Analyses of publicly available <i>Hungatella hathewayi</i> genomes revealed genetic distances indicating they belong to more than one species

Hernández-Juárez, Laura E.; Camorlinga, Margarita; Méndez‐Tenorio, Alfonso; Calderón, Judith Flores; Huang, Bihua C.; Bandoy, DJ Darwin; Weimer, Bart C.; Torres, Javier

doi:10.1080/21505594.2021.1950955

Cited by 9 publications

(10 citation statements)

References 48 publications

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“…Genetic distance is one of the common indicators of genetic differentiation among plant populations [ 56 ]. In the present study, we found that the genetic distance between the wild ancient tea tree populations at adjacent altitudes was small, and genetic distance over large altitude difference was larger.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity of the wild ancient tea tree (Camellia taliensis) populations at different altitudes in Qianjiazhai

Wang

Cheng

et al. 2023

PLoS ONE

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In this study, the genetic diversity and population structure of 4 wild ancient tea tree (Camellia taliensis) populations at different altitudes (2,050, 2,200, 2,350, and 2,500 m) in Qianjiazhai Nature Reserve, Zhenyuan country, Yunnan province, were investigated using EST-SSR molecular markers to compare their genetic variation against altitude. In total, 182 alleles were detected across all loci, ranging from 6 to 25. The top one informative SSR was CsEMS4 with polymorphism information content (PIC) of 0.96. The genetic diversity of this species was high, with 100% of loci being polymorphic, an average Nei’s gene diversity (H) of 0.82, and Shannon’s information index (I) of 1.99. By contrast, at the population level, the genetic diversity of wild ancient tea tree was relatively low, with values of H and I being 0.79 and 1.84, respectively. Analysis of molecular variance (AMOVA) revealed a minor genetic differentiation (12.84%) among populations, and most of the genetic variation (87.16%) was detected within populations. Using population structure analysis, we found that the germplasm of wild ancient tea tree was divided into three groups, and there was a substantial gene exchange among these three groups at different altitudes. Divergent habitats caused by altitudes and high gene flow played important roles in genetic diversity of wild ancient tea tree populations, which will provide new opportunities for promoting their protection and potential utilization.

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Section: Discussionmentioning

confidence: 99%

Genetic diversity of the wild ancient tea tree (Camellia taliensis) populations at different altitudes in Qianjiazhai

Wang

Cheng

et al. 2023

PLoS ONE

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“…The pangenome analysis indicated that the strains described herein should be considered as new species. Additionally, the genetic distance cut-off (OrthoANI values) and core genes similarity (%) should be established for Bartonella , as previously conducted for Hungatella hathewayi , a necessary step toward evaluating the intrageneric diversity [ 18 ].…”

Section: Discussionmentioning

confidence: 99%

“…Isolates were selected and the gDNA was extracted after lysis using Qiagen DNeasy blood and tissue kits [ 14 ]. Each sample was used to produce a sequencing library with gDNA that was of sufficient quality (A 260/280 and A 260/230 > 1.5) with an average insert size of 350 bp according to the KAPA HyperPlus Kit protocol as described previously [ 16 , 17 , 18 , 19 ]. All samples were sequenced using HiSeq XTEN Sequencing System (Illumina, San Diego, CA, USA) [ 20 , 21 ].…”

Section: Methodsmentioning

confidence: 99%

“…A whole-genome-based phylogenetic tree was reconstructed using RAxML (v8.2.11) [ 30 ] implemented in PATRIC [ 31 ]. Whole-genome average nucleotide identity (ANI) was calculated between genomes of members of the genus Bartonella using the software Orthologous Average Nucleotide Identity Tool (OAT v.0.93.1) [ 18 , 32 ]. Delimitation of species using OrthoANI results was based on Goris et al [ 33 ] and Ciufo et al [ 34 ], considering <95% values as novel species [ 19 ].…”

