TreeDyn: towards dynamic graphics and annotations for analyses of trees

Chevenet, François; Brun, Catherine; Bañuls, Anne‐Laure; Jacq, Bernard; Christen, Richard

doi:10.1186/1471-2105-7-439

Cited by 956 publications

(639 citation statements)

References 31 publications

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“…The reliability for the internal branches was assessed using the approximate likelihood ratio test (aLRT -SHLike) (Anisimova and Gascuel, 2006). Graphical representation and editing of the phylogenetic trees were performed with TreeDyn (v 198.3) (Chevenet et al, 2006). …”

Section: Dna Isolation and Phylogenetic Analysis Of A Phagocytophilumentioning

confidence: 99%

Infection of Ixodes spp. tick cells with different Anaplasma phagocytophilum isolates induces the inhibition of apoptotic cell death

Alberdi

Ayllón

Cabezas-Cruz

et al. 2015

Ticks and Tick-borne Diseases

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Anaplasma phagocytophilum is an intracellular rickettsial pathogen transmitted by Ixodes spp. ticks, which causes granulocytic anaplasmosis in humans, horses and dogs and tick-borne fever (TBF) in ruminants. In the United States, human granulocytic anaplasmosis (HGA) is highly prevalent while TBF has not been reported. However, in Europe the situation is the opposite, with high prevalence for TBF in sheep and low prevalence of HGA. The origin of these differences has not been identified and our hypothesis is that different A. phagocytophilum isolates impact differently on tick vector

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Section: Dna Isolation and Phylogenetic Analysis Of A Phagocytophilumentioning

confidence: 99%

Infection of Ixodes spp. tick cells with different Anaplasma phagocytophilum isolates induces the inhibition of apoptotic cell death

Alberdi

Ayllón

Cabezas-Cruz

et al. 2015

Ticks and Tick-borne Diseases

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“…Phylogeny was determined with PhyML using the GTR substitution model with 100 bootstraps (Anisimova & Gascuel, 2006;Guindon & Gascuel, 2003). The resultant phylogenetic tree was generated with TreeDyn (Chevenet et al, 2006). These tools were accessed through phylogeny.fr (Dereeper et al, 2008).…”

mentioning

confidence: 99%

Liberibacter crescens gen. nov., sp. nov., the first cultured member of the genus Liberibacter

Fagen

Leonard

Coyle

et al. 2014

International Journal of Systematic and Evolutionary Microbiology

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The Gram-stain-negative, rod-shaped bacterial isolate BT-1T is the closest relative to the genus ‘Candidatus Liberibacter ’ cultured to date. BT-1T was recovered from the phloem sap of a defoliating mountain papaya in Puerto Rico. The BT-1T 16S rRNA gene sequence showed that strain BT-1T is most closely related to members of the genus ‘Ca. Liberibacter ’ sharing 94.7 % 16S rRNA gene sequence similarity with ‘Ca. Liberibacter americanus ’ and ‘Ca. Liberibacter asiaticus ’. Additionally, average nucleotide identity, 16S rRNA gene sequences and conserved protein sequences supported inclusion of the previously described species of the genus ‘Ca. Liberibacter ’ in a genus with BT-1T. The prominent fatty acids of isolate BT-1T were C18 : 1ω7c (77.2 %), C16 : 0 OH (4.8 %), C18 : 0 (4.4 %) and C16 : 0 (3.5 %). Both physiological and genomic characteristics support the creation of the genus Liberibacter , as well as the novel species Liberibacter crescens gen. nov., sp. nov. with type strain BT-1T ( = ATCC BAA-2481T = DSM 26877T).

