scholarly journals The complete chloroplast genome sequence of Quercus ningangensis and its phylogenetic implication

2021 ◽  
Vol 66 (2) ◽  
pp. 155-165
Author(s):  
Tian-Rui Wang ◽  
Zheng-Wei Wang ◽  
Yi-Gang Song ◽  
Gregor Kozlowski
Keyword(s):  
Sequence Divergence ◽  
Phylogenetic Position ◽  
Future Research ◽  
Structural Variations ◽  
Genetic Characteristics ◽  
Repeat Elements ◽  
Codon Composition ◽  
Maximum Likelihood Methods ◽  
Phylogenetic Evolution ◽  
Cp Genome

Quercus ningangensis is an economically and ecologically important tree species belonging to the family Fagaceae. In this study, the complete chloroplast (cp) genome of Q. ningangensis was sequenced and assembled, and 18 published cp genomes of Quercus were retrieved for genomic analyses (including sequence divergence, repeat elements, and structure) and phylogenetic inference. With this study, we found that complete cp genomes in Quercus are conserved, and we discovered a codon composition bias, which may be related to genomic content and genetic characteristics. In addition, we detected considerable structural variations in the expansion and contraction of inverted repeat regions. Six regions with relatively high variable (matK-rps16, psbC, ycf3 intron, rbcL, petA-psbJ, and ycf1) were detected by conducting a sliding window analysis, which has a high potential for developing effective genetic markers. Phylogenetic analysis based on Bayesian inference and maximum likelihood methods resulted in a robust phylogenetic tree of Quercus with high resolution for nearly all identified nodes. The phylogenetic relationships showed that the phylogenetic position of Q. ningangensis was located between Q. sichourensis and Q. acuta. The results of this study contribute to future research into the phylogenetic evolution of Quercus section Cyclobalanopsis (Fagaceae).

No longer endemic to Africa: Kribiodosis Kieffer, 1921 (Diptera, Chironomidae) new to Oriental China with a phylogeny and expanded adult generic diagnoses

Zootaxa ◽  
2021 ◽  
Vol 5072 (6) ◽  
pp. 560-574
Author(s):  
WU HAN ◽  
JIE LIU ◽  
YIFAN LUO ◽  
HONGQU TANG
Keyword(s):  
New Species ◽  
Mixed Model ◽  
Dna Barcode ◽  
Sister Group ◽  
Phylogenetic Position ◽  
Generic Diagnosis ◽  
Likelihood Methods ◽  
Core Member ◽  
Maximum Likelihood Methods ◽  
African Genus

Kribiodosis Kieffer, 1921, an African genus of Chironomini (Diptera: Chironomidae), is newly recorded from the Oriental region through a new species K. cantonensis sp. n. Detailed descriptions of the male, female and a DNA barcode are provided. With the inclusion of the new species bearing scutal tubercle and fused tibial comb, the generic diagnosis needs revision and expansion. The phylogenetic position of Kribiodosis within the tribe Chironomini is explored based on five concatenated genetic makers (18S, 28S, CAD1, CAD4 and COI-3P) using both mixed-model Bayesian inference and maximum likelihood methods. Kribiodosis is placed as a core member of the Microtendipes group but its precise sister group remains unclear. Inclusion of the analysis of Nilodosis Kieffer, another Chironomini genus with an African-Oriental distribution, reveals an unexpected robust position as sister to a large and diverse inclusive group of many Chironomini.  

scholarly journals Predictors of suicidal thoughts and behavior in children: results from penalized logistic regression analyses in the ABCD study

2021 ◽  
Author(s):  
Laura S. van Velzen ◽  
Yara J. Toenders ◽  
Aina Avila-Parcet ◽  
Richard Dinga ◽  
Jill A. Rabinowitz ◽  
...  
Keyword(s):  
Logistic Regression ◽  
Mental Health Treatment ◽  
Future Research ◽  
Control Group ◽  
Operating Characteristics ◽  
Genetic Characteristics ◽  
Healthy Control ◽  
History Of ◽  
Social Environmental ◽  
Penalized Logistic Regression

