scholarly journals Gene encoding the CTP synthetase as an appropriate molecular tool for identification and phylogenetic study of the family Bifidobacteriaceae

2018 ◽  
Vol 7 (4) ◽  
pp. e00579 ◽  
Author(s):  
Jiří Killer ◽  
Chahrazed Mekadim ◽  
Radko Pechar ◽  
Věra Bunešová ◽  
Jakub Mrázek ◽  
...  
Keyword(s):  
Phylogenetic Study ◽  
Ctp Synthetase ◽  
Gene Encoding ◽  
Molecular Tool ◽  
The Family

scholarly journals Novel Organization of Genes Involved in Prophage Excision Identified in the Temperate Lactococcal Bacteriophage TP901-1

1999 ◽  
Vol 181 (23) ◽  
pp. 7291-7297 ◽  
Author(s):  
Anne Breüner ◽  
Lone Brøndsted ◽  
Karin Hammer
Keyword(s):  
Basic Protein ◽  
Genetic Material ◽  
Gene Encoding ◽  
Low Frequencies ◽  
Uracil Phosphoribosyltransferase ◽  
Phage Integrase ◽  
The Family ◽  
Phage Protein ◽  
Selection Of

ABSTRACT In this work, the phage-encoded proteins involved in site-specific excision of the prophage genome of the temperate lactococcal bacteriophage TP901-1 were identified. The phage integrase is required for the process, and a low but significant frequency of excision is observed when the integrase is the only phage protein present. However, 100% excision is observed when the phage protein Orf7 is provided as well as the integrase. Thus, Orf7 is the TP901-1 excisionase, and it is the first excisionase identified that is used during excisive recombination catalyzed by an integrase belonging to the family of extended resolvases. Orf7 is a basic protein of 64 amino acids, and the corresponding gene (orf7) is the third gene in the early lytic operon. This location of an excisionase gene of a temperate bacteriophage has never been described before. The experiments are based on in vivo excision of specifically designed excision vectors carrying the TP901-1 attP site which are integrated intoattB on the chromosome of Lactococcus lactis. Excision of the vectors was investigated in the presence of different TP901-1 genes. In order to detect very low frequencies of excision, a method for positive selection of loss of genetic material based upon the upp gene (encoding uracil phosphoribosyltransferase) was designed, since upp mutants are resistant to fluorouracil. By using this system, frequencies of excision on the order of 10−5 per cell could easily be measured. The described selection principle may be of general use for many organisms and also for types of deletion events other than excision.

Phylogeny of the family Pasteurellaceae based on rpoB sequences

2004 ◽  
Vol 54 (4) ◽  
pp. 1393-1399 ◽  
Author(s):  
Bożena Korczak ◽  
Henrik Christensen ◽  
Stefan Emler ◽  
Joachim Frey ◽  
Peter Kuhnert
Keyword(s):  
16S Rdna ◽  
Dna Hybridization ◽  
Gene Encoding ◽  
Phylogenetic Studies ◽  
Study Selection ◽  
Gene Sequence Analysis ◽  
Rdna Sequencing ◽  
The Family ◽  
Type Strains ◽  
Selection Of

Sequences of the gene encoding the β-subunit of the RNA polymerase (rpoB) were used to delineate the phylogeny of the family Pasteurellaceae. A total of 72 strains, including the type strains of the major described species as well as selected field isolates, were included in the study. Selection of universal rpoB-derived primers for the family allowed straightforward amplification and sequencing of a 560 bp fragment of the rpoB gene. In parallel, 16S rDNA was sequenced from all strains. The phylogenetic tree obtained with the rpoB sequences reflected the major branches of the tree obtained with the 16S rDNA, especially at the genus level. Only a few discrepancies between the trees were observed. In certain cases the rpoB phylogeny was in better agreement with DNA–DNA hybridization studies than the phylogeny derived from 16S rDNA. The rpoB gene is strongly conserved within the various species of the family of Pasteurellaceae. Hence, rpoB gene sequence analysis in conjunction with 16S rDNA sequencing is a valuable tool for phylogenetic studies of the Pasteurellaceae and may also prove useful for reorganizing the current taxonomy of this bacterial family.

