scholarly journals Divergence among Genes Encoding the Elongation Factor Tu of Yersinia Species

2008 ◽  
Vol 190 (22) ◽  
pp. 7548-7558 ◽  
Author(s):  
Sandra Isabel ◽  
Éric Leblanc ◽  
Maurice Boissinot ◽  
Dominique K. Boudreau ◽  
Myrian Grondin ◽  
...  
Keyword(s):  
Gene Conversion ◽  
Phylogenetic Trees ◽  
Gene Evolution ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Elongation Factor Tu ◽  
Phylogenetic Information ◽  
Yersinia Species ◽  
The Family ◽  
Genes Encoding

ABSTRACT Elongation factor Tu (EF-Tu), encoded by tuf genes, carries aminoacyl-tRNA to the ribosome during protein synthesis. Duplicated tuf genes (tufA and tufB), which are commonly found in enterobacterial species, usually coevolve via gene conversion and are very similar to one another. However, sequence analysis of tuf genes in our laboratory has revealed highly divergent copies in 72 strains spanning the genus Yersinia (representing 12 Yersinia species). The levels of intragenomic divergence between tufA and tufB sequences ranged from 8.3 to 16.2% for the genus Yersinia, which is significantly greater than the 0.0 to 3.6% divergence observed for other enterobacterial genera. We further explored tuf gene evolution in Yersinia and other Enterobacteriaceae by performing directed sequencing and phylogenetic analyses. Phylogenetic trees constructed using concatenated tufA and tufB sequences revealed a monophyletic genus Yersinia in the family Enterobacteriaceae. Moreover, Yersinia strains form clades within the genus that mostly correlate with their phenotypic and genetic classifications. These genetic analyses revealed an unusual divergence between Yersinia tufA and tufB sequences, a feature unique among sequenced Enterobacteriaceae and indicative of a genus-wide loss of gene conversion. Furthermore, they provided valuable phylogenetic information for possible reclassification and identification of Yersinia species.

European bumblebees (Hymenoptera: Bombini)- phylogenetic relationships inferred from DNA sequences

2002 ◽  
Vol 33 (4) ◽  
pp. 361-386 ◽  
Author(s):  
Vest Pedersen
Keyword(s):  
Maximum Likelihood ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Elongation Factor ◽  
Nuclear Gene ◽  
The Other ◽  
Elongation Factor 1Α ◽  
Nucleotide Bias

AbstractThe phylogenetics of 40 taxa of European bumblebees were analysed based on PCR amplified and direct sequenced DNA from one region of the mitochondrial gene Cytochrome Oxidase I (1046 bp) and for 26 taxa from two regions in the nuclear gene Elongation Factor 1α (1056 bp). The sequences were aligned to the corresponding sequences in the honey bee. Phylogenetic analyses based on parsimony, as well as maximum likelihood, indicate that the bumblebees can be separated into several well-supported clades. Most of the terminal clades correspond very well with the clades known from former phylogenetic analyses based on morphology and recognized as the subgenera: Mendacibombus, Confusibombus, Psithyrus, Thoracobombus, Megabombus, Rhodobombus, Kallobombus, Alpinobombus, Subterraneobombus, Alpigenobombus, Pyrobombus, Bombus and Melanobombus. All the cuckoo bumblebees form a well-supported clade, the subgenus Psithyrus, within the true bumblebees. All the analyses place Kallobombus as the most basal taxon in contradiction to former analyses. The other deeper nodes of the phylogenetic trees, which are weakly supported, deviate significantly from former published trees - especially the trees based on mtCO-I. Presumably, the reasons are that multiple hits and the strong bias of the bases A and T blur the relationships in the deepest part of the trees. Analyses of the region in mtCO-I show a very strong A+T bias (A+T= 75%), which also indicate preferences in the use of codons with A or T in third positions. In closely related entities, there is only a weak transversion bias (A+T). In the studied regions in EF 1-α, no nucleotide bias is observed. The observed differences in bases between the investigated taxa are relatively small and the gene is too conserved to solve all the questions that the analyses of the deeper nodes using mtCO-I raise.