AbstractDespite numerous efforts to predict suicide risk in children, the ability to reliably identify youth that will engage in suicide thoughts or behaviors (STB) has remained remarkably unsuccessful. To further knowledge in this area, we apply a novel machine learning approach and examine whether children with STB could be differentiated from children without STB based on a combination of sociodemographic, physical health, social environmental, clinical psychiatric, cognitive, biological and genetic characteristics. The study sample included 5,885 unrelated children (50% female, 67% white) between 9 and 11 years old from the Adolescent Brain Cognitive Development (ABCD) study. Both parents and youth reported on children’s STB and based on these reports, we divided children into three subgroups: 1. children with current or past STB, 2. children with psychiatric disorder but no STB (clinical controls) and 3. healthy control children. We performed binomial penalized logistic regression analysis to distinguish between groups. The analyses were performed separately for child-reported STB and parent-reported STB. Results showed that we were able to distinguish the STB group from healthy controls and clinical controls (area under the receiver operating characteristics curve (AUROC) range: 0.79-0.81 and 0.70-0.78 respectively). However, we could not distinguish children with suicidal ideation from those who attempted suicide (AUROC range 0.49-0.59). Factors that differentiated the STB group from the clinical control group included family conflict, prodromal psychosis symptoms, impulsivity, depression severity and a history of mental health treatment. Future research is needed to determine if these variables prospectively predict subsequent suicidal behavior.

scholarly journals Melatonin in plants: what we know and what we don’t

2021 ◽  
Vol 5 ◽  
Author(s):  
Zixin Zhang ◽  
Yang Zhang
Keyword(s):  
Abiotic Stresses ◽  
Growth And Development ◽  
Current Knowledge ◽  
Future Research ◽  
Signal Transduction Pathways ◽  
Biotic And Abiotic Stresses ◽  
Research Directions ◽  
Genetic Characteristics ◽  
Future Research Directions ◽  
Biosynthesis Regulation

Abstract Melatonin is an endogenous micromolecular compound of indoleamine with multiple physiological functions in various organisms. In plants, melatonin is involved in growth and development, as well as in responses to biotic and abiotic stresses. Furthermore, melatonin functions in phytohormone-mediated signal transduction pathways. There are multiple melatonin biosynthesis pathways, and the melatonin content in plants is greatly affected by intrinsic genetic characteristics and external environmental factors. Although melatonin biosynthesis has been extensively studied in model plants, it remains uncharacterized in most plants. This article focuses on current knowledge on the biosynthesis, regulation and application of melatonin, particularly for fruit quality and preservation. In addition, it highlights the links between melatonin and other hormones, as well as future research directions.

scholarly journals Distribution of Microbes Producing Antimicrobial ε-Poly-l-Lysine Polymers in Soil Microflora Determined by a Novel Method

2002 ◽  
Vol 68 (7) ◽  
pp. 3575-3581 ◽  
Author(s):  
Masanobu Nishikawa ◽  
Ken'ichi Ogawa
Keyword(s):  
Screening Method ◽  
Agar Plate ◽  
Soil Microflora ◽  
Phylogenetic Position ◽  
Structural Variations ◽  
Modified Polymer ◽  
Concentric Zone ◽  
Molecular Masses ◽  
Novel Method ◽  
Horizontal Transfers

ABSTRACT We developed a simple and sensitive screening method to investigate the distribution of microbes producing an antimicrobial poly(amino acid), ε-poly-l-lysine (ε-PL), in microflora. An acidic dye, Poly R-478, incorporated in an agar plate detected ε-PL producers by electrostatic interaction with the secreted basic polymers. All ε-PL producers, isolated after careful and sufficient screening of soil microflora, belonged exclusively to two groups of bacteria of the family Streptomycetaceae and ergot fungi. They were characterized based on the density and diameter of the concentric zone formed by the secreted polymers. The density depended on each isolate. The increase in the diameter of the concentric zone per unit of time varied among isolates and was negatively correlated with the molecular weight. Although the distribution of ε-PL producers was extremely limited, their products were structurally varied. The molecular masses of the secreted polymers among the isolates ranged from 0.8 to 2.0 kDa. There were also isolates producing unknown polymers inconsistent with the correlation or producing a mixture of polymers with original and modified structures. A chemically modified polymer was an ε-PL derivative, as determined by mass spectrometry. Since the structural variations had no relation to the phylogenetic position of the isolates, it is possible that enzymes involved in the synthesis diversified after putative horizontal transfers of relevant genes.

scholarly journals Phylogenetic analysis of Trichostrongylus vitrinus isolates from southwest Iran

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Mohammad Amin Ghatee ◽  
Seyed Ali Asghar Malek Hosseini ◽  
Masoud Marashifard ◽  
Mehdi Karamian ◽  
Walter Robert Taylor ◽  
...  
Keyword(s):  
New Zealand ◽  
South African ◽  
Phylogenetic Position ◽  
Nucleotide Polymorphisms ◽  
Colonial Era ◽  
Genetic Characteristics ◽  
Clade B ◽  
Political Relationships ◽  
The Uk ◽  
Southwest Iran