scholarly journals Review on the molecular study of the Diplozoidae: analyses of currently available genetic data, what it tells us, and where to go from here

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Quinton Marco Dos Santos ◽  
Annemariè Avenant-Oldewage
Keyword(s):  
Sequence Data ◽  
Molecular Study ◽  
Turn Of The Century ◽  
Phylogenetic Study ◽  
Online Databases ◽  
Crucial Component ◽  
The Family ◽  
Molecular Information ◽  
Taxonomic Approach ◽  
Species Descriptions

Abstract The use of molecular tools in the study of parasite taxonomy and systematics have become a substantial and crucial component of parasitology. Having genetic characterisation at the disposal of researchers has produced mostly useful, and arguably more objective conclusions. However, there are several groups for which limited genetic information is available and, coupled with the lack of standardised protocols, renders molecular study of these groups challenging. The Diplozoidae are fascinating and unique monogeneans parasitizing mainly freshwater cyprinid fishes in Europe, Asia and Africa. This group was studied from a molecular aspect since the turn of the century and as such, limitations and variability concerning the use of these techniques have not been clearly defined. In this review, all literature and molecular information, primarily from online databases such as GenBank, were compiled and scrupulously analysed for the Diplozoidae. This was done to review the information, detect possible pitfalls, and provide a “checkpoint” for future molecular studies of the family. Hindrances detected are the availability of sequence data for only a limited number of species, frequently limited to a single sequence per species, and the heavy reliance on one non-coding ribosomal marker (ITS2 rDNA) which is difficult to align objectively and displays massive divergences between taxa. Challenging species identification and limited understanding of diplozoid species diversity and plasticity are also likely restricting factors, all of which hamper the accurate taxonomic and phylogenetic study of this group. Thus, a more integrated taxonomic approach through the inclusion of additional markers, application of more rigorous morphological assessment, more structured barcoding techniques, alongside thorough capturing of species descriptions including genetypes, genophore vouchers and reference collections in open sources are encouraged. The pitfalls highlighted are not singular to the Diplozoidae, and the study of other groups may benefit from the points raised here as well.

Complementary description of Africoseius lativentris and placement of Africoseius in Podocinidae (Acari, Mesostigmata) based on molecular and morphological evidences

2019 ◽  
Vol 24 (10) ◽  
pp. 2369-2394 ◽  
Author(s):  
Diana Rueda-Ramírez ◽  
Jandir C. Santos ◽  
Nazer Famah Sourassou ◽  
Peterson R. Demite ◽  
Andrés Puerta-gonzález ◽  
...  
Keyword(s):  
Taxonomic Position ◽  
Phylogenetic Study ◽  
Similar Data ◽  
Free Living ◽  
Paulo State ◽  
Rdna Sequences ◽  
The Family ◽  
28S Rdna Sequences ◽  
Similarities And Differences ◽  
Longitudinal Extension