Saprobic Dothideomycetes in Thailand: Phaeoseptum hydei sp. nov., a new terrestrial ascomycete in Phaeoseptaceae

Phytotaxa ◽  
2020 ◽  
Vol 449 (2) ◽  
pp. 149-163
Author(s):  
DHANUSHKA N. WANASINGHE ◽  
PETER E. MORTIMER ◽  
CHANOKNED SENWANNA ◽  
RATCHADAWAN CHEEWANGKOON
Keyword(s):  
Novel Species ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
University Campus ◽  
Translation Elongation ◽  
Delonix Regia ◽  
The Family ◽  
Elongation Factor 1 Alpha ◽  
Vertical Septum ◽  
Elongation Factor 1

During a survey of saprobic microfungi in Thailand, a dothideomycetous fungus was found on a dead twig of Delonix regia, on the Chiang Mai University campus. This fungus is characterized by fully immersed ascomata under a small blackened pseudoclypeus, pseudoparenchymatous peridium, cellular pseudoparaphyses, cylindrical-clavate asci with a distinct pedicel, overlapping 3–4-seriate, pale to dark brown, broadly fusoid, 7–9-transversally septate ascospores with a vertical septum in nearly all median cells. Multigene phylogenetic analyses, using partial sequences from the 28S nrRNA gene (LSU), 18S nrRNA gene (SSU), internal transcribed spacer regions and intervening 5.8S nrRNA gene (ITS) of the nrDNA operon and the translation elongation factor 1-alpha region (TEF) demonstrated a monophyletic affiliation of the new strain, accommodating the species of Phaeoseptum in the family Phaeoseptaceae. With further morphological and phylogenetic investigations, we justify the new fungus as a novel species, Phaeoseptum hydei in Phaeoseptaceae. Detailed descriptions and illustrations are provided for Phaeoseptum hydei and this novel species compared with the remaining species found in the genus. An updated checklist of microfungi recorded on Delonix regia from around the world is also provided.

scholarly journals Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov. and Veillonellales ord. nov.

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3203-3215 ◽  
Author(s):  
Chantal Campbell ◽  
Mobolaji Adeolu ◽  
Radhey S. Gupta
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Core Protein ◽  
Phylogenetic Analyses ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Conserved Signature Indels ◽  
The Family ◽  
Genomic Analyses

The class Negativicutes is currently divided into one order and two families on the basis of 16S rRNA gene sequence phylogenies. We report here comprehensive comparative genomic analyses of the sequenced members of the class Negativicutes to demarcate its different evolutionary groups in molecular terms, independently of phylogenetic trees. Our comparative genomic analyses have identified 14 conserved signature indels (CSIs) and 48 conserved signature proteins (CSPs) that either are specific for the entire class or differentiate four main groups within the class. Two CSIs and nine CSPs are shared uniquely by all or most members of the class Negativicutes, distinguishing this class from all other sequenced members of the phylum Firmicutes. Four other CSIs and six CSPs were specific characteristics of the family Acidaminococcaceae, two CSIs and four CSPs were uniquely present in the family Veillonellaceae, six CSIs and eight CSPs were found only in Selenomonas and related genera, and 17 CSPs were identified uniquely in Sporomusa and related genera. Four additional CSPs support a pairing of the groups containing the genera Selenomonas and Sporomusa. We also report detailed phylogenetic analyses for the Negativicutes based on core protein sequences and 16S rRNA gene sequences, which strongly support the four main groups identified by CSIs and by CSPs. Based on the results from different lines of investigation, we propose a division of the class Negativicutes into an emended order Selenomonadales containing the new families Selenomonadaceae fam. nov. and Sporomusaceae fam. nov. and two new orders, Acidaminococcales ord. nov. and Veillonellales ord. nov., respectively containing the families Acidaminococcaceae and Veillonellaceae.

