Phylogenetic analysis of the genera Streptomyces and Kitasatospora based on partial RNA polymerase β-subunit gene (rpoB) sequences

The RNA polymerase β-subunit genes (rpoB) of 67 Streptomyces strains, representing 57 species, five Kitasatospora strains and Micromonospora echinospora KCTC 9549 were partially sequenced using a pair of rpoB PCR primers. Among the streptomycetes, 99·7–100 % similarity within the same species and 90·2–99·3 % similarity at the interspecific level were observed by analysis of the determined rpoB sequences. The topology of the phylogenetic tree based on rpoB sequences was similar to that of 16S rDNA. The five Kitasatospora strains formed a stable monophyletic clade and a sister group to the clade comprising all Streptomyces species. Although there were several discrepancies in the details, considerable agreement was found between the results of rpoB analysis and those of numerical phenetic classification. This study demonstrates that analysis of rpoB can be used as an alternative genetic method in parallel to conventional taxonomic methods, including numerical phenetic and 16S rDNA analyses, for the phylogenetic analyses of the genera Streptomyces and Kitasatospora.

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Bacterial diversity of soil under eucalyptus assessed by 16S rDNA sequencing analysis

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2006001000008 ◽

2006 ◽

Vol 41 (10) ◽

pp. 1507-1516 ◽

Cited By ~ 15

Author(s):

Érico Leandro da Silveira ◽

Rodrigo Matheus Pereira ◽

Denilson César Scaquitto ◽

Eliamar Aparecida Nascimbém Pedrinho ◽

Silvana Pómpeia Val-Moraes ◽

...

Keyword(s):

Bacterial Diversity ◽

16S Rdna ◽

Phylogenetic Analyses ◽

Chemical Properties ◽

Pcr Primers ◽

Native Forest ◽

Sequencing Analysis ◽

Soil Dna ◽

Rdna Sequencing ◽

The Impact

Studies on the impact of Eucalyptus spp. on Brazilian soils have focused on soil chemical properties and isolating interesting microbial organisms. Few studies have focused on microbial diversity and ecology in Brazil due to limited coverage of traditional cultivation and isolation methods. Molecular microbial ecology methods based on PCR amplified 16S rDNA have enriched the knowledge of soils microbial biodiversity. The objective of this work was to compare and estimate the bacterial diversity of sympatric communities within soils from two areas, a native forest (NFA) and an eucalyptus arboretum (EAA). PCR primers, whose target soil metagenomic 16S rDNA were used to amplify soil DNA, were cloned using pGEM-T and sequenced to determine bacterial diversity. From the NFA soil 134 clones were analyzed, while 116 clones were analyzed from the EAA soil samples. The sequences were compared with those online at the GenBank. Phylogenetic analyses revealed differences between the soil types and high diversity in both communities. Soil from the Eucalyptus spp. arboretum was found to have a greater bacterial diversity than the soil investigated from the native forest area.

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Phylogenetic relationships of the lower Cyclorrhapha (Diptera: Brachycera) based on 28S rDNA sequences

Insect Systematics & Evolution ◽

10.1163/187631202x00235 ◽

2002 ◽

Vol 33 (4) ◽

pp. 445-456 ◽

Cited By ~ 14

Author(s):

