Molecular evidence for a polyphyletic genus Japonia (Architaenioglossa: Cyclophoridae) and with the description of a new genus and two new species

Zootaxa ◽  
2008 ◽  
Vol 1792 (1) ◽  
pp. 22 ◽  
Author(s):  
YEN-CHEN LEE ◽  
KUANG-YANG LUE ◽  
WEN-LUNG WU
Keyword(s):  
Phylogenetic Trees ◽  
New Genus ◽  
Morphological Diversity ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
Mitochondrial Cytochrome Oxidase Subunit ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Mitochondrial Cytochrome Oxidase ◽  
The 16S Rrna Gene

Cyclophoridae is the dominant family of operculated terrestrial snails in East Asia. The group consists of four subfamilies and approximately 300 species that are currently classified into 34 genera. The species occupy various habitatsand show a high morphological diversity. The molecular phylogenetic relationships of this group have not previously been discussed. In order to uncover the relationships within the family, we sequenced parts of the mitochondrial cytochrome oxidase subunit I (COI) and of the 16S rRNA gene from 32 species of 10 genera of cyclophorid and established the phylogenetic tree using neighbor joining, Bayesian and maximum likelihood analyses to construct phylogenetic trees. The results based on mtDNA sequences suggest that the genera Cyclophorus, Cyclotus, Leptopoma, and Cyathopoma are monophyletic while the traditional genus Japonia appeared polyphyletic and then J. zebra should be moved to the new genus Pilosphaera. In addition, Pilosphaera yentoensis n. sp. and Japonia boonkioensis n. sp. are described in this paper.

Molecular data provide new insights into the phylogeny of Cladonotinae (Orthoptera: Tetrigoidea) from China with the description of a new genus and species

Zootaxa ◽  
2020 ◽  
Vol 4809 (3) ◽  
pp. 547-559
Author(s):  
RONG-JIAO ZHANG ◽  
CONG-LIN ZHAO ◽  
FEI-PENG WU ◽  
WEI-AN DENG
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Relationships ◽  
New Genus ◽  
Molecular Data ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Mitochondrial Cytochrome Oxidase Subunit ◽  
Close Relationship ◽  
Phylogenetic Framework ◽  
Mitochondrial Cytochrome Oxidase

Considerable effort has been devoted to elucidating the phylogenetic relationships of tetrigides. However, there is still no commonly accepted phylogenetic hypothesis. Therefore, the phylogenetic relationships among some subfamilies remain unclear; e.g., Cladonotinae is a controversial group, in which the phylogenetic relationships between genera and the boundaries of some of the included genera are unclear, causing some of the taxa to be difficult to identify. Therefore, an in-depth phylogenetic analysis of Cladonotinae is urgently needed. In this study, a robust phylogenetic framework for the tetrigides was reconstructed based on the combined mitochondrial cytochrome oxidase subunit I (COI), 16S ribosomal RNA (16S rRNA), and nuclear 18S ribosomal RNA (18S rRNA) gene sequences of 25 species belonging to 16 genera of Tetrigoidea from China, which included 13 species from 8 genera of Cladonotinae. Phylogenetic inferences were performed using the combined dataset and Bayesian inference (BI) and Maximum Parsimony (MP) methods, and the phylogenetic tree of Cladonotinae was reconstructed. All inferences based on the results of the present study supported the Cladonotinae subfamily as a polyphyletic group; within the Cladonotinae subfamily, Tetradinodula, and Tuberfemurus were closely related to Tetriginae, while Austrohancockia and Gibbotettix showed a close relationship to the Scelimenidae subfamily. Additionally, a new genus and new species of the Cladonotinae subfamily are described and illustrated: Hainantettix Deng, gen. nov. and Hainantettix strictivertex Deng, sp. nov. 

scholarly journals Winogradskyella poriferorum sp. nov., a novel member of the family Flavobacteriaceae isolated from a sponge in the Bahamas

2005 ◽  
Vol 55 (4) ◽  
pp. 1589-1592 ◽  
Author(s):  
Stanley C. K. Lau ◽  
Mandy M. Y. Tsoi ◽  
Xiancui Li ◽  
Ioulia Plakhotnikova ◽  
Sergey Dobretsov ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Gliding Motility ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Phenotypic Characteristics ◽  
The Bahamas ◽  
The Family ◽  
Winogradskyella Poriferorum ◽  
The 16S Rrna Gene