Blautia liquoris sp. nov., isolated from the mud in a fermentation cellar used for the production of Chinese strong-flavour liquor

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Ling-Fei Lu ◽  
Yang Yang ◽  
Li-Juan Chai ◽  
Zhen-Ming Lu ◽  
Li-Qiang Zhang ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Carbon Sources ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Link Type ◽  
The Family

A novel Gram-positive, non-motile, non-flagellated, strictly anaerobic, non-spore-forming and dumbbell-shaped, coccoid- or chain-shaped bacterium, designated strain LZLJ-3T, was isolated from a mud fermentation cellar which has been used for the production of Chinese strong-flavour liquor for over 100 years. Strain LZLJ-3T grew at 20–40 °C (optimum, 37 °C), at pH 6.0–8.0 (optimum, pH 8.0) and with NaCl concentrations up to 1 % (w/v; optimum, 0 %). Phylogenetic trees established based on 16S rRNA gene sequences showed that strain LZLJ-3T belonged to the genus Blautia of the family Lachnospiraceae, with the highest sequence similarity to Blautia stercoris GAM6-1T (91.7 %) and Blautia faecicola KGMB01111T (91.7 %). Comparative genome analysis showed that the orthologous average nucleotide identity (OrthoANI) and genome-to-genome distance (GGD) values between strain LZLJ-3T and B. stercoris GAM6-1T were respectively 69.1 and 22.9 %; the OrthoANI and GGD values between strain LZLJ-3T and B. faecicola KGMB01111T were respectively 70.86 and 36 % . The DNA G+C content of strain LZLJ-3T genome was 42.1 mol%. The predominant celluar fatty acids (>10 %) of strain LZLJ-3T were C16 : 0 FAME (27.9 %), C14 : 0 FAME (17.6 %) and C16 : 0 DMA (13.0 %). Arabinose, glucose and maltose could be utilized by strain LZLJ-3T as sole carbon sources for growth, with weak utilization of raffinose and l-fucose. API ZYM analysis gave positive reactions with α-galactosidase, β-galactosidase, α-glucosidase and β-glucosidase. The major end product of glucose fermentation was acetic acid. Based on the results of phenotypic, genotypic and phylogenetic analyses, strain LZLJ-3T is considered to represent a novel species of Blautia , for which the name Blautia liquoris sp. nov. is proposed. The type strain is LZLJ-3T (=KCTC 25163T=CGMCC 1.5299T=JCM 34225T).

scholarly journals Comparative Mitogenomic Analysis of the Eurydema Genus in the Context of Representative Pentatomidae (Hemiptera: Heteroptera) Taxa

2019 ◽  
Vol 19 (6) ◽  
Author(s):  
Wanqing Zhao ◽  
Qing Zhao ◽  
Min Li ◽  
Jiufeng Wei ◽  
Xianhong Zhang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Mitochondrial Genomes ◽  
Rna Structures ◽  
Protein Coding ◽  
Transfer Rnas ◽  
The Family ◽  
Maximum Likelihood Methods