Brian M. Wiegmann ◽

Kenneth P. Collins

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Sister Group ◽

28S Rdna ◽

Morphological Data ◽

Monophyletic Clade ◽

Rdna Sequences ◽

28S Rdna Sequences

AbstractCyclorrhaphan Diptera are an extremely successful clade of ecologically and phylogenenetically important flies. Despite their significance the relationships among lower cyclorrhaphans ('Aschiza') remain controversial in spite of several morphologically based phylogenetic analyses. We sequenced a 2.7-kb fragment of 28S rDNA for taxa representing all lower cyclorrhaphan families (except Ironomyiidae), four schizophoran families, and seven empidoid out-group taxa. Phylogenetic analysis of these data strongly supports a monophyletic Cyclorrhapha (including the enigmatic taxon Opetia nigra) that is divided into two clades - a well-supported Eumuscomorpha (Syrphidae + Pipunculidae + Schizophora), and a weakly-supported Platypezoidea (all non-Eumuscomorpha). Consequently, the former grouping known as Aschiza, which included syrphids and pipunculids, is not a valid monophyletic clade. Within Platypezoidea, most of our analyses place Lonchopteridae as sister group to Opetiidae, and strongly support the monophyly of Sciadoceridae + Phoridae. Among the Eumuscomorpha we do not recover the monophyly of Syrphoidea (Syrphidae + Pipunculidae). Instead, all analyses place Pipunculidae as the sister group to Schizophora. This novel finding has never been proposed based on morphological data and will require more data (both molecular and morphological) and taxa to confirm.

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Phylogenetic Analysis of Nonthermophilic Members of the Kingdom Crenarchaeota and Their Diversity and Abundance in Soils

Applied and Environmental Microbiology ◽

10.1128/aem.64.11.4333-4339.1998 ◽

1998 ◽

Vol 64 (11) ◽

pp. 4333-4339 ◽

Cited By ~ 159

Author(s):

Daniel H. Buckley ◽

Joseph R. Graber ◽

Thomas M. Schmidt

Keyword(s):

16S Rrna ◽

16S Rdna ◽

Phylogenetic Analyses ◽

Pcr Primers ◽

Soil Samples ◽

Molecular Techniques ◽

Rrna Gene ◽

Rdna Sequences ◽

16S Rdna Sequences ◽

Long Term Ecological Research

ABSTRACT Within the last several years, molecular techniques have uncovered numerous 16S rRNA gene (rDNA) sequences which represent a unique and globally distributed lineage of the kingdom Crenarchaeotathat is phylogenetically distinct from currently characterized crenarchaeotal species. rDNA sequences of members of this novel crenarchaeotal group have been recovered from low- to moderate-temperature environments (−1.5 to 32°C), in contrast to the high-temperature environments (temperature, >80°C) required for growth of the currently recognized crenarchaeotal species. We determined the diversity and abundance of the nonthermophilic members of the Crenarchaeota in soil samples taken from cultivated and uncultivated fields located at the Kellogg Biological Station’s Long-Term Ecological Research site (Hickory Corners, Mich.). Clones were generated from 16S rDNA that was amplified by using broad-specificity archaeal PCR primers. Twelve crenarchaeotal sequences were identified, and the phylogenetic relationships between these sequences and previously described crenarchaeotal 16S rDNA sequences were determined. Phylogenetic analyses included nonthermophilic crenarchaeotal sequences found in public databases and revealed that the nonthermophilic Crenarchaeota group is composed of at least four distinct phylogenetic clusters. A 16S rRNA-targeted oligonucleotide probe specific for all known nonthermophilic crenarchaeotal sequences was designed and used to determine their abundance in soil samples. The nonthermophilicCrenarchaeota accounted for as much as 1.42% ± 0.42% of the 16S rRNA in the soils analyzed.

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Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

Systematic Botany ◽

10.1600/036364419x15710776741477 ◽

2019 ◽

Vol 44 (4) ◽

pp. 930-942

Author(s):

Geraldine A. Allen ◽

Luc Brouillet ◽

John C. Semple ◽

Heidi J. Guest ◽

Robert Underhill

Keyword(s):

North American ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Sister Group ◽

Morphological Evidence ◽

South American ◽

New Combinations ◽

The North ◽

Hybridization Event ◽

Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

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Molecular analysis of the mitochondrial markers COI, 12S rDNA and 16S rDNA for six species of Iranian scorpions

BMC Research Notes ◽

10.1186/s13104-021-05449-3 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Parisa Soltan-Alinejad ◽

Javad Rafinejad ◽

Farrokh Dabiri ◽

Piero Onorati ◽

Olle Terenius ◽

...

