scholarly journals Symphyonema bifilamentata sp. nov., the Right Fischerella ambigua 108b: Half a Decade of Research on Taxonomy and Bioactive Compounds in New Light

2021 ◽  
Vol 9 (4) ◽  
pp. 745
Author(s):  
Patrick Jung ◽  
Paul M. D’Agostino ◽  
Burkhard Büdel ◽  
Michael Lakatos
Keyword(s):  
Small Molecules ◽  
Bioactive Compounds ◽  
Bioactive Metabolites ◽  
Phylogenetic Position ◽  
Cyanobacterial Strain ◽  
Protein Coding ◽  
The Family ◽  
True Branching Cyanobacteria ◽  
The Right ◽  
True Branching

Since 1965 a cyanobacterial strain termed ‘Fischerella ambigua 108b’ was the object of several studies investigating its potential as a resource for new bioactive compounds in several European institutes. Over decades these investigations uncovered several unique small molecules and their respective biosynthetic pathways, including the polychlorinated triphenyls of the ambigol family and the tjipanazoles. However, the true taxonomic character of the producing strain remained concealed until now. Applying a polyphasic approach considering the phylogenetic position based on the 16S rRNA and the protein coding gene rbcLX, secondary structures and morphological features, we present the strain ‘Fischerella ambigua 108b’ as Symphyonema bifilamentata sp. nov. 97.28. Although there is the type species (holotype) S. sinense C.-C. Jao 1944 there is no authentic living strain or material for genetic analyses for the genus Symphyonema available. Thus we suggest and provide an epitypification of S. bifilamentata sp. nov. 97.28 as a valid reference for the genus Symphyonema. Its affiliation to the family Symphyonemataceae sheds not only new light on this rare taxon but also on the classes of bioactive metabolites of these heterocytous and true-branching cyanobacteria which we report here. We show conclusively that the literature on the isolation of bioactive products from this organism provides further support for a clear distinction between the secondary metabolism of Symphyonema bifilamentata sp. nov. 97.28 compared to related and other taxa, pointing to the assignment of this organism into a separate genus.

scholarly journals Phylogenetic placement of Paratrichaptum and reconsideration of Gloeophyllales

2020 ◽  
Vol 5 (1) ◽  
pp. 119-130 ◽  
Author(s):  
C.-C. Chen ◽  
B. Cao ◽  
T. Hattori ◽  
B.-K. Cui ◽  
C.-Y. Chen ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Strong Support ◽  
Brown Rot ◽  
Phylogenetic Position ◽  
Nuclear Rdna ◽  
Protein Coding ◽  
Phylogenetic Placement ◽  
The Family ◽  
Ancestral States ◽  
Relic Species

Paratrichaptum accuratum is a large conspicuous polypore fungus growing on dead or living angiosperm trees in subtropical-boreal areas of China, Indonesia, Japan, and Taiwan. The present study places P. accuratum in the family Gloeophyllaceae that belongs to the order Gloeophyllales within Agaricomycetes (Basidiomycota), based on evidence derived from morphological and ecological characteristics, and phylogenetic analyses of sequences of nuclear rDNA regions (5.8S, nuc 18S, nuc 28S) and protein-coding genes (rpb1, rpb2, and tef1). The analyses presented in this study also give strong support for including Jaapia in Gloeophyllaceae and Gloeophyllales. Thus, the names Jaapiaceae and Jaapiales are considered here as synonyms of Gloeophyllaceae and Gloeophyllales. Since Paratrichaptum represents the earliest diverging lineage in Gloeophyllales, pileate basidiocarps and brown rot appear to be ancestral states of Gloeophyllales. Paratrichaptum accuratum may represent a relic species, according to its phylogenetic position, peculiar distribution pattern and rare occurrence.

scholarly journals Extensive plastome reduction and loss of photosynthesis genes in Diphelypaea coccinea, a holoparasitic plant of the family Orobanchaceae