A Gram-negative, rod-shaped bacterium (designated strain UST030701-295T) with fast gliding motility was isolated from the surface of the sponge Lissodendoryx isodictyalis in the Bahamas. Colonies of UST030701-295T were yellow in colour, 2–4 mm in diameter, convex with a smooth surface and entire margins. UST030701-295T was heterotrophic, strictly aerobic and required NaCl for growth (1·0–4·0 %). Growth was observed at pH 6·0–10·0 and at 12–44 °C. Phylogenetic analysis of the 16S rRNA gene sequence placed UST030701-295T within the genus Winogradskyella of the family Flavobacteriaceae, sharing 94·7–95·8 % similarity with the three recognized members of the genus. The G+C content of the DNA was 32·8 mol% and the predominant fatty acids were iso-C15 : 1, iso-C15 : 0, iso-C15 : 0 2-OH, iso-C15 : 0 3-OH, iso-C16 : 0 3-OH, C16 : 1 ω7 and iso-C17 : 0 3-OH (together representing 75·4 % of the total); these data supported the affiliation of UST030701-295T to the genus Winogradskyella. UST030701-295T differed from the three recognized species of Winogradskyella in 7–17 traits. Molecular evidence together with phenotypic characteristics suggests that UST030701-295T represents a novel species within the genus Winogradskyella, for which the name Winogradskyella poriferorum sp. nov. is proposed. The type strain is UST030701-295T (=NRRL B-41101T=JCM 12885T).

scholarly journals Endobacter medicaginis gen. nov., sp. nov., isolated from alfalfa nodules in an acidic soil

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1760-1765 ◽  
Author(s):  
Martha Helena Ramírez-Bahena ◽  
Carmen Tejedor ◽  
Isidro Martín ◽  
Encarna Velázquez ◽  
Alvaro Peix
Keyword(s):  
Type Species ◽  
New Genus ◽  
Culture Media ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The 16S Rrna Gene

A bacterial strain designated M1MS02T was isolated from a surface-sterilized nodule of Medicago sativa in Zamora (Spain). The 16S rRNA gene sequence of this strain showed 96.5 and 96.2 % similarity, respectively, with respect to Gluconacetobacter liquefaciens IFO 12388T and Granulibacter bethesdensis CGDNIH1T from the family Acetobacteraceae . The novel isolate was a Gram-stain-negative, non-sporulating, aerobic coccoid to rod-shaped bacterium that was motile by a subpolar flagellum. The major fatty acid was C18 : 1ω7c and the major ubiquinone was Q-10. The lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, two aminophospholipids, three aminolipids, four glycolipids, two phospholipids and one lipid. Strain M1MS02T was catalase-positive and oxidase- and urease-negative. Acetate and lactate were not oxidized. Acetic acid was produced from ethanol in culture media supplemented with 2 % CaCO3. Ammonium sulphate was assimilated in glucose medium. The strain produced dihydroxyacetone from glycerol. Phylogenetic and phenotypic analyses commonly used to differentiate genera within the family Acetobacteraceae showed that strain M1MS02T should be classified as representing a novel species of a new genus within this family, for which the name Endobacter medicaginis gen. nov., sp. nov. is proposed. The type strain of the type species is M1MS02T ( = LMG 26838T = CECT 8088T). To our knowledge, this is the first report of a member of the Acetobacteraceae occurring as a legume nodule endophyte.

