/sexual morph connection from GuangDong Province, China

Phytotaxa ◽  
2019 ◽  
Vol 419 (1) ◽  
pp. 28-38 ◽  
Author(s):  
KE-KE ZHANG ◽  
SINANG HONGSANAN ◽  
DANUSHKA S. TENNAKOON ◽  
SHENG-LI TIAN ◽  
NING XIE
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Guangdong Province ◽  
Distinct Species ◽  
Bootstrap Support ◽  
Comprehensive Description ◽  
High Bootstrap ◽  
Asexual Morphs

Phaeosphaeria chinensis sp. nov. was found on dead leaves, collected from Guangdong Province, China. Morphology of the new species was compared with other Phaeosphaeria species and related genera of Phaeosphaeriaceae. Phylogenetic analyses of combined ITS, LSU, SSU and TEF-1 sequence data based on maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) revealed that P. chinensis as a distinct species within the Phaeosphaeria with high bootstrap support. The comparison of the new species with other Phaeosphaeria species and a comprehensive description and micrographs are provided. The linkage of sexual and asexual morphs of the new species is also showed.

scholarly journals Veterinary Fusarioses within the United States

2016 ◽  
Vol 54 (11) ◽  
pp. 2813-2819 ◽  
Author(s):  
Kerry O'Donnell ◽  
Deanna A. Sutton ◽  
Nathan Wiederhold ◽  
Vincent A. R. G. Robert ◽  
Pedro W. Crous ◽  
...  
Keyword(s):  
United States ◽  
Dna Sequence ◽  
Species Complex ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Distinct Species ◽  
The United States ◽  
Content Type ◽  
Dna Sequence Data ◽  
Species Complexes

Multilocus DNA sequence data were used to assess the genetic diversity and evolutionary relationships of 67Fusariumstrains from veterinary sources, most of which were from the United States. Molecular phylogenetic analyses revealed that the strains comprised 23 phylogenetically distinct species, all but two of which were previously known to infect humans, distributed among eight species complexes. The majority of the veterinary isolates (47/67 = 70.1%) were nested within theFusarium solanispecies complex (FSSC), and these included 8 phylospecies and 33 unique 3-locus sequence types (STs). Three of the FSSC species (Fusarium falciforme,Fusarium keratoplasticum, andFusariumsp. FSSC 12) accounted for four-fifths of the veterinary strains (38/47) and STs (27/33) within this clade. Most of theF. falciformestrains (12/15) were recovered from equine keratitis infections; however, strains ofF. keratoplasticumandFusariumsp. FSSC 12 were mostly (25/27) isolated from marine vertebrates and invertebrates. Our sampling suggests that theFusarium incarnatum-equisetispecies complex (FIESC), with eight mycoses-associated species, may represent the second most important clade of veterinary relevance withinFusarium. Six of the multilocus STs within the FSSC (3+4-eee, 1-b, 12-a, 12-b, 12-f, and 12-h) and one each within the FIESC (1-a) and theFusarium oxysporumspecies complex (ST-33) were widespread geographically, including three STs with transoceanic disjunctions. In conclusion, fusaria associated with veterinary mycoses are phylogenetically diverse and typically can only be identified to the species level using DNA sequence data from portions of one or more informative genes.

scholarly journals “Candidatus Finniella” (Rickettsiales, Alphaproteobacteria), Novel Endosymbionts of Viridiraptorid Amoeboflagellates (Cercozoa, Rhizaria)

2015 ◽  
Vol 82 (2) ◽  
pp. 659-670 ◽  
Author(s):  
Sebastian Hess ◽  
Andreas Suthaus ◽  
Michael Melkonian
Keyword(s):  
Rrna Gene ◽  
The Novel ◽  
Single Nucleotide ◽  
Content Type ◽  
Obligate Intracellular ◽  
Wide Range ◽  
Candidate Species ◽  
Novel Bacteria ◽  
Obligate Intracellular Bacteria