Keyword(s):

16S Rdna ◽

Phylogenetic Analyses ◽

Coi Gene ◽

Diagnostic Tools ◽

Morphological Identification ◽

Species Determination ◽

Important Species ◽

Mitochondrial Markers ◽

12S Rdna ◽

Rdna Sequences

Abstract Objectives Annually, 1.2 million humans are stung by scorpions and severely affected by their venom. Some of the scorpion species of medical importance have a similar morphology to species with low toxicity. To establish diagnostic tools for surveying scorpions, the current study was conducted to generate three mitochondrial markers, Cytochrome Oxidase I (COI gene), 12S rDNA and 16S rDNA for six species of medically important Iranian scorpions: Androctonus crassicauda, Hottentotta saulcyi, Mesobuthus caucasicus, M. eupeus, Odontobuthus doriae, and Scorpio maurus. Results Phylogenetic analyses of the obtained sequences corroborated the morphological identification. For the first time, 12S rDNA sequences are reported from Androctonus crassicauda, Hottentotta saulcyi, Mesobuthus caucasicus and M. eupeus and also the 16S rDNA sequence from Hottentotta saulcyi. We conclude that the mitochondrial markers are useful for species determination among these medically important species of scorpions.

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Phenotypically and Genotypically Heterogeneous Strains of Pseudomonas syringae Associated With Alfalfa Leaf Spot Disease in Iran

Plant Disease ◽

10.1094/pdis-06-19-1153-re ◽

2019 ◽

Vol 103 (12) ◽

pp. 3199-3208 ◽

Cited By ~ 2

Author(s):

Maryam Ansari ◽

S. Mohsen Taghavi ◽

Sadegh Zarei ◽

Soraya Mehrb-Moghadam ◽

Hamzeh Mafakheri ◽

...

Keyword(s):

Host Range ◽

Pseudomonas Syringae ◽

Leaf Spot ◽

Phylogenetic Analyses ◽

Housekeeping Genes ◽

Pcr Primers ◽

Phylogenetic Position ◽

Leaf Spot Disease ◽

Bacterial Strains ◽

Alfalfa Leaf

In this study, we provide a polyphasic characterization of 18 Pseudomonas spp. strains associated with alfalfa leaf spot symptoms in Iran. All of the strains were pathogenic on alfalfa, although the aggressiveness and symptomology varied among the strains. All strains but one were pathogenic on broad bean, cucumber, honeydew, and zucchini, whereas only a fraction of the strains were pathogenic on sugar beet, tomato, and wheat. Syringomycin biosynthesis genes (syrB1 and syrP) were detected using the corresponding PCR primers in all of the strains isolated from alfalfa. Phylogenetic analyses using the sequences of four housekeeping genes (gapA, gltA, gyrB, and rpoD) revealed that all of the strains except one (Als34) belong to phylogroup 2b of P. syringae sensu lato, whereas strain Als34 placed within phylogroup 1 close to the type strain of P. syringae pv. apii. Among the phylogroup 2b strains, nine strains were phylogenetically close to the P. syringae pv. aptata clade, whereas the remainder were scattered among P. syringae pv. atrofaciens and P. syringae pv. syringae strains. Pathogenicity and host range assays of the bacterial strains evaluated in this study on a set of taxonomically diverse plant species did not allow us to assign a “pathovar” status to the alfalfa strains. However, these results provide novel insight into the host range and phylogenetic position of the alfalfa-pathogenic members of P. syringae sensu lato, and they reveal that phenotypically and genotypically heterogeneous strains of the pathogen cause bacterial leaf spot of alfalfa.

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Affinities of the Boletus chromapes group to Royoungia and the description of two new genera, Harrya and Australopilus

Australian Systematic Botany ◽

10.1071/sb12028 ◽

2012 ◽

Vol 25 (6) ◽

pp. 418 ◽

Cited By ~ 23

Author(s):

Roy E. Halling ◽

Mitchell Nuhn ◽

Todd Osmundson ◽

Nigel Fechner ◽

James M. Trappe ◽

...