Abstract The family Pentatomidae, the largest within the superfamily Pentatomoidae, comprises about 5,000 species; many of which are economically important pests. Although the phylogeny of Pentatomidae species has been studied using various molecular markers, their phylogenetic relationships remain controversial. Recently, mitochondrial genomes (mitogenomes) have been extensively employed to examine the phylogenetics and evolution of different insects, and in this study, we sequenced complete/near-complete mitochondrial genomes from five shield bug species of Eurydema to gain a better understanding of phylogenetic relationships in the Pentatomidae. The five mitogenomes ranged in length from 15,500 to 16,752 bp and comprised 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region. We compared mitogenomic characteristics of the Pentatomidae and constructed phylogenetic trees using Bayesian inference and maximum likelihood methods. Our results showed that gene arrangements, base composition, start/stop codons, gene overlaps, and RNA structures were conserved within the Pentatomidae and that congeneric species shared more characteristics. Saturation and heterogeneity analyses revealed that our PCGs and PCGRNA datasets were valid for phylogenetic analysis. Phylogenetic analyses showed consistent topologies based on BI and ML methods. These analyses strongly supported that Eurydema species belong to the tribe Strachiini, and formed a sister group with Pentatomini. The relationships among Eurydema species were shown to be consistent with their morphological features. (Strachiini + Pentatomini) was found to be a stable sibling of the clade comprising Cappaeini, Graphosomini, and Carpocorini. Furthermore, our results indicated that Graphosoma rubrolineatum (Heteroptera: Pentatomidae) belongs to the Pentatominae and not the Podopinae.

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 Neptunomyces aureus gen. et sp. nov. (Didymosphaeriaceae, Pleosporales) isolated from algae in Ria de Aveiro, Portugal

MycoKeys ◽  
2019 ◽  
Vol 60 ◽  
pp. 31-44 ◽  
Author(s):  
Micael F. M. Gonçalves ◽  
Tânia F. L. Vicente ◽  
Ana C. Esteves ◽  
Artur Alves
Keyword(s):  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Its Region ◽  
Physiological Data ◽  
New Taxon ◽  
Translation Elongation ◽  
Ria De Aveiro ◽  
The Family ◽  
Elongation Factor 1 Alpha ◽  
Elongation Factor 1

A collection of fungi was isolated from macroalgae of the genera Gracilaria, Enteromorpha and Ulva in the estuary Ria de Aveiro in Portugal. These isolates were characterized through a multilocus phylogeny based on ITS region of the ribosomal DNA, beta-tubulin (tub2) and translation elongation factor 1 alpha (tef1-α) sequences, in conjunction with morphological and physiological data. These analyses showed that the isolates represented an unknown fungus for which a new genus, Neptunomycesgen. nov. and a new species, Neptunomyces aureussp. nov. are proposed. Phylogenetic analyses supported the affiliation of this new taxon to the family Didymosphaeriaceae.

scholarly journals Phylogenetic position of Pleurogenoides species (Plagiorchiida: Pleurogenidae) from the duodenum of Indian skipper frog, Euphlyctis cyanophlyctis (Amphibia: Dicroglossidae) inhabiting the Western Ghats, India

2020 ◽  
Vol 57 (1) ◽  
pp. 71-77
Author(s):  
A. Chaudhary ◽  
K. Shinad ◽  
P. K. Prasadan ◽  
H. S. Singh
Keyword(s):  
Western Ghats ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Pcr Amplification ◽  
Molecular Study ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Digenetic Trematodes ◽  
The Family ◽  
The Western Ghats

SummaryTwo species of digenetic trematodes of the genus Pleurogenoides viz., P. cyanophlyctiShinad & Prasadan (2018a) and P. euphlyctiShinad & Prasadan (2018b) have been described from India. Information regarding the molecular data of various species of the genus Pleurogenoides Travassos, 1921 is virtually lacking. This study addresses the application of molecular markers to validate the phylogenetic position of P. cyanophlycti and P. euphlycti. In the present study, two species P. cyanophlycti and P. euphlycti were collected between January 2016 to October 2017, infecting the freshwater frogs inhabiting the Western Ghats, India. In the present study, the two species were identifi ed morphologically and by PCR amplification of the 28S ribosomal RNA gene. Phylogenetic tree results clearly demonstrate that both P. cyanophlycti and P. euphlycti belongs to the family Pleurogenidae Looss, 1899. Based on these results, we presented and discussed the phylogenetic relationships of P. cyanophlycti and P. euphlycti within family Pleurogenidae from India. Phylogenetic analyses showed that P. cyanophlycti and P. euphlycti cluster according to their vertebrate host and revealed an important congruence between the phylogenetic trees of Pleurogenoides and of their vertebrate hosts. P. cyanophlycti and P. euphlycti clearly constitute a separate, sister branch with other species of the genera, Pleurogenoides, Pleurogenes (=Candidotrema), Prosotocus and Brandesia. The present study firstly provides important information about the molecular study and phylogenetic analysis of P. cyanophlycti and P. euphlycti. This study will also serve as a baseline for Pleurogenoides species identifi cation for further studies.