ABSTRACTTheRickettsiales(Alphaproteobacteria) are obligate intracellular bacteria that colonize a wide range of eukaryotic hosts, including diverse metazoa and protists. Here, we characterize rickettsial endosymbionts discovered in the cytoplasm of the algivorous amoeboflagellatesViridiraptor invadensandOrciraptor agilis(Viridiraptoridae, Cercozoa, Rhizaria), supplying evidence of free-living, phagotrophic members of the Cercozoa serving as hosts forRickettsiales. According to 16S rRNA gene phylogenies, the bacteria represent two closely related but distinct genotypes within a deep-branching rickettsial clade, which contains the genera “CandidatusOdyssella,” “CandidatusParacaedibacter,” and “CandidatusCaptivus.” Using the full-cycle rRNA approach, we detected the novel bacteria in four of nine viridiraptorid strains tested. Furthermore, two specific oligonucleotide probes with a single-nucleotide-difference discriminated both bacterial genotypes by fluorescencein situhybridization (FISH). We establish the candidate species “CandidatusFinniella inopinata” (found inViridiraptor invadens) and “CandidatusFinniella lucida” (found inOrciraptor agilis) for the novel bacteria and propose a new, provisional family ofRickettsiales, “CandidatusParacaedibacteraceae.”

Molecular systematics of Australian rhinolophid bats (Chiroptera : Rhinolophidae)

1998 ◽  
Vol 46 (3) ◽  
pp. 203 ◽  
Author(s):  
S. J. B. Cooper ◽  
T. B. Reardon ◽  
J. Skilins
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Distinct Species ◽  
Surprising Result ◽  
Separate Species ◽  
Phylogenetic Species Concept ◽  
South Wales ◽  
Mtdna Sequence ◽  
Geographic Populations

Genetic variation in two morphologically distinct species of Australian Rhinolophus, R. megaphyllus, and R. philippinensis, and a third putative species (‘the intermediate’) were examined using allozyme electrophoresis and sequencing of the mitochondrial DNA (mtDNA) control region with the aim of resolving their taxonomic status. The surprising result was that no fixed allozymic differences and low allozyme divergence existed among these three taxa over 45 loci examined. In contrast, levels of intra-generic divergence among eight species of Rhinolophus showed up to 50% fixed allozyme differences between species, indicating that low allozyme divergence was not a common feature of the genus and that the three Australian taxa are likely to be monophyletic and recently diverged. Phylogenetic analyses of mtDNA sequence data revealed that populations of R. megaphyllus and R. philippinensis from Sabah, New Guinea, and Australia were represented by distinct mtDNA clades and that the two species are polyphyletic. These data suggest a reclassification of the different geographic populations of R. megaphyllus and R. philippinensis as separate species on the basis of a phylogenetic species concept. Within Australia, three distinct mtDNA clades were found, one of which showed ‘the intermediate’ in paraphyly with R. philippinensis from Queensland, but does not resolve the taxonomic status of ‘the intermediate’. Two mtDNA clades were also found representing R. megaphyllus from Queensland and R. megaphyllus from Victoria and New South Wales respectively. The finding of genetic subdivision along the east coast of Australia in an apparently continuously distributed bat species raises questions of the origin and historical biogeography of these bats in Australia.

scholarly journals Multigene phylogeny of the scyphozoan jellyfish family Pelagiidae reveals that the common U.S. Atlantic sea nettle comprises two distinct species (Chrysaora quinquecirrhaandC. chesapeakei)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3863 ◽  
Author(s):  
Keith M. Bayha ◽  
Allen G. Collins ◽  
Patrick M. Gaffney
Keyword(s):  
Gulf Of Mexico ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Source Region ◽  
Historical Review ◽  
Distinct Species ◽  
Chrysaora Quinquecirrha ◽  
Western Africa ◽  
Sea Nettle ◽  
The U.S