Keyword(s):

New Genus ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Elongation Factor ◽

Sister Group ◽

Molecular Data ◽

Translation Elongation ◽

Spore Deposit ◽

Large Subunit Rdna ◽

Translation Elongation Factor 1Α

Harrya is described as a new genus of Boletaceae to accommodate Boletus chromapes, a pink-capped bolete with a finely scabrous stipe adorned with pink scabers, a chrome yellow base and a reddish-brown spore deposit. Phylogenetic analyses of large-subunit rDNA and translation elongation factor 1α confirmed Harrya as a unique generic lineage with two species, one of which is newly described (H. atriceps). Some Chinese taxa were recently placed in a separate genus, Zangia, supported by both morphology and molecular data. Multiple accessions from Queensland, Australia, support the synonymy of at least three species in a separate Australian clade in the new genus, Australopilus. The truffle-like Royoungia is also supported as a separate lineage in this clade of boletes. Even though it lacks stipe characters, it possesses the deep, bright yellow to orange pigments in the peridium. Additional collections from Zambia and Thailand represent independent lineages of uncertain phylogenetic placement in the Chromapes complex, but sampling is insufficient for formal description of new species. Specimens from Java referable to Tylopilus pernanus appear to be a sister group of the Harrya lineage.

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Morphological and molecular characterization of Buzionema lutgardae n. sp. (Nematoda: Oxyuridomorpha: Thelastomatidae) from the cockroach Byrsotria sp. (Blattaria: Blaberidae) in Cuba

Zootaxa ◽

10.11646/zootaxa.4965.2.11 ◽

2021 ◽

Vol 4965 (2) ◽

pp. 385-395

Author(s):

JANS MORFFE ◽

NAYLA GARCÍA ◽

KOICHI HASEGAWA ◽

RAMON A. CARRENO

Keyword(s):

New Species ◽

Molecular Characterization ◽

Sister Group ◽

Cylindrical Part ◽

28S Rdna ◽

Monophyletic Clade ◽

Basal Bulb ◽

Morphological And Molecular Characterization

Buzionema lutgardae n. sp. (Nematoda: Oxyuridomorpha: Thelastomatidae) is described from the cockroach Byrsotria sp. (Blattaria: Blaberidae), endemic to Cuba. Females of B. lutgardae n. sp. are shorter than those of B. validum Kloss, 1966 (1600–2150 µm vs. 3131–3378 µm), but the oesophagus is comparatively longer (b = 2.96–3.77 vs. 4.65–4.87). The lateral alae of the new species extend from ca. the midpoint of the cylindrical part of the procorpus to the level of the anus in contrast to the base of the basal bulb to the level of the anus in B. validum. The males of B. lutgardae n. sp. are shorter than those of B. validum (780–940 µm vs. 1177–1423 µm) and their lateral alae end at some distance before the cloaca instead the level of the cloaca in B. validum. The phylogeny of B. lutgardae n. sp. is inferred by the D2-D3 domains of the 28S rDNA. B. lutgardae n. sp. and B. validum form a monophyletic clade with strong nodal support, as sister-group of the genus Leidynema Schwenck in Travassos, 1929.

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Unraveling the Etiology of North American Grapevine Yellows (NAGY): Novel NAGY Phytoplasma Sequevars Related to ‘Candidatus Phytoplasma pruni’

Plant Disease ◽

10.1094/pdis-11-14-1185-re ◽

2015 ◽

Vol 99 (8) ◽

pp. 1087-1097 ◽

Cited By ~ 19

Author(s):

Robert E. Davis ◽

Ellen L. Dally ◽

Yan Zhao ◽

Ing-Ming Lee ◽

Wei Wei ◽

...