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7830 ◽  
Author(s):  
Eugeny V. Gruzdev ◽  
Vitaly V. Kadnikov ◽  
Alexey V. Beletsky ◽  
Andrey V. Mardanov ◽  
Nikolai V. Ravin
Keyword(s):  
Genome Evolution ◽  
Plastid Genome ◽  
Housekeeping Genes ◽  
Parasitic Plants ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Trna Genes ◽  
Protein Coding ◽  
The Family ◽  
Plastid Genome Evolution

Background Parasitic plants have the ability to obtain nutrients from their hosts and are less dependent on their own photosynthesis or completely lose this capacity. The reduction in plastid genome size and gene content in parasitic plants predominantly results from loss of photosynthetic genes. Plants from the family Orobanchaceae are used as models for studying plastid genome evolution in the transition from an autotrophic to parasitic lifestyle. Diphelypaea is a poorly studied genus of the Orobanchaceae, comprising two species of non-photosynthetic root holoparasites. In this study, we sequenced the plastid genome of Diphelypaea coccinea and compared it with other Orobanchaceae, to elucidate patterns of plastid genome evolution. In addition, we used plastid genome data to define the phylogenetic position of Diphelypaea spp. Methods The complete nucleotide sequence of the plastid genome of D. coccinea was obtained from total plant DNA, using pyrosequencing technology. Results The D. coccinea plastome is only 66,616 bp in length, and is highly rearranged; however, it retains a quadripartite structure. It contains only four rRNA genes, 25 tRNA genes and 25 protein-coding genes, being one of the most highly reduced plastomes among the parasitic Orobanchaceae. All genes related to photosynthesis, including the ATP synthase genes, had been lost, whereas most housekeeping genes remain intact. The plastome contains two divergent, but probably intact clpP genes. Intron loss had occurred in some protein-coding and tRNA genes. Phylogenetic analysis yielded a fully resolved tree for the Orobanchaceae, with Diphelypaea being a sister group to Orobanche sect. Orobanche.

scholarly journals Highly rearranged mitochondrial genome in Falcolipeurus lice (Phthiraptera: Philopteridae) from endangered eagles

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Yu Nie ◽  
Yi-Tian Fu ◽  
Yu Zhang ◽  
Yuan-Ping Deng ◽  
Wei Wang ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Gene Rearrangements ◽  
Posterior Probabilities ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
Louse Species ◽  
Mt Genome ◽  
Rna Genes

Abstract Background Fragmented mitochondrial (mt) genomes and extensive mt gene rearrangements have been frequently reported from parasitic lice (Insecta: Phthiraptera). However, relatively little is known about the mt genomes from the family Philopteridae, the most species-rich family within the suborder Ischnocera. Methods Herein, we use next-generation sequencing to decode the mt genome of Falcolipeurus suturalis and compare it with the mt genome of F. quadripustulatus. Phylogenetic relationships within the family Philopteridae were inferred from the concatenated 13 protein-coding genes of the two Falcolipeurus lice and members of the family Philopteridae using Bayesian inference (BI) and maximum likelihood (ML) methods. Results The complete mt genome of F. suturalis is a circular, double-stranded DNA molecule 16,659 bp in size that contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and three non-coding regions. The gene order of the F. suturalis mt genome is rearranged relative to that of F. quadripustulatus, and is radically different from both other louse species and the putative ancestral insect. Phylogenetic analyses revealed clear genetic distinctiveness between F. suturalis and F. quadripustulatus (Bayesian posterior probabilities = 1.0 and bootstrapping frequencies = 100), and that the genus Falcolipeurus is sister to the genus Ibidoecus (Bayesian posterior probabilities = 1.0 and bootstrapping frequencies = 100). Conclusions These datasets help to better understand gene rearrangements in lice and the phylogenetic position of Falcolipeurus and provide useful genetic markers for systematic studies of bird lice. Graphic abstract

scholarly journals A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis

2020 ◽  
Author(s):  
Eiichi Shoguchi ◽  
Girish Beedessee ◽  
Kanako Hisata ◽  
Ipputa Tada ◽  
Haruhi Narisoko ◽  
...  
Keyword(s):  
Thermal Tolerance ◽  
Genomic Structure ◽  
Gc Content ◽  
Genomic Diversity ◽  
Phylogenetic Position ◽  
Neighboring Gene ◽  
Protein Coding ◽  
The Family ◽  
Genomic Resource ◽  
Conserved Gene