BackgroundSpecies of the scyphozoan family Pelagiidae (e.g.,Pelagia noctiluca,Chrysaora quinquecirrha) are well-known for impacting fisheries, aquaculture, and tourism, especially for the painful sting they can inflict on swimmers. However, historical taxonomic uncertainty at the genus (e.g., new genusMawia) and species levels hinders progress in studying their biology and evolutionary adaptations that make them nuisance species, as well as ability to understand and/or mitigate their ecological and economic impacts.MethodsWe collected nuclear (28SrDNA) and mitochondrial (cytochromecoxidase I and16SrDNA) sequence data from individuals of all four pelagiid genera, including 11 of 13 currently recognized species ofChrysaora. To examine species boundaries in the U.S. Atlantic sea nettleChrysaora quinquecirrha, specimens were included from its entire range along the U.S. Atlantic and Gulf of Mexico coasts, with representatives also examined morphologically (macromorphology and cnidome).ResultsPhylogenetic analyses show that the genusChrysaorais paraphyletic with respect to other pelagiid genera. In combined analyses,Mawia, sampled from the coast of Senegal, is most closely related toSanderia malayensis, andPelagiaforms a close relationship to a clade of PacificChrysaoraspecies (Chrysaora achlyos, Chrysaora colorata,Chrysaora fuscescens, andChrysaora melanaster).Chrysaora quinquecirrhais polyphyletic, with one clade from the U.S. coastal Atlantic and another in U.S. Atlantic estuaries and Gulf of Mexico. These genetic differences are reflected in morphology, e.g., tentacle and lappet number, oral arm length, and nematocyst dimensions. Caribbean sea nettles (Jamaica and Panama) are genetically similar to the U.S. Atlantic estuaries and Gulf of Mexico clade ofChrysaora quinquecirrha.DiscussionOur phylogenetic hypothesis for Pelagiidae contradicts current generic definitions, revealing major disagreements between DNA-based and morphology-based phylogenies. A paraphyleticChrysaoraraises systematic questions at the genus level for Pelagiidae; accepting the validity of the recently erected genusMawia, as well as past genera, will require the creation of additional pelagiid genera. Historical review of the species-delineating genetic and morphological differences indicates thatChrysaora quinquecirrhaDesor 1848 applies to the U.S. Coastal AtlanticChrysaoraspecies (U.S. Atlantic sea nettle), while the nameC. chesapeakeiPapenfuss 1936 applies to the U.S. Atlantic estuarine and Gulf of Mexico Chrysaora species (Atlantic bay nettle). We provide a detailed redescription, with designation of a neotype forChrysaora chesapeakei, and clarify the description ofChrysaora quinquecirrha. Since CaribbeanChrysaoraare genetically similar toChrysaora chesapeakei, we provisionally term themChrysaorac.f.chesapeakei. The presence ofMawia benovicioff the coast of Western Africa provides a potential source region for jellyfish introduced into the Adriatic Sea in 2013.

scholarly journals bModelTest: Bayesian phylogenetic site model averaging and model comparison

2015 ◽  
Author(s):  
Remco R Bouckaert ◽  
Alexei J Drummond
Keyword(s):  
Model Comparison ◽  
Ad Hoc ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Model Averaging ◽  
Sources Of Information ◽  
Nucleotide Sequence Data ◽  
Site Model ◽  
Wide Range ◽  
Substitution Models

AbstractBackground:Reconstructing phylogenies through Bayesian methods has many benefits, which include providing a mathematically sound framework, providing realistic estimates of uncertainty and being able to incorporate different sources of information based on formal principles. Bayesian phylogenetic analyses are popular for interpreting nucleotide sequence data, however for such studies one needs to specify a site model and associated substitution model. Often, the parameters of the site model is of no interest and an ad-hoc or additional likelihood based analysis is used to select a single site model.Results:bModelTest allows for a Bayesian approach to inferring and marginalizing site models in a phylogenetic analysis. It is based on trans-dimensional Markov chain Monte Carlo (MCMC) proposals that allow switching between substitution models as well as estimating the posterior probability for gamma-distributed rate heterogeneity a proportion of invariable sites and unequal base frequencies. The model can be used with the full set of time-reversible models on nucleotides, but we also introduce and demonstrate the use of two subsets of time-reversible substitution models.Conclusion:With the new method the site model can be inferred (and marginalized) during the MCMC analysis and does not need to be pre-determined, as is now often the case in practice, by likelihood-based methods. The method is implemented in the bModelTest package of the popular BEAST 2 software, which is open source, licensed under the GNU Lesser General Public License and allows joint site model and tree inference under a wide range of models.

scholarly journals Morphologic and Molecular Characterization of a Demodex (Acari: Demodicidae) Species from White-Tailed Deer (Odocoileus virginianus)

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Michael J. Yabsley ◽  
Sarah E. Clay ◽  
Samantha E. J. Gibbs ◽  
Mark W. Cunningham ◽  
Michaela G. Austel
Keyword(s):  
Odocoileus Virginianus ◽  
18S Rrna ◽  
Association Studies ◽  
Phylogenetic Analyses ◽  
Skin Irritation ◽  
Black Bear ◽  
Distinct Species ◽  
Rrna Gene ◽  
Adult Males ◽  
Wide Range