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“…For the neighbour-joining analysis, a distance matrix was calculated using Kimura's two-parameter correction and bootstraps were performed using 1000 replications. Phylogenetic trees were drawn using TreeDyn (Chevenet et al, 2006) or SeaView. A consensus phylogenetic tree is shown in Supplementary Fig.…”

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confidence: 99%

Winogradskyella exilis sp. nov., isolated from the starfish Stellaster equestris, and emended description of the genus Winogradskyella

Ivanova

Christen

Gorshkova

et al. 2010

International Journal of Systematic and Evolutionary Microbiology

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A pale-yellowish-pigmented strain, 022-2-26 T , was isolated from a starfish, Stellaster equestris. Cells of strain 022-2-26 T were Gram-negative short rods that were chemo-organotrophic, alkalitolerant and mesophilic. The predominant menaquinone was MK-6. The major cellular fatty acids were iso-C 15 : 0 , iso-C 15 : 1 , C 15 : 0 , iso-C 15 : 0 2-OH and iso-C 17 : 0 3-OH (together representing 87 % of the total fatty acids). The DNA G+C content was 30.1 mol%. A 16S rRNA gene sequence of the isolate was determined and phylogenetic analyses revealed that strain 022-2-26 T formed a robust clade (neighbour-joining algorithm with a bootstrap value of 95 % and parsimony and maximum-likelihood algorithms) with type strains of species in the genus Winogradskyella. The closest phylogenetic neighbour of strain 022-2-26 T was Winogradskyella poriferorum UST030701-295 T (96 % 16S rRNA gene sequence similarity; 59 differences between sequences). On the basis of the phenotypic and chemotaxonomic characteristics and the phylogenetic evidence, it is proposed that strain 022-2-26 T represents a novel species, Winogradskyella exilis sp. nov. The type strain is 022-2-26 T (5KMM 6013 T 5CIP 109976 T ).The genus Winogradskyella was created within the family Flavobacteriaceae in 2005 to accommodate three species, Winogradskyella thalassocola, W. epiphytica and W. eximia, marine bacteria respectively isolated from the green alga Acrosiphonia sonderi and the brown algae Chorda filum and Laminaria japonica (Nedashkovskaya et al., 2005). A fourth species was described shortly afterwards: Winogradskyella poriferorum, isolated from a sponge (Lau et al., 2005). We report here the polyphasic characterization of a novel bacterium isolated from the starfish Stellaster equestris.The starfish was collected with dragging equipment in October 1998 at a depth of 100 m (30 % salinity, 15 u C) in the South China Sea (26 u 28.39 N 122 u 29.09 E). The starfish was pre-rinsed in sterilized seawater and a piece (about 3 g) of tegument tissue was removed aseptically. Strain 022-2-26 T was isolated from the tissue homogenates by plating samples (0.1 ml) on agar plates of marine agar 2216 (MA; Oxoid) and on medium B. Medium B contained (w/v) 0.2 % Bacto peptone (Difco), 0.2 % casein hydrolysate (Merck), 0.2 % Bacto yeast extract (Oxoid), 0.1 % glucose, 0.02 % KH 2 PO 4 , 0.005 % MgSO 4 . 7H 2 O and 1.5 % Bacto agar (Oxoid) in 50 % (v/v) natural seawater and 50 % (v/v) distilled water at pH 7.5-7.8, as described elsewhere (Ivanova et al., 1996).The phenotypic properties used for the characterization of Flavobacterium species were determined by using standard procedures (Smibert & Krieg, 1994) and as described elsewhere (McMeekin et al., 1971;Ivanova et al., 1996Ivanova et al., , 1998Ivanova et al., , 2005Bernardet et al., 2002). Strain 022-2-26 T was cultured at 22-24 u C. To test for spreading growth and gliding motility, strain 022-2-26 T was grown on medium B with the peptone content reduced to 0.02 % (0.2 g l 21 ). Gliding motility was verified by using ...

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TreeDyn: towards dynamic graphics and annotations for analyses of trees

Cited by 956 publications

References 31 publications

Infection of Ixodes spp. tick cells with different Anaplasma phagocytophilum isolates induces the inhibition of apoptotic cell death

Infection of Ixodes spp. tick cells with different Anaplasma phagocytophilum isolates induces the inhibition of apoptotic cell death

Liberibacter crescens gen. nov., sp. nov., the first cultured member of the genus Liberibacter

Winogradskyella exilis sp. nov., isolated from the starfish Stellaster equestris, and emended description of the genus Winogradskyella

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