scholarly journals Aurantimonas ureilytica sp. nov., isolated from an air sample

2007 ◽  
Vol 57 (8) ◽  
pp. 1717-1720 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Seung-Hee Yoo ◽  
Jae-Ho Joa ◽  
Ki Hwan Lee ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Family ◽  
Air Sample ◽  
Aurantimonas Coralicida ◽  
Ubiquinone 10 ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A novel strain, designated 5715S-12T, was isolated from an air sample collected from Suwon region, Republic of Korea, using R2A medium. The cells were strictly aerobic, Gram-negative, motile, short rods. Comparison of the 16S rRNA gene sequence of strain 5715S-12T showed the highest sequence similarities to Aurantimonas altamirensis S21BT (95.9 %) and Aurantimonas coralicida WP1T (95.4 %). Phylogenetic trees indicated that the strain formed a cluster with members of the family Aurantimonadaceae (A. altamirensis, A. coralicida and Fulvimarina pelagi). The major fatty acid was C18 : 1 ω7c. The predominant isoprenoid quinone was ubiquinone 10 (Q-10). Diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylglycerol, phosphatidylcholine and four unknown lipids were found as the polar lipid components. The DNA G+C content was 67.0 mol%. On the basis of the phenotypic and phylogenetic features studied, we propose that strain 5715S-12T be assigned to a novel species of the genus Aurantimonas, for which the name Aurantimonas ureilytica sp. nov. (type strain 5715S-12T =KACC 11607T =DSM 18598T) is proposed.

scholarly journals Molecular phylogeny of the family Vorticellidae (Ciliophora, Peritrichia) using combined datasets with a special emphasis on the three morphologically similar genera Carchesium, Epicarchesium and Apocarchesium

2011 ◽  
Vol 61 (4) ◽  
pp. 1001-1010 ◽  
Author(s):  
Ping Sun ◽  
John C. Clamp ◽  
Dapeng Xu ◽  
Yasushi Kusuoka ◽  
Manabu Hori
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Rrna Gene ◽  
Evolutionary Divergence ◽  
Ssu Rrna ◽  
Generic Level ◽  
Ssu Rrna Gene ◽  
The Family ◽  
Molecular Phylogenetic

Little is known about the phylogeny of the family Vorticellidae at the generic level because few comprehensive analyses of molecular phylogenetic relationships between members of this group have, so far, been done. As a result, the phylogenetic positions of some genera that were based originally on morphological analyses remain controversial. In the present study, we performed phylogenetic analyses of vorticellids based on the sequence of the small-subunit (SSU) rRNA gene, including one species of the genus Apocarchesium, for which no sequence has previously been reported. Phylogenetic trees were reconstructed with SSU rRNA gene sequences by using four different methods (Bayesian analysis, maximum-likelihood, neighbour-joining and maximum-parsimony) and had a consistent branching pattern. Members of the genera Vorticella (except V. microstoma) and Carchesium formed a clearly defined, well supported clade that was divergent from the clade comprising members of the genera Pseudovorticella and Epicarchesium, suggesting that the differences in the silverline system (transverse vs reticulate) among vorticellids may be the result of genuine evolutionary divergence. Members of the newly established genus Apocarchesium clustered within the family Vorticellidae basal to the clade containing members of the genera Pseudovorticella and Epicarchesium and were distinct from members of the genus Carchesium, supporting the validity of Apocarchesium as a novel genus. Additional phylogenetic analyses of 21 strains representing seven genera from the families Vorticellidae and Zoothamniidae were performed with single datasets (ITS1–5.8S–ITS2, ITS2 alone) and combined datasets (SSU rRNA+ITS1–5.8S–ITS2, SSU rRNA+ITS2) to explore further the phylogenetic relationship between the three morphologically similar genera Carchesium, Epicarchesium and Apocarchesium, using characteristics not included in previous analyses. The phylogenetic trees reconstructed with combined datasets were more robust and therefore more reliable than those based on single datasets and supported the results of trees based on SSU rRNA sequences.

scholarly journals Perexilibacter aurantiacus gen. nov., sp. nov., a novel member of the family ‘Flammeovirgaceae’ isolated from sediment

2007 ◽  
Vol 57 (5) ◽  
pp. 964-968 ◽  
Author(s):  
Jaewoo Yoon ◽  
Shu Ishikawa ◽  
Hiroaki Kasai ◽  
Akira Yokota
Keyword(s):  
New Genus ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
The Family ◽  
Republic Of Palau ◽  
The 16S Rrna Gene