Abstract Background Trichostrongylus is one of the most important zoonotic trichostrongylid nematodes, infecting mostly livestock. Data on its genetic characteristics are lacking in Iran. Methods We determined the phylogenetic relationships of Trichostrongylus species in three counties of Kohgiloyeh and Boyerahmad (K-B) province, southwest Iran. Small intestine and abomasum of 70 sheep and goats were investigated. Results A total of 35 isolates of Trichostrongylus worms were detected and all were genetically identified as Trichostrongylus vitrinus. Analysis of 321 bp of the internal transcribed spacer 2 (ITS2) of ribosomal DNA revealed 16 genotypes. All genotypes were single nucleotide polymorphisms, including some hypervariable points. All sequences were trimmed to 170 bp, compared with sequences on GenBank including short sequences from other endemic foci of Iran and other countries and all isolates were used to generate a maximum likelihood phylogenetic tree, which consisted of two clades A and B. Clade A included isolates from Iran, Russia, New Zealand, Australia and the UK; clade B only contained South African isolates. Most clade A isolates (north, southwest and west Iran, Russia, New Zealand, Australia and UK) were in a similar phylogenetic position. One subclade was detected in clade A (isolates from Southwest Iran, New Zealand and UK). Conclusions We hypothesize that drug resistant T. vitrinus may account for its exclusive detection in our samples. The high similarity of genotypes from Iran, New Zealand and UK may be due to their close political relationships during the colonial era. More research is needed to understand better the phylogeny of T. vitrinus and its relationship with drug resistance and human transmission.

scholarly journals Ixodes kangdingensis (Acari: Ixodidae), a new species from the Siberian weasel, Mustela sibirica (Carnivora: Mustelidae) in China

2017 ◽  
Vol 3 ◽  
Author(s):  
TIANYU GUO ◽  
YI SUN ◽  
GUANG XU ◽  
LANCE A. DURDEN
Keyword(s):  
New Species ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Divergence ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Closely Related Species ◽  
Ixodes Arboricola ◽  
A New Species

SUMMARY The female and nymph of Ixodes (Pholeoixodes) kangdingensis n. sp. are described based on both morphology and analysis of 16S rRNA gene sequences. Specimens of this new tick species were collected from a Siberian weasel (Mustela sibirica) in Kangding County, Sichuan Province, China. The morphological features of the female and nymph are unique to distinguish I. kangdingensis n. sp. from other members of the subgenus Pholeoixodes, including the presence of distinctly shaped cornua, anterior and posterior processes on palpal article I and a large angular projection on each side of the hypostome. Partial sequence of 16S rRNA gene grouped this species with Ixodes arboricola and Ixodes lividus with sequence divergence of new species from I. arboricola 4·16% and from I. lividus 8·49%. Data on the phylogenetic position, hosts, geographic distribution and key to females of closely related species are also provided.

Paraphyly of Chinese Amolops (Anura, Ranidae) and phylogenetic position of the rare Chinese frog, Amolops tormotus

Zootaxa ◽  
2007 ◽  
Vol 1531 (1) ◽  
pp. 49-55 ◽  
Author(s):  
HONG-XIA CAI ◽  
JING CHE ◽  
JUN-FENG PANG ◽  
ER-MI ZHAO ◽  
YA-PING ZHANG
Keyword(s):  
Morphological Characteristics ◽  
Sister Group ◽  
Phylogenetic Position ◽  
12S Rrna ◽  
Sister Group Relationship ◽  
Likelihood Methods ◽  
New Classification ◽  
Maximum Likelihood Methods ◽  
Species Groups ◽  
Relationship Of

In order to evaluate the five species groups of Chinese Amolops based on morphological characteristics, and to clarify the phylogenetic position of the concave-eared torrent frog Amolops tormotus, we investigated the phylogeny of Amolops by maximum parsimony, Bayesian Inference, and maximum likelihood methods using two mitochondrial DNA fragments (12S rRNA, 16S rRNA). Our results supported a sister group relationship of Amolops ricketti and Amolops hainanensis. However, the grouping of Amolops mantzorum and Amolops monticola needs to be resolved with more data. Amolops tormotus was nested in genus Odorrana. Thus, recognition of the A. tormotus group is unwarranted and A. tormotus should be referred to genus Odorrana as O. tormota. This species is the sister group of O. nasica plus O. versabilis. The new classification implies that the genus Wurana is to be considered as junior subjective synonym of Odorrana.