Keyword(s):

16S Rdna ◽

North American ◽

Phylogenetic Analyses ◽

New York State ◽

16S Rrna Genes ◽

Rrna Genes ◽

Vitis Vinifera L ◽

Polymorphism Analysis ◽

Ribosomal Protein Genes ◽

Grapevine Yellows

North American grapevine yellows (NAGY) disease has sometimes been attributed to infection of Vitis vinifera L. by Prunus X-disease phytoplasma (‘Candidatus Phytoplasma pruni’) but this attribution may not be fully adequate. In this study, phytoplasma strains related to ‘Ca. Phytoplasma pruni’ were found in NAGY-diseased grapevines in Maryland, Pennsylvania, Virginia, Ohio, Missouri, and New York State. Based on restriction fragment length polymorphism analysis of 16S ribosomal RNA gene (16S rDNA) sequences, the strains (termed NAGYIII strains) were classified in group 16SrIII (X-disease group) but they contained a recognition site for the restriction endonuclease MseI that is not present in the 16S rDNA of ‘Ca. Phytoplasma pruni’. The 16S rDNA of the strains differed by three or four nucleotides from that of ‘Ca. Phytoplasma pruni’, indicating that they belonged to two novel 16S rDNA sequevars, designated NAGYIIIα and NAGYIIIβ. Both sequevars differed from ‘Ca. Phytoplasma pruni’ by a single base in each of three regions corresponding to species-unique (signature) sequences described for ‘Ca. Phytoplasma pruni’. Phylogenetic analyses of 16S rRNA genes and SecY proteins, and single-nucleotide polymorphism analyses of secY and ribosomal protein genes, further distinguished the two grapevine sequevar lineages from one another and from ‘Ca. Phytoplasma pruni’. The NAGYIIIα and NAGYIIIβ sequevars also differed from ‘Ca. Phytoplasma pruni’ in regions of the folded SecY protein that are predicted to be near or exposed at the outer surface of the phytoplasma membrane. No evidence indicated that diseased grapevines contained any phytoplasma strain conforming to ‘Ca. Phytoplasma pruni’ sensu stricto. Because the NAGYIII sequevars have not been reported in X-disease, a question is raised as to whether NAGYIII and Prunus X-disease are caused by different phytoplasma genotypes.

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Mimaporia, a new genus of Epicopeiidae (Lepidoptera), with description of a new species from Vietnam

Zootaxa ◽

10.11646/zootaxa.4254.5.3 ◽

2017 ◽

Vol 4254 (5) ◽

pp. 537 ◽

Cited By ~ 5

Author(s):

CHIA-HSUAN WEI ◽

SHEN-HORN YEN

Keyword(s):

New Species ◽

New Genus ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Taxonomic Status ◽

Sister Group ◽

Morphological Evidence ◽

New Taxon ◽

The Family ◽

A New Species

The Epicopeiidae is a small geometroid family distributed in the East Palaearctic and Oriental regions. It exhibits high morphological diversity in body size and wing shape, while their wing patterns involve in various complex mimicry rings. In the present study, we attempted to describe a new genus, and a new species from Vietnam, with comments on two assumed congeneric novel species from China and India. To address its phylogenetic affinity, we reconstructed the phylogeny of the family by using sequence data of COI, EF-1α, and 28S gene regions obtained from seven genera of Epicopeiidae with Pseudobiston pinratanai as the outgroup. We also compared the morphology of the new taxon to other epicopeiid genera to affirm its taxonomic status. The results suggest that the undescribed taxon deserve a new genus, namely Mimaporia gen. n. The species from Vietnam, Mimaporia hmong sp. n., is described as new to science. Under different tree building strategies, the new genus is the sister group of either Chatamla Moore, 1881 or Parabraxas Leech, 1897. The morphological evidence, which was not included in phylogenetic analyses, however, suggests its potential affinity with Burmeia Minet, 2003. This study also provides the first, although preliminary, molecular phylogeny of the family on which the revised systematics and interpretation of character evolution can be based.

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