Morphological details of specimens collected from several localities in Brazil and identified as Africoseius lativentris (Karg 1982) are provided. The taxonomic position of Africoseius Krantz, 1962 has been debated over the years, with repeated changes in its familial placement. A phylogenetic study based on 18S and 28S rDNA sequences of the Brazilian population of A. lativentris collected at Jaboticabal, São Paulo State, and similar data of 70 taxa representing 11 families of Gamasina indicated that Africoseius is a member of the well-supported Podocinidae (sensu Lindquist et al. 2009) clade. The main morphological similarities and differences between Africoseius and the group of species until now placed in Podocinidae sensu Lindquist et al. (2009) are listed. Apomorphic characteristics uniting those taxa include the hypotrichous condition of tibia I (eight and nine setae instead of ten or more in other free-living Gamasina) and the insertions of av2 and pv2, considerably more distal on tarsi II and III than in the majority of the free-living Gamasina. Within Podocinidae, a new subfamily, Africoseiinae, is proposed, based on uniquely apomorphic characteristics of the setae ad4 and pd4 (sensu  Evans 1969) of tarsi II–IV absent, and setae av4 and pv4 of same basitarsi long, incurved and close to each other and to a posterior longitudinal extension of the peripodomeric suture and on the attenuated form of the lateral (rather than the medial) hypostomatic setae. This subfamily is currently represented by Africoseius areolatus Krantz and Africoseius lativentris (Karg 1982), while all other presently known species of the family are now placed in the subfamily Podocininae.

Regarding the taxonomic status of Ophyra Robineau-Desvoidy (Diptera: Muscidae): A molecular approach

Zootaxa ◽  
2004 ◽  
Vol 712 (1) ◽  
pp. 1 ◽  
Author(s):  
GUILHERME SCHNELL E. SCHUEHLI ◽  
CLAUDIO JOSÉ BARROS DE CARVALHO ◽  
BRIAN M. WIEGMANN
Keyword(s):  
Elongation Factor ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Systematic Position ◽  
Mitochondrial Genes ◽  
Phylogenetic Study ◽  
Molecular Approach ◽  
The Family ◽  
The Subject ◽  
Elongation Factor 1

The muscid genus Ophyra has long been the subject of debate over its placement within the family. However, a phylogenetic study has never been conducted that would clarify its systematic position. In the present paper, phylogenetic relationships are examined between Ophyra albuquerquei and related muscid genera. The mitochondrial genes Cytochrome Oxidase I and II and tRNA-Leu were used combined with the nuclear genes CAD and Elongation Factor 1 to compose a matrix with 2989 characters (716 parsimonyinformative). These characters were analyzed under parsimony resulting in a single most parsimonious tree. Contrary to some recent classifications, our molecular data suggest the placement of Ophyra albuquerquei within the Muscinae in a separate position from the azeliine genus Hydrotaea.

An intronless gene encoding a potential member of the family of receptors coupled to guanine nucleotide regulatory proteins

Nature ◽  
1987 ◽  
Vol 329 (6134) ◽  
pp. 75-79 ◽  
Author(s):  
Brian K. Kobilka ◽  
Thomas Frielle ◽  
Sheila Collins ◽  
Theresa Yang-Feng ◽  
Tong Sun Kobilka ◽  
...  
Keyword(s):  
Regulatory Proteins ◽  
Guanine Nucleotide ◽  
Gene Encoding ◽  
Intronless Gene ◽  
The Family ◽  
Guanine Nucleotide Regulatory Proteins ◽  
Potential Member

scholarly journals Biodiversity and phylogeny of Ammotheidae (Arthropoda: Pycnogonida)

2017 ◽  
Author(s):  
Romain Sabroux ◽  
Laure Corbari ◽  
Franz Krapp ◽  
Céline Bonillo ◽  
Stéphanie Le Prieur ◽  
...  
Keyword(s):  
Type Species ◽  
Base Composition ◽  
Phylogenetic Signal ◽  
Mitochondrial Gene ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Gene Encoding ◽  
The Family ◽  
Statistical Support ◽  
Selection Of

