scholarly journals Congruence of evolutionary relationships inside the Leuconostoc–Oenococcus–Weissella clade assessed by phylogenetic analysis of the 16S rRNA gene, dnaA, gyrB, rpoC and dnaK

2007 ◽  
Vol 57 (2) ◽  
pp. 276-286 ◽  
Author(s):  
Ivo M. Chelo ◽  
Líbia Zé-Zé ◽  
Rogério Tenreiro
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Inference ◽  
Evolutionary Relationships ◽  
Rrna Gene ◽  
Phylogenetic Structure ◽  
The 16S Rrna Gene ◽  
Combined Data ◽  
Good Agreement

The phylogenetic structure of the Leuconostoc–Oenococcus–Weissella clade was evaluated by comparison of 16S rRNA gene, dnaA, gyrB, rpoC and dnaK sequence analysis. Phylogenies obtained with the different genes were in overall good agreement and a well-supported, almost fully resolved phylogenetic tree was obtained when the combined data were analysed in a Bayesian approach. A rapid basal diversification of the three genera is suggested. Evolutionary rates of the 16S rRNA gene in these genera seem to be different and specifically related to the evolution of this group, revealing the importance of this sequence in the constitution of the present taxonomy, but preventing its straightforward use in phylogenetic inference.

‘Candidatus Phytoplasma balanitae’ associated with witches’ broom disease of Balanites triflora

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 636-640 ◽  
Author(s):  
Nang Kyu Kyu Win ◽  
Seung-Yeol Lee ◽  
Assunta Bertaccini ◽  
Shigetou Namba ◽  
Hee-Young Jung
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

A phytoplasma was identified in naturally infected wild Balanites triflora plants exhibiting typical witches’ broom symptoms (Balanites witches’ broom: BltWB) in Myanmar. The 16S rRNA gene sequence revealed that BltWB phytoplasma had the highest similarity to that of ‘Candidatus Phytoplasma ziziphi’ and it was also closely related to that of ‘Candidatus Phytoplasma ulmi ’. Phylogenetic analysis of the 16S rRNA gene sequences indicated that the BltWB phytoplasma clustered as a discrete subclade with Elm yellows phytoplasmas. RFLP analysis of the 16S rRNA gene including the 16S–23S spacer region differentiated the BltWB phytoplasma from ‘Ca. P. ziziphi ’, ‘Ca. P. ulmi ’ and ‘Candidatus Phytoplasma trifolii ’. Analysis of additional ribosomal protein (rp) and translocase protein (secY) gene sequences and phylogenetic analysis of BltWB showed that this phytoplasma was clearly distinguished from those of other ‘Candidatus Phytoplasma ’ taxa. Taking into consideration the unique plant host and the restricted geographical occurrence in addition to the 16S rRNA gene sequence similarity, the BltWB phytoplasma is proposed to represent a novel taxon, ‘Candidatus Phytoplasma balanitae’.

scholarly journals Chryseomicrobium aureum sp. nov., a bacterium isolated from activated sludge

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2682-2687 ◽  
Author(s):  
Shi-Kai Deng ◽  
Xiao-Mei Ye ◽  
Cui-Wei Chu ◽  
Jin Jiang ◽  
Jian He ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

A Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, aerobic bacterial strain, designated BUT-2T, was isolated from activated sludge of one herbicide-manufacturing wastewater-treatment facility in Kunshan, Jiangsu province, China, and subjected to polyphasic taxonomic studies. Analysis of the 16S rRNA gene sequence indicated that strain BUT-2T shared the highest similarity with Chryseomicrobium amylolyticum (98.98 %), followed by Chryseomicrobium imtechense (98.88 %), with less than 96 % similarlity to members of the genera Paenisporosarcina , Planococcus , Sporosarcina and Planomicrobium . Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain BUT-2T clustered with C. amylolyticum JC16T and C. imtechense MW10T, occupying a distinct phylogenetic position. The major fatty acid (>10 % of total fatty acids) type of strain BUT-2T was iso-C15 : 0. The quinone system comprised menaquinone MK-7 (77.8 %), MK-6 (11.9 %) and MK-8 (10.3 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and some unidentified phospholipids. The cell-wall peptidoglycan type of strain BUT-2T was l-Orn-d-Glu. The genomic DNA G+C content of strain BUT-2T was 48.5 mol%. Furthermore, the DNA–DNA relatedness in hybridization experiments against the reference strain was lower than 70 %, confirming that strain BUT-2T did not belong to previously described species of the genus Chryseomicrobium . On the basis of its morphological, physiological and chemotaxonomic characteristics as well as phylogenetic analysis, strain BUT-2T is considered to represent a novel species of the genus Chryseomicrobium , for which the name Chryseomicrobium aureum sp. nov. is proposed. The type strain is BUT-2T ( = CCTCC AB2013082T = KACC 17219T).