scholarly journals Genetic Classification of “Rickettsia heilongjiangii” and “Rickettsia hulinii,” Two Chinese Spotted Fever Group Rickettsiae

2000 ◽  
Vol 38 (9) ◽  
pp. 3498-3501 ◽  
Author(s):  
J. Z. Zhang ◽  
M. Y. Fan ◽  
Y. M. Wu ◽  
P. E. Fournier ◽  
V. Roux ◽  
...  
Keyword(s):  
Spotted Fever ◽  
Phylogenetic Position ◽  
Spotted Fever Group ◽  
Neighbor Joining ◽  
Likelihood Methods ◽  
Genetic Classification ◽  
Repeat Units ◽  
Statistical Bootstrap ◽  
Maximum Likelihood Methods

To determine the phylogenetic position of two new rickettsial strains isolated from ticks in China, 16S ribosomal DNA,gltA, and ompA (apart from the tandem repeat units) genes were amplified by PCR and sequenced. The phylogenetic relationships between these strains and other rickettsiae were inferred from the comparison of sequences of the three genes by the parsimony, neighbor-joining, and maximum-likelihood methods. The results demonstrated that the 054 strain, a rickettsia pathogenic in humans, and the HL-93 strain were related and clustered together withRickettsia japonica. Significant statistical bootstrap values (100 and 92%) supported the nodes in this cluster. Based on previous genotypic and antigenic data and the phylogenetic analysis presented here, the 054 and HL-93 strains should be considered as new species, and we formally propose that they be named “Rickettsia heilongjiangii” and “Rickettsia hulinii,” respectively.

scholarly journals The epidemiology of BSE in cattle herds in Great Britain. II. Model construction and analysis of transmission dynamics

1997 ◽  
Vol 352 (1355) ◽  
pp. 803-838 ◽  
Author(s):  
N. M. Ferguson ◽  
C. A. Donnelly ◽  
M. E. J. Woolhouse ◽  
R. M. Anderson
Keyword(s):  
Great Britain ◽  
Northern Ireland ◽  
Horizontal Transmission ◽  
Research Priorities ◽  
Epidemiological Data ◽  
Future Research ◽  
Spongiform Encephalopathy ◽  
Model Parameters ◽  
Maximum Likelihood Methods ◽  
Cattle Herds

Mathematical models that describe the key processes determining the pattern of the bovine spongiform encephalopathy (BSE) epidemic in British cattle are derived that allow for infection from feed as well as maternal and direct horizontal transmission. Heterogeneous susceptibility classes are also incorporated into the analysis. Maximum likelihood methods are used to estimate parameters and to obtain confidence intervals from available experimental and epidemiological data. A comprehensive sensitivity analysis of all model parameters and distributional assumptions is presented. Additional validation is provided by fitting the model to independent data collected in Northern Ireland. Model estimates and predictions based on BSE case data for Great Britain and Northern Ireland, together with their implications, are reviewed, and future research priorities discussed.

scholarly journals DNAskew: Statistical Analysis of Base Compositional Asymmetry and Prediction of Replication Boundaries in the Genome Sequences

2004 ◽  
Vol 36 (1) ◽  
pp. 16-20 ◽  
Author(s):  
Xiang-Ru Ma ◽  
Shao-Bo Xiao ◽  
Ai-Zhen Guo ◽  
Jian-Qiang Lü ◽  
Huan-Chun Chen
Keyword(s):  
Statistical Analysis ◽  
Base Composition ◽  
Script Language ◽  
Genome Sequences ◽  
Strand Asymmetry ◽  
Rule Type ◽  
Codon Composition ◽  
Dna Strands ◽  
Phylogenetic Evolution ◽  
Relationship Of

Abstract Sueoka and Lobry declared respectively that, in the absence of bias between the two DNA strands for mutation and selection, the base composition within each strand should be A=T and C=G (this state is called Parity Rule type 2, PR2). However, the genome sequences of many bacteria, vertebrates and viruses showed asymmetries in base composition and gene direction. To determine the relationship of base composition skews with replication orientation, gene function, codon usage biases and phylogenetic evolution, in this paper a program called DNAskew was developed for the statistical analysis of strand asymmetry and codon composition bias in the DNA sequence. In addition, the program can also be used to predict the replication boundaries of genome sequences. The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. DNAskew was written in Perl script language and implemented on the LINUX operating system. It works quickly with annotated or unannotated sequences in GBFF (GenBank flatfile) or fasta format. The source code is freely available for academic use at http://www.epizooty.com/pub/stat/DNAskew.

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