Abstract Photosynthetic dinoflagellates of the Family Symbiodiniaceae live symbiotically with many organisms that inhabit coral reefs and are currently classified into fifteen groups, including seven genera. Draft genomes from four genera, Symbiodinium, Breviolum, Fugacium, and Cladocopium, which have been isolated from corals, have been reported. However, no genome is available from the genus Durusdinium, which occupies an intermediate phylogenetic position in the Family Symbiodiniaceae and is well known for thermal tolerance (resistance to bleaching). We sequenced, assembled, and annotated the genome of Durusdinium trenchii, isolated from the coral, Favia speciosa, in Okinawa, Japan. Assembled short reads amounted to 670 Mbp with ∼47% GC content. This GC content was intermediate among taxa belonging to the Symbiodiniaceae. Approximately 30,000 protein-coding genes were predicted in the D. trenchii genome, fewer than in other genomes from the Symbiodiniaceae. However, annotations revealed that the D. trenchii genome encodes a cluster of genes for synthesis of mycosporine-like amino acids (MAAs), which absorb UV radiation. Interestingly, a neighboring gene in the cluster encodes a GMC (glucose-methanol-choline) oxidoreductase with an FAD (flavin adenine dinucleotide) domain that is also found in Symbiodinium tridacnidorum. This conservation seems to partially clarify an ancestral genomic structure in the Symbiodiniaceae and its loss in late-branching lineages, including Breviolum and Cladocopium, after splitting from the Durusdinium lineage. Our analysis suggests that approximately half of the taxa in the Symbiodiniaceae may maintain the ability to synthesize MAAs. Thus, this work provides a significant genomic resource for understanding the genomic diversity of Symbiodiniaceae in corals.

scholarly journals Highly Rearranged Mitochondrial Genome in Falcolipeurus lice (Phthiraptera: Philopteridae) from Endangered Eagles

2021 ◽  
Author(s):  
Yu Nie ◽  
Yi-Tian Fu ◽  
Yu Zhang ◽  
Yuan-Ping Deng ◽  
Ya Tu ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Gene Rearrangements ◽  
Posterior Probabilities ◽  
Genome Sequences ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
Mt Genome ◽  
Rna Genes

Abstract Background: Fragmented mitochondrial (mt) genomes and extensive mt gene rearrangements have been frequently reported from parasitic lice (Insecta: Phthiraptera). However, relatively little is available about the mt genomes from the family Philopteridae that is the most species-rich family within the suborder Ischnocera. Methods: Herein, we use next-generation sequencing to decode the mt genome sequences of Falcolipeurus suturalis and compared it with the mt genome sequences of F. quadripustulatus. Phylogenetic relationship of the concatenated amino acid sequence data for 13 protein-coding genes of the two Falcolipeurus lice and selected members of the family Philopteridae was evaluated using Bayesian inference (BI).Results: The complete mt genome of F. suturalis is a circular double-stranded DNA molecule of 16,659 bp, and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, as well as three putative non-coding regions. The gene order in F. suturalis mt genome was rearranged compared with that of F. quadripustulatus, and they were radical different from other louse species and the ancestral insect. Phylogenetic analyses revealed that the clear genetic distinctiveness between F. suturalis and F. quadripustulatus (Bayesian posterior probabilities=1.0), and the genus Falcolipeurus is more closely related to the genus Ibidoecus than to other genera (Bayesian posterior probabilities=1.0). Conclusions: These novel datasets will help to better understand the gene rearrangements and phylogenetic position of Falcolipeurus and provide useful genetic markers for systematics and phylogenetic studies of bird lice.