A strictly aerobic, Gram-negative, gliding, dull-orange-pigmented, rod-shaped bacterium, designated strain Shu-F-UV2-2T, was isolated from sediment (Carp Island, Republic of Palau) and was the focus of a polyphasic taxonomic study. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated to the family ‘Flammeovirgaceae’ of the phylum Bacteroidetes and that it showed highest sequence similarity (85.5 %) to Flammeovirga yaeyamensis NBRC 100898T. The novel isolate could be differentiated phenotypically and physiologically from recognized members of the family ‘Flammeovirgaceae’. The G+C content of the DNA was 43.0 mol%, MK-7 was the major menaquinone and iso-C15 : 0, C16 : 1 ω7c and C16 : 1 ω5c were the major fatty acids. On the basis of this polyphasic evidence, it was concluded that strain Shu-F-UV2-2T represents a novel species in a new genus of the family ‘Flammeovirgaceae’, for which the name Perexilibacter aurantiacus gen. nov., sp. nov. is proposed. The type strain is Shu-F-UV2-2T (=MBIC06993T=IAM 15413T=KCTC 12867T).

A molecular phylogenetic approach for unravelling the taxonomic status of Basilaphelenchus persicus n. gen., n. sp. (Aphelenchoididae: Tylaphelenchinae)

Nematology ◽  
2018 ◽  
Vol 20 (6) ◽  
pp. 567-582 ◽  
Author(s):  
Majid Pedram ◽  
Natsumi Kanzaki ◽  
Robin M. Giblin-Davis ◽  
Ebrahim Pourjam
Keyword(s):  
New Genus ◽  
Small Body ◽  
Taxonomic Status ◽  
Cephalic Region ◽  
Rrna Gene ◽  
Phylogenetic Studies ◽  
Sister Clade ◽  
The Family ◽  
Lsu Rrna Gene ◽  
Molecular Phylogenetic

Summary Basilaphelenchus persicus n. gen., n. sp. is described and illustrated based on morphological and molecular phylogenetic studies. The new genus belongs to the family Aphelenchoididae and is characterised mainly by the small body size of females (297-393 μm) and males (304-331 μm), high cephalic region in both sexes, fine 5.5-7.8 μm long stylet that is barely visible in mounted specimens yet clear in fresh individuals, stylet with a linear conus and weak shaft ending in three elongate, posteriorly directed, knobs, small spherical metacorpus with posteriorly located (at 72-75% of metacorpus) weak but distinct valve, monodelphic-prodelphic reproductive system with a long post-vulval uterine sac containing large rounded sperm cells, a vulva lacking any flap apparatus, conical tail of female usually ventrally bent at tip and male tail ventrally bent as in the female, lacking the P1 supplement, but with three pairs of caudal papillae, and small arcuate spicules with rounded condylus and small pointed rostrum. The new genus is similar to both Tylaphelenchus and Pseudaphelenchus in the possession of a raised cephalic region and a small spherical metacorpus, placing it in the subfamily Tylaphelenchinae. It is also typologically similar to Aphelenchoides. Molecular phylogenetic studies using both SSU and LSU rRNA gene sequences (both partial) revealed that the new genus formed a robustly supported sister clade with Pseudaphelenchus spp. and had a basal placement to this clade and, probably, to all other aphelenchoidids. Tylaphelenchus grosmannae is transferred to the new genus as B. grosmannae n. comb. and A. christinae n. comb. (= T. christinae) is proposed. The taxonomic status of Tylaphelenchus is discussed and T. sinodendroni n. comb. (= A. sinodendroni) proposed.

Xiangella phaseoli gen. nov., sp. nov., a member of the family Micromonosporaceae

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2138-2145 ◽  
Author(s):  
Xiangjing Wang ◽  
Feiyu Jia ◽  
Chongxi Liu ◽  
Junwei Zhao ◽  
Liang Wang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
New Genus ◽  
Gene Sequence ◽  
Gene Signature ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The 16S Rrna Gene