Demodex mites, although usually nonpathogenic, can cause a wide range of dermatological lesions ranging from mild skin irritation and alopecia to severe furunculosis. Recently, a case of demodicosis from a white-tailed deer (Odocoileus virginianus) revealed a Demodex species morphologically distinct from Demodex odocoilei. All life cycle stages were considerably larger than D. odocoilei and although similar in size to D. kutzeri and D. acutipes from European cervids, numerous morphometrics distinguished the four species. Adult males and females were 209.1±13.1 and 225.5±13.4 μm in length, respectively. Ova, larva, and nymphs measured 65.1±4.1, 124.9±11.6, and 205.1±19.4 μm in length, respectively. For phylogenetic analyses, a portion of the 18S rRNA gene was amplified and sequenced from samples of the WTD Demodex sp., two Demodex samples from domestic dogs, and Demodex ursi from a black bear. Phylogenetic analyses indicated that the WTD Demodex was most similar to D. musculi from laboratory mice. A partial sequence from D. ursi was identical to the WTD Demodex sequence; however, these two species can be differentiated morphologically. This paper describes a second Demodex species from white-tailed deer and indicates that 18S rRNA is useful for phylogenetic analysis of most Demodex species, but two morphologically distinct species had identical partial sequences. Additional gene targets should be investigated for phylogenetic and parasite-host association studies.

scholarly journals Benchmarking topological accuracy of bacterial phylogenomic workflows using in silico evolution

2021 ◽  
Author(s):  
Boas CL van der Putten ◽  
Niek AH Huijsmans ◽  
Daniel R Mende ◽  
Constance Schultsz
Keyword(s):  
De Novo ◽  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Phylogenetic Reconstruction ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
De Novo Genome Assembly ◽  
Relevant Alternatives ◽  
Wide Range ◽  
Similar Accuracy

Phylogenetic analyses are widely used in microbiological research, for example to trace the progression of bacterial outbreaks based on whole-genome sequencing data. In practice, multiple analysis steps such as de novo assembly, alignment and phylogenetic inference are combined to form phylogenetic workflows. Comprehensive benchmarking of the accuracy of complete phylogenetic workflows is lacking. To benchmark different phylogenetic workflows, we simulated bacterial evolution under a wide range of evolutionary models, varying the relative rates of substitution, insertion, deletion, gene duplication, gene loss and lateral gene transfer events. The generated datasets corresponded to a genetic diversity usually observed within bacterial species (≥95% average nucleotide identity). We replicated each simulation three times to assess replicability. In total, we benchmarked seventeen distinct phylogenetic workflows using 8 different simulated datasets. We found that recently developed k-mer alignment methods such as kSNP and SKA achieve similar accuracy as reference mapping. The high accuracy of k-mer alignment methods can be explained by the large fractions of genomes these methods can align, relative to other approaches. We also found that the choice of de novo assembly algorithm influences the accuracy of phylogenetic reconstruction, with workflows employing SPAdes or SKESA outperforming those employing Velvet. Finally, we found that the results of phylogenetic benchmarking are highly variable between replicates. We conclude that for phylogenomic reconstruction k-mer alignment methods are relevant alternatives to reference mapping at species level, especially in the absence of suitable reference genomes. We show de novo genome assembly accuracy to be an underappreciated parameter required for accurate phylogenomic reconstruction.

scholarly journals Phylogenetic placement of Iodosphaeriaceae (Xylariales, Ascomycota), designation of an epitype for the type species of Iodosphaeria, I. phyllophila, and description of I. foliicola sp. nov.

2021 ◽  
Author(s):  
A.N. Miller ◽  
M. Réblová
Keyword(s):  
Maximum Likelihood ◽  
Type Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Monophyletic Group ◽  
Its Sequence ◽  
Phylogenetic Placement ◽  
Wide Range ◽  
Single Genus

The Iodosphaeriaceae is represented by the single genus, Iodosphaeria, which is composed of nine species with superficial, black, globose ascomata covered with long, flexuous, brown hairs projecting from the ascomata in a stellate fashion, unitunicate asci with an amyloid apical ring or ring lacking and ellipsoidal, ellipsoidal-fusiform or allantoid, hyaline, aseptate ascospores. Members of Iodosphaeria are infrequently found worldwide as saprobes on various hosts and a wide range of substrates. Only three species have been sequenced and included in phylogenetic analyses, but the type species, I. phyllophila, lacks sequence data. In order to stabilize the placement of the genus and family, an epitype for the type species was designated after obtaining ITS sequence data and conducting maximum likelihood and Bayesian phylogenetic analyses. Iodosphaeria foliicola occurring on overwintered Alnus sp. leaves is described as new. Five species in the genus form a well-supported monophyletic group, sister to the Pseudosporidesmiaceae in the Xylariales. Selenosporella-like and/or ceratosporium-like synasexual morphs were experimentally verified or found associated with ascomata of seven of the nine accepted species in the genus. Taxa included and excluded from Iodosphaeria are discussed.

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