Section: Methodsmentioning

confidence: 99%

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Genomic Characterization of Three Novel Bartonella Strains in a Rodent and Two Bat Species from Mexico

et al. 2023

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Rodents and bats are the most diverse mammal group that host Bartonella species. In the Americas, they were described as harboring Bartonella species; however, they were mostly characterized to the genotypic level. We describe here Bartonella isolates obtained from blood samples of one rodent (Peromyscus yucatanicus from San José Pibtuch, Yucatan) and two bat species (Desmodus rotundus from Progreso, and Pteronotus parnellii from Chamela-Cuitzmala) from Mexico. We sequenced and described the genomic features of three Bartonella strains and performed phylogenomic and pangenome analyses to decipher their phylogenetic relationships. The mouse-associated genome was closely related to Bartonella vinsonii. The two bat-associated genomes clustered into a single distinct clade in between lineages 3 and 4, suggesting to be an ancestor of the rodent-associated Bartonella clade (lineage 4). These three genomes showed <95% OrthoANI values compared to any other Bartonella genome, and therefore should be considered as novel species. In addition, our analyses suggest that the B. vinsonii complex should be revised, and all B. vinsonii subspecies need to be renamed and considered as full species. The phylogenomic clustering of the bat-associated Bartonella strains and their virulence factor profile (lack of the Vbh/TraG conjugation system remains of the T4SS) suggest that it should be considered as a new lineage clade (L5) within the Bartonella genus.

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“…WGS was performed using the methods from the 100K Pathogen Genome Project [ 14 , 15 ]. Briefly, high-molecular-weight genomic DNA (gDNA) was extracted from banked bacterial isolate colonies using the Wizard Genomic DNA Jit (Promega, Madison, WI; cat#A1460) as described previously [ 16 ].…”

Section: Methodsmentioning

confidence: 99%

Characteristics of Extended-Spectrum β-Lactamase Producing Enterobacterales Isolated from Dogs and Cats, 2011–2021

Woerde

Reagan

Byrne

et al. 2023

Veterinary Sciences

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The rising prevalence of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales is a significant threat to animal and human health. This study aims to describe the clinical features, antimicrobial susceptibility patterns, and genotypic features of infections associated with ESBL-producing Enterobacterales in dogs and cats seen at a tertiary referral veterinary teaching hospital. Enterobacterales isolated from dogs and cats that underwent ESBL testing during the study period were identified using a search of the hospital antimicrobial susceptibility test software database. Medical records of confirmed ESBL isolates were reviewed, and the source of infection, clinical findings, and antimicrobial susceptibility were recorded. Genomic DNA from bacterial isolates was evaluated for antimicrobial resistance genes with whole genome sequencing. Thirty ESBL-producing isolates were identified based on phenotypic testing (twenty-nine from dogs, one from a cat); twenty-six were Escherichia coli and the remainder were Klebsiella spp. Bacterial cystitis was the most commonly identified (8/30, 27%) clinical problem associated with infection. Resistance to three or more antimicrobial classes was identified in 90% (27/30) of isolates, and all isolates were susceptible to imipenem. Over 70% of isolates were susceptible to piperacillin-tazobactam, amikacin, and cefoxitin. BlaCTX-M-15 was the most common ESBL gene identified, present in 13/22 (59%) isolate genomes. A wide range of clinical infections were identified. Piperacillin-tazobactam and amikacin may be alternatives to carbapenem therapy. Further, larger-scale studies are needed.

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Analyses of publicly available Hungatella hathewayi genomes revealed genetic distances indicating they belong to more than one species

Abstract: Torres (2021) Analyses of publicly available Hungatellahathewayi genomes revealed genetic distances indicating they belong to more than one species

Cited by 9 publications

References 48 publications

Genetic diversity of the wild ancient tea tree (Camellia taliensis) populations at different altitudes in Qianjiazhai

Genetic diversity of the wild ancient tea tree (Camellia taliensis) populations at different altitudes in Qianjiazhai

Genomic Characterization of Three Novel Bartonella Strains in a Rodent and Two Bat Species from Mexico

Characteristics of Extended-Spectrum β-Lactamase Producing Enterobacterales Isolated from Dogs and Cats, 2011–2021

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