The complete mitochondrial genome of Pseudanoplocephala crawfordi and a comparison with closely related cestode species

2015 ◽  
Vol 90 (5) ◽  
pp. 588-595 ◽  
Author(s):  
G.H. Zhao ◽  
H.B. Wang ◽  
Y.Q. Jia ◽  
W. Zhao ◽  
X.F. Hu ◽  
...  
Keyword(s):  
Complete Mitochondrial Genome ◽  
Taxonomic Status ◽  
Amino Acid Sequences ◽  
Health Concern ◽  
Phylogenetic Position ◽  
Protein Coding ◽  
Economic Significance ◽  
The Family ◽  
Mt Genome ◽  
Rna Genes

AbstractPseudanoplocephala crawfordi is an important zoonotic cestode of economic significance and public health concern. In spite of its significance as a pathogen, the systematics, genetics, epidemiology and biology of this parasite remain poorly understood. In the present study, we sequenced and characterized the complete mitochondrial (mt) genome of P. crawfordi, which is 14,192 bp long and encodes 36 genes, including 12 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes. Phylogenetic analysis of the concatenated amino acid sequences using the Bayesian inference (BI) method showed that P. crawfordi was closely related to the family Hymenolepididae. Considering that the taxonomic status of P. crawfordi has been controversial when based only on morphological features, the mt genome obtained here will provide novel molecular markers to ascertain the phylogenetic position of this parasite accurately.

scholarly journals The First Two Complete Mitochondrial Genomes of Neoephemeridae (Ephemeroptera): Comparative Analysis and Phylogenetic Implication for Furcatergalia

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1875
Author(s):  
Ran Li ◽  
Zhenxing Ma ◽  
Changfa Zhou
Keyword(s):  
Phylogenetic Trees ◽  
Purifying Selection ◽  
Sister Group ◽  
Phylogenetic Position ◽  
Sister Group Relationship ◽  
General Reference ◽  
Protein Coding ◽  
The Family ◽  
Conserved Gene ◽  
Relationship Of

Mayflies of the family Neoephemeridae are widespread in the Holarctic and Oriental regions, and its phylogenetic position is still unstable in the group Furcatergalia (mayflies with fringed gills). In the present study, we determined the complete mitogenomes of two species, namely Potamanthellus edmundsi and Pulchephemera projecta, of this family. The lengths of two mitogenomes were 15,274 bp and 16,031 bp with an A + T content of 73.38% and 73.07%, respectively. Two neoephemerid mitogenomes had a similar gene size, base composition, and codon usage of protein-coding genes (PCGs), and the sequenced gene arrangements were consistent with the putative ancestral insect mitogenomes as understood today. The most variable gene of Furcatergalia mitogenomes was ND2, while the most conserved gene was COI. Meanwhile, the analysis of selection pressures showed that ND6 and ATP8 exhibited a relaxed purifying selection, and COI was under the strongest purifying selection. Phylogenetic trees reconstructed based on two concatenated nucleotide datasets using both maximum likelihood (ML) and Bayesian inference (BI) estimations yielded robust identical topologies. These results corroborated the monophyly of seven studied families and supported the family Leptophlebiidae as being of the basal lineage of Furcatergalia. Additionally, the sister-group relationship of Caenidae and Neoephemeridae was well supported. Methodologically, our present study provides a general reference for future phylogenetic studies of Ephemeroptera at the mitogenome level.

SYSTEMIC CAUSES OF THE APPEARANCE OF “COBRA EFFECT” IN THE MANAGEMENT OF SOCIO-ECONOMIC DEVELOPMENT

2019 ◽  
Vol 86 (3) ◽  
pp. 51-61
Author(s):  
M. S. Mokiy ◽  
E. K. Borzenko
Keyword(s):  
Economic Development ◽  
Economic System ◽  
Gross National Product ◽  
The Family ◽  
Social And Economic Development ◽  
Socio Economic Development ◽  
Energy Consuming ◽  
The Right ◽  
Goals And Objectives ◽  
Least Energy