A novel endophytic actinomycete, designated strain NEAU-J5T was isolated from roots of snap bean (Phaseolus vulgaris L.). Comparative analysis of the 16S rRNA gene sequence indicated that NEAU-J5T is phylogenetically related to members of the family Micromonosporaceae . The whole-cell sugars were galactose, mannose and glucose. The predominant menaquinones were MK-9(H4) and MK-9(H6). The major fatty acids were C16 : 0, C18 : 0, C17 : 1ω7c, iso-C15 : 0 and C17 : 0. The phospholipids were phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol and phosphatidylinositol mannoside. The DNA G+C content was 72.2 mol%. On the basis of the morphological and chemotaxonomic characteristics, phylogenetic analysis and characteristic patterns of 16S rRNA gene signature nucleotides, strain NEAU-J5T represents a novel species of a new genus within the family Micromonosporaceae , for which the name Xiangella phaseoli gen. nov., sp. nov. is proposed. The type strain of Xiangella phaseoli is strain NEAU-J5T ( = CGMCC 4.7038T = DSM 45730T).

scholarly journals Halarchaeum acidiphilum gen. nov., sp. nov., a moderately acidophilic haloarchaeon isolated from commercial solar salt

2010 ◽  
Vol 60 (11) ◽  
pp. 2513-2516 ◽  
Author(s):  
Hiroaki Minegishi ◽  
Akinobu Echigo ◽  
Shuhei Nagaoka ◽  
Masahiro Kamekura ◽  
Ron Usami
Keyword(s):  
New Genus ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
New Genus And Species ◽  
Solar Salt ◽  
The Family ◽  
Optimum Ph ◽  
The 16S Rrna Gene ◽  
Moderately Acidophilic

A novel halophilic archaeon, strain MH1-52-1T, was isolated from solar salt imported from Australia. Cells were pleomorphic, non-motile and Gram-negative. Strain MH1-52-1T required at least 3.0 M NaCl and 1 mM Mg2+ for growth. Strain MH1-52-1T was able to grow at pH 4.0–6.0 (optimum, pH 4.4–4.5) and 15–45 °C (optimum, 37 °C). The diether phospholipids phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, derived from both C20C20 and C20C25 archaeol, were present. Four unidentified glycolipids were also detected. The 16S rRNA gene sequence showed the highest similarity to that of Halobacterium noricense A1T (91.7 %); there were lower levels of similarity to other members of the family Halobacteriaceae. The G+C content of its DNA was 61.4 mol%. Based on our phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolate should be classified as a representative of a new genus and species, for which the name Halarchaeum acidiphilum gen. nov., sp. nov. is proposed. The type strain of Halarchaeum acidiphilum is MH1-52-1T (=JCM 16109T =DSM 22442T =CECT 7534T).

scholarly journals Aureibacter tunicatorum gen. nov., sp. nov., a marine bacterium isolated from a coral reef sea squirt, and description of Flammeovirgaceae fam. nov.

2011 ◽  
Vol 61 (10) ◽  
pp. 2342-2347 ◽  
Author(s):  
Jaewoo Yoon ◽  
Kyoko Adachi ◽  
Sanghwa Park ◽  
Hiroaki Kasai ◽  
Akira Yokota
Keyword(s):  
Marine Bacterium ◽  
New Genus ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
The Novel ◽  
Sea Squirt ◽  
Golden Yellow ◽  
The Family ◽  
The 16S Rrna Gene

Two aerobic, Gram-reaction-negative, golden-yellow pigmented and rod-shaped bacteria, designated strains A5Q-118T and A5Q-27, were isolated from an unidentified sea squirt that thrives in the coral reefs off the coast of Okinawa, Japan. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolates were affiliated with the family ‘Flammeovirgaceae’ of the phylum Bacteroidetes. Strains A5Q-118T and A5Q-27 shared 100 % sequence similarity with each other and showed <92 % similarity with other cultivated members of the family ‘Flammeovirgaceae’. The novel isolates were phenotypically and physiologically different from strains described previously. The DNA G+C content was 35.5–36.2 mol%, MK-7 was the major menaquinone and iso-C15 : 0 and C16 : 1ω5c were the major fatty acids. Based on the results of this polyphasic taxonomic study, it was concluded that strains A5Q-118T and A5Q-27 represent a novel species in a new genus of the family ‘Flammeovirgaceae’, for which the name Aureibacter tunicatorum gen. nov., sp. nov. is proposed. Proposal for designation of the Flammeovirgaceae fam. nov. is also presented. The type strain of Aureibacter tunicatorum is A5Q-118T ( = KCTC 23232T  = NBRC 107587T).

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