scholarly journals Phylogenetic analysis and delineation of phytoplasmas based on secY gene sequences

2010 ◽  
Vol 60 (12) ◽  
pp. 2887-2897 ◽  
Author(s):  
I.-M. Lee ◽  
K. D. Bottner-Parker ◽  
Y. Zhao ◽  
R. E. Davis ◽  
N. A. Harrison
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
Resolving Power ◽  
Rrna Gene ◽  
Similarity Coefficients ◽  
Gene Sequences ◽  
Pattern Similarity ◽  
The 16S Rrna Gene

The secY gene sequence is more variable than that of the 16S rRNA gene. Comparative phylogenetic analyses with 16S rRNA and secY gene sequences from 80 and 83 phytoplasma strains, respectively, were performed to assess the efficacy of these sequences for delineating phytoplasma strains within each 16Sr group. The phylogenetic interrelatedness among phytoplasma taxa inferred by secY gene-based phylogeny was nearly congruent with that inferred by 16S rRNA gene-based phylogeny. Phylogenetic analysis based on the secY gene permitted finer differentiation of phytoplasma strains, however. The secY gene-based phylogeny not only readily resolved 16Sr subgroups within a given 16Sr group, but also delineated distinct lineages irresolvable by 16S rRNA gene-based phylogeny. Such high resolving power makes the secY gene a more useful genetic marker than the 16S rRNA gene for finer differentiation of closely related phytoplasma strains based on RFLP analysis with selected restriction enzymes. Such strains were readily identified by collective secY RFLP patterns. The genetic interrelationships among these strains were determined by pattern similarity coefficients, which coincided with delineations by phylogenetic analysis. This study also revealed two heterogeneous spc operons present in the phytoplasma clade. This latter finding may have significant implications for phytoplasma evolution.

scholarly journals Phylogenetic Analysis of the 16S rRNA Gene of Anaplasma Species Detected from Japanese Serows (Capricornis crispus)

2009 ◽  
Vol 71 (12) ◽  
pp. 1677-1679 ◽  
Author(s):  
Makoto SATO ◽  
Ikuo NISHIZAWA ◽  
Masatoshi FUJIHARA ◽  
Takashi NISHIMURA ◽  
Kazuei MATSUBARA ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
The 16S Rrna Gene

scholarly journals Isolation of Gemmata-Like and Isosphaera-Like Planctomycete Bacteria from Soil and Freshwater

2002 ◽  
Vol 68 (1) ◽  
pp. 417-422 ◽  
Author(s):  
Jenny Wang ◽  
Cheryl Jenkins ◽  
Richard I. Webb ◽  
John A. Fuerst
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Double Membrane ◽  
Gemmata Obscuriglobus ◽  
Genus Two ◽  
The 16S Rrna Gene

ABSTRACT New cultured strains of the planctomycete division (order Planctomycetales) of the domain Bacteria related to species in the genera Gemmata and Isosphaera were isolated from soil, freshwater, and a laboratory ampicillin solution. Phylogenetic analysis of the 16S rRNA gene from eight representative isolates showed that all the isolates were members of the planctomycete division. Six isolates clustered with Gemmata obscuriglobus and related strains, while two isolates clustered with Isosphaera pallida. A double-membrane-bounded nucleoid was observed in Gemmata-related isolates but not in Isosphaera-related isolates, consistent with the ultrastructures of existing species of each genus. Two isolates from this study represent the first planctomycetes successfully cultivated from soil.

scholarly journals Flavobacterium restrictum sp. nov., Flavobacterium rhamnosiphilum sp. nov., and Flavobacterium zepuense sp. nov. isolated from glaciers