The article on the basis of extrapolation of system laws of management of social and economic development illustrates the system reason of the Cobra effect, that is, a situation where, despite the rather attractive goals that managers formulate, the result of the activities of subordinates is opposite to what was intended. The main problem of management is the development of a system of indicators, in which, working on the indicator, employees would change the state in the right direction. The reason for the Cobra effect is the manifestation of systemic patterns of socio-economic development. The main system regularity is the desire of the system for stability and self-preservation. This state of the system is achieved using the least energy-consuming way. It is shown that any worker, realizing system regularities, aspires to stability and self-preservation. Therefore, the employee is always forced to work for achieving the indicator. The article analyzes the manifestation of these laws at the level of enterprises and state. When managers understand these patterns explicitly or covertly, changes in the economic system are moving in the right direction. It is shown that the existing system of target indicators used as indicators to assess the effectiveness of management does not meet the goals and objectives of socio-economic development. At the meso- and macrolevel, absolute, volumetric indicators, such as gross national product and others, reduce the range of benefits to the population. The article defines the vector of change in the system of indicators for assessing the effectiveness of management at the regional and state levels, based on the fact that the key element is the family. At the same time, the targets should be indicators to assess the availability of benefits for households.

Temulawak (Curcuma  xanthorrhizaRoxb.) belongs to the family Zingiberaceae, has been empirically used as herbal medicines. The research was aimed to evaluate three promising lines of Temulawak based on their high bioactive contents (xanthorrhizol and curcuminoid) and its in vitro bioactivity (antioxidant and toxicity), and to obtain information on agrobiophysic environmental condition which produced high bioactive compounds. The xanthorrhizol and curcuminoid contents were measured by HPLC. In vitro antioxidant and toxicity were determined by DPPH (1,1-diphenyl-2-picryl-hydrazyl) method and BSLT (Brine Shrimp Lethality Test). The result showed that promising line A produced the highest yield of bioactive and bioactivity, i.e. 0.157 and 0.056 g plant-1of xanthorrizol and curcuminoid respectively. The IC50 of antioxidant activity was 65.09 mg L-1and LC50of toxicity was 69.05 mg L-1. In this study, Cipenjo had the best temulawak performance than two other locations. According to the agrobiophysic parameters, Cipenjo environmental condition was suitable for temulawak cultivation with temperature 28-34 ºC, rainfall ± 223.97 mm year-1 and sandy clay soil. Keywords: antioxidant, curcuminoid, promising lines, temulawak, xanthorrhizol

1970 ◽  
Vol 40 (2) ◽  
Author(s):  
Waras Nurcholis ◽  
Edy Djauhari Purwakusumah ◽  
Mono Rahardjo ◽  
Latifah K. Darusman
Keyword(s):  
Antioxidant Activity ◽  
Bioactive Compounds ◽  
Brine Shrimp ◽  
Clay Soil ◽  
Herbal Medicines ◽  
Environmental Condition ◽  
In Vitro Bioactivity ◽  
The Family ◽  
Promising Line

Temulawak (Curcuma  xanthorrhizaRoxb.) belongs to the family Zingiberaceae, has been empirically used as herbal medicines. The research was aimed to evaluate three promising lines of Temulawak based on their high bioactive contents (xanthorrhizol and curcuminoid) and its in vitro bioactivity (antioxidant and toxicity), and to obtain information on agrobiophysic environmental condition which produced high bioactive compounds. The xanthorrhizol and curcuminoid contents were measured by HPLC. In vitro antioxidant and toxicity were determined by DPPH (1,1-diphenyl-2-picryl-hydrazyl) method and BSLT (Brine Shrimp Lethality Test). The result showed that promising line A produced the highest yield of bioactive and bioactivity, i.e. 0.157 and 0.056 g plant-1of xanthorrizol and curcuminoid respectively. The IC50 of antioxidant activity was 65.09 mg L-1and LC50of toxicity was 69.05 mg L-1. In this study, Cipenjo had the best temulawak performance than two other locations. According to the agrobiophysic parameters, Cipenjo environmental condition was suitable for temulawak cultivation with temperature 28-34 ºC, rainfall ± 223.97 mm year-1 and sandy clay soil. Keywords: antioxidant, curcuminoid, promising lines, temulawak, xanthorrhizol

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