Iridaceae 'Out of Australasia'? Phylogeny, Biogeography, and Divergence Time Based on Plastid DNA Sequences

2008 ◽  
Vol 33 (3) ◽  
pp. 495-508 ◽  
Author(s):  
Peter Goldblatt ◽  
Aaron Rodriguez ◽  
M. P. Powell ◽  
Jonathan T. Davies ◽  
John C. Manning ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Secondary Growth ◽  
Divergence Time ◽  
Plastid Dna ◽  
Morphological Characters ◽  
Evolutionary Patterns ◽  
Related Family ◽  
The Family

The current infrafamilial taxonomy of the Iridaceae recognizes four subfamilies; Isophysidoideae (1: 1); Nivenioideae (6: ca. 92), Iridoideae (29: 890), and Crocoideae (29: 1032). Phylogenetic analyses of sequences of five plastid DNA regions, rbcL, rps4, trnL–F, matK, and rps16, confirm most aspects of this classification and the evolutionary patterns that they imply, importantly the sisiter relationship of Isophysidoideae to the remainder of the family and the monophyly of Iridoideae. Subfamily Nivenioideae is, however, paraphyletic; Crocoideae is consistently found nested within it, sister to the core Nivenioideae, the woody Klattia, Nivenia, and Witsenia. This clade is sister to Aristea, which in turn is sister to the Madagascan Geosiris, and then to the Australasian Patersonia. We treat Aristea, Geosiris, and Patersonia as separate subfamilies, Aristeoideae and the new Geosiridaceae and Patersonioideae, rendering Nivenioideae and Crocoideae monophyletic. The alternative, uniting a widely circumscribed Nivenioideae and Crocoideae, seems undesirable because Nivenioideae have none of the numerous synapomorphies of Crocoideae, and that subfamily includes more than half the total species of Iridaceae. Main synapomorphies of Crocoideae are: pollen operculate; exine perforate; ovule campylotropous; root xylem vessels with simple perforations; rootstock a corm; inflorescence usually a spike; plants deciduous. Four more derived features of Crocoideae are shared only with core Nivenioideae: flowers long-lived; perianth tube well developed; flowers sessile; and septal nectaries present. The genera of the latter subfamily are evergreen shrubs, have monocot-type secondary growth, tangentially flattened seeds, and the inflorescence unit is a binate rhipidium. The latter feature unites core Nivenioideae with Aristea, Geosiris, and Patersonia, which have fugaceous flowers and, with few exceptions, a blue perianth. Molecular-based phylogenetic trees using sequences from five plastid DNA regions now show discrete generic clusters within Crocoideae and Iridoideae, the foundation for the tribal classification. The five tribe classification of Iridoideae, initially based on morphological characters and subsequently supported by a four plastid DNA region sequence analysis, continues to receive support using additional DNA sequences. Application of molecular clock techniques to our phylogeny indicates that the Iridaceae differentiated in the late Cretaceous and diverged from the next most closely related family, Doryanthaceae circa 82 mya, thus during the Campanian. The Tasmanian Isophysis is the only extant member of the clade sister to the remainder of the Iridaceae, from which it may have diverged 66 mya, in the Maastrichtian. The generic phylogeny shows the proximal clades of the family are all Australasian, which corroborates past hypotheses that the Iridaceae originated in Antarctica-Australasia, although its subsequent radiation occurred elsewhere, notably in southern Africa and temperate and highland South America at the end of the Eocene or later.

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