2020 ◽  
Vol 70 (8) ◽  
pp. 4583-4590 ◽  
Author(s):  
Guo-Qing Zhang ◽  
Lei-Lei Yang ◽  
Qing Liu ◽  
Hong-Can Liu ◽  
Yu-Guang Zhou ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Rrna Gene ◽  
The Tibetan Plateau ◽  
Content Type ◽  
Pr China ◽  
The 16S Rrna Gene

Three strains, designated as LB1R34T, LB3P52T and ZT4R6T, were isolated from glaciers located on the Tibetan Plateau, PR China. The strains were Gram-stain-negative, aerobic, rod-shaped, non-motile and yellow. Phylogenetic analysis based on the 16S rRNA gene and genomic sequences indicated that they were related to the members of the genus Flavobacterium . The 16S rRNA gene sequences similarities between the three strains were 92.31–96.93 %. The average nucleotide identity values and digital DNA–DNA hybridization values between these three strains and their closest relatives were 76.80–91.33 % and 21.3–44.2 %, respectively. LB1R34T, LB3P52T and ZT4R6T contained MK-6 as the major menaquinone, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and iso-C15 : 0 as the major fatty acids. Phosphatidylethanolamine was present in their polar lipids profiles. On the basis of the phenotypic characteristics, he results of phylogenetic analysis and genotypic data, three novel species, Flavobacterium restrictum sp. nov. (type strain=LB1 R34T=CGMCC 1.11493T=NBRC 113650T), Flavobacterium rhamnosiphilum sp. nov. (type strain=LB3 P52T=CGMCC 1.11446T=NBRC 113776T) and Flavobacterium zepuense sp. nov. (type strain=ZT4 R6T=CGMCC 1.11919T=NBRC 113653T) are proposed.

scholarly journals Alloactinosynnema album gen. nov., sp. nov., a member of the family Actinosynnemataceae isolated from soil

2010 ◽  
Vol 60 (1) ◽  
pp. 39-43 ◽  
Author(s):  
Li-Jie Yuan ◽  
Yu-Qin Zhang ◽  
Li-Yan Yu ◽  
Hong-Yu Liu ◽  
Yan Guan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Family ◽  
Distinct Lineage ◽  
Diamino Acid ◽  
Signature Pattern ◽  
The 16S Rrna Gene

The taxonomic position of a Gram-stain-positive, aerobic strain, designated 03-9939T, isolated from a soil sample collected from Xinjiang Province, China, was established using a polyphasic approach. Whole-cell hydrolysates of strain 03-9939T contained galactose and ribose as diagnostic sugars and meso-diaminopimelic acid as the diamino acid. The predominant menaquinone was MK-9(H4). The phospholipids consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine. The major fatty acids were iso-C16 : 0 (61.5 %) and iso-C16 : 1 H (11.6 %). The genomic DNA G+C content was 68.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 03-9939T should be placed within the family Actinosynnemataceae, in which the strain formed a distinct lineage. Signature nucleotides in the 16S rRNA gene sequence showed that the strain contained a genus-specific diagnostic nucleotide signature pattern. The combination of phylogenetic analysis, phenotypic characteristics and chemotaxonomic data supported the conclusion that strain 03-9939T represents a novel species in a new genus of the family Actinosynnemataceae, for which the name Alloactinosynnema album gen. nov., sp. nov. is proposed. Strain 03-9939T (=DSM 45114T =KCTC 19294T =CCM 7461T) is the type strain of Alloactinosynnema album.

scholarly journals Taxonomy of the canine Mollicutes by 16S rRNA gene and 16S/23S rRNA intergenic spacer region sequence comparison

2004 ◽  
Vol 54 (2) ◽  
pp. 537-542 ◽  
Author(s):  
Victoria J. Chalker ◽  
Joe Brownlie
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Comparison ◽  
Intergenic Spacer ◽  
23S Rrna ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Intergenic Spacer Region ◽  
The 16S Rrna Gene

The taxonomy of canine Mollicutes is described, based on phylogenetic analysis of 16S rRNA gene and 16S/23S rRNA intergenic spacer (IGS) region sequences. The nucleotide sequences of the 16S rRNA gene of two untyped mycoplasmas and the IGS region of 11 Mycoplasma species were determined and used for phylogenetic analysis. The two untyped Mycoplasma strains, HRC 689 and VJC 358, were found to be distinct from all known canine mycoplasmas and all published mycoplasma 16S rRNA gene sequences.

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