The family Ammotheidae is the most diversified group of the class Pycnogonida, with 297 species described in 20 genera. Its monophyly and intergeneric relationships have been highly debated in previous studies. Here, we investigated the phylogeny of Ammotheidae using specimens from poorly studied areas. We sequenced the mitochondrial gene encoding the first subunit of cytochrome c oxidase (CO1) from 104 specimens. The complete nuclear 18S rRNA gene was sequenced from a selection of 80 taxa to provide further phylogenetic signal. The base composition in CO1 shows a higher heterogeneity in Ammotheidae than in other families, which may explain their apparent polyphyly in the CO1 tree. Although deeper nodes of the tree receive no statistical support, Ammotheidae was found to be monophyletic and divided into two clades, here defined as distinct subfamilies: Achelinae comprises the genera Achelia Hodge, 1864, Ammothella Verrill, 1900, Nymphopsis Haswell, 1884 and Tanystylum Miers, 1879; and Ammotheinae includes the genera Ammothea Leach, 1814, Acheliana Arnaud, 1971, Cilunculus Loman, 1908, Sericosura Fry & Hedgpeth, 1969 and also Teratonotum gen. nov., including so far only the type species Ammothella stauromata Child, 1982. The species Cilunculus gracilis Nakamura & Child, 1991 is reassigned to Ammothella, forming the binomen Ammothella gracilis (Nakamura & Child, 1991) comb. nov. Additional taxonomic re-arrangements are suggested for the genera Achelia, Acheliana, Ammothella and Cilunculus.

scholarly journals Phylogenetic Systematics of Pterostichites (Carabidae)

2019 ◽  
Vol 2 ◽  
Author(s):  
Kipling Will
Keyword(s):  
Northern Hemisphere ◽  
Phylogenetic Study ◽  
Phylogenetic Systematics ◽  
The Family

As typically comprised, Pterostichitae includes about 10% of the species described in Carabidae. The phylogenetic study of the family Carabidae headed up by D. Maddison (OSU) that includes 550 carabid species covers all major clades of pterostichites and their putative relatives in Harpalinae. I will present results for the Pterostichitae from that analysis, focusing on relationships among major clades in the Northern Hemisphere (Pterostichina, Zabrina, Sphodrina) and the placement of more distantly related taxa (e.g., Abacetini, Drimostomatini). As analyses of the data have not yet been completed, there will be additional discoveries this summer, about which I will report in my talk.

scholarly journals Phylogeny and Taxonomic of Xylaria Associated With Fallen Fruits and Seeds in China

2021 ◽  
Author(s):  
Hai-Xia Ma ◽  
Zi-Kun Song ◽  
Xiao-Yan Pan ◽  
Zhi Qu ◽  
Si-Yu Ma ◽  
...  
Keyword(s):  
New Taxa ◽  
Phylogenetic Study ◽  
Similar Species ◽  
The Family ◽  
First Time ◽  
Β Tubulin

Abstract A study of the phylogeny and taxonomy of Xylaria species associated with fallen fruits and seeds within the genus Xylaria and among gernera of the family Xylariaceae based on ITS, RPB2, and β-tubulin sequences of 97 species from Xylaria and 7 other genera of the Xylariaceae were analyzed. The 7 genera included Amphirosellinia, Astrocystis, Kretzschmaria, Nemania, Podosordaria, Poronia, and Rosellinia. The results of our phylogenetic study showed that Xylaria species were distributed among five major clades, X1, X2, X3, X4, and X5. Clade X1 encompassed exclusively those Xylaria speices associated with termite nests, clade X2 composed Xylaria speices growing on leaves, fibrous pericarps and some on wood, clade X3 contained endocarp-inhabiting Xylaria species, clade X4 composed primarily of wood-inhabiting Xylaria speices, clade X5 composed primarily of species of Xylaria associated with leguminous pods. Xylaria appears to be a paraphyletic genus, with most of 7 genera included in it. Nine new taxa associated with fallen fruits and seeds, namely X. aleuriticola, X. cordiicola, X. meliicola, X. microcarpa, X. rogersii, X. schimicola, X. terminaliicola, X. theaceicola, and X. wallichii, are described, illustrated, and compared to morphologically similar species. Four species, X. carpophila, X. liquidambaris, X. oxyacanthae, and X. xanthinovelutina, were reported in China for the first time. A key to all the accepted species associated with fallen fruits and seeds in Xylaria from China was given.

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