Phylogenetic position of the genera Caryandoides, Paratoacris, Fer and Longchuanacris (Orthoptera:Acrididae) revealed by complete mitogenome sequences

2021 ◽  
Vol 35 (7) ◽  
pp. 725
Author(s):  
Xiang Zeng ◽  
Haiyang Xu ◽  
Jingxiao Gu ◽  
Benyong Mao ◽  
Zhilin Chen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Bayesian Inference ◽  
Phylogenetic Trees ◽  
Morphological Characters ◽  
Phylogenetic Position ◽  
Depth Study ◽  
Complete Mitogenome ◽  
Relationship Of ◽  
The Relationship ◽  
Generation Sequencing

Many taxa in the Acrididae have controversial phylogenetic positions. A typical example of such controversies is the phylogenetic positions of the genera Caryandoides, Paratoacris, Fer and Longchuanacris, as well as some other related taxa, which were placed in Oxyinae by some authors, but were considered members of the subfamily Catantopinae by others. In this study, the complete mitogenomes of nine species were sequenced using next-generation sequencing, the characteristics of the newly sequenced mitogenomes are presented briefly, and the phylogeny of the Oxyinae and Catantopinae are reconstructed using a selected dataset of mitogenome sequences under maximum likelihood and Bayesian inference frameworks. The results show that the four controversial genera were consistently assigned to the subfamily Oxyinae rather than Catantopinae in all phylogenetic trees deduced from different datasets under different frameworks, and this finding is entirely consistent with their morphological characters. Therefore, it is more appropriate to place them in Oxyinae rather than Catantopinae. In addition, the results from our analysis also confirm the membership of the genus Apalacris in Coptacrinae rather than Catantopinae, and indicate the uncertainty in the phylogenetic position of the genus Traulia, and a more in-depth study is necessary to resolve the relationship of Traulia with other catantopine groups or Coptacrinae.

scholarly journals Phylogenetic Position of the Genus Alulacris (Orthoptera: Acrididae: Melanoplinae: Podismini) Revealed by Complete Mitogenome Evidence

Insects ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 918
Author(s):  
Haiyang Xu ◽  
Benyong Mao ◽  
Sergey Yu. Storozhenko ◽  
Yuan Huang ◽  
Zhilin Chen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Phylogenetic Trees ◽  
Morphological Character ◽  
Morphological Characters ◽  
Phylogenetic Position ◽  
High Quality ◽  
Sequencing Cost ◽  
Complete Mitogenome ◽  
Data Source ◽  
Generation Sequencing

Whole mitogenomes are a useful data source for a wide variety of research goals due to the vastly cheaper sequencing cost and the far less demanding high-quality templates. The mitogenome has demonstrated great potential in resolving phylogenetic questions in Orthoptera at different taxonomic scales as well as exploring patterns of molecular and morphological character evolutions. In this study, the complete mitogenome of Alulacris shilinensis (Zheng, 1977) was sequenced using next-generation sequencing, the characteristics of the mitogenome are presented briefly, and the phylogeny of the Melanoplinae and Catantopinae was reconstructed using a selected dataset of mitogenome sequences under maximum likelihood and Bayesian inference frameworks. The results show that the genus was consistently assigned to the subfamily Melanoplinae rather than Catantopinae in all phylogenetic trees deduced from different datasets under different frameworks, and this finding is entirely consistent with its morphological characters. Therefore, it is more appropriate to place the genus Alulacris in Melanoplinae rather than in Catantopinae.

Phylogeny and taxonomy of Meeboldia, Sinodielsia and their relatives (Apiaceae: Apioideae) inferred from nrDNA ITS, plastid DNA intron (rpl16 and rps16) sequences and morphological characters

Phytotaxa ◽  
2021 ◽  
Vol 482 (2) ◽  
pp. 121-142
Author(s):  
WEI GOU ◽  
XIAN-LIN GUO ◽  
SONG-DONG ZHOU ◽  
XING-JIN HE
Keyword(s):  
Phylogenetic Trees ◽  
Morphological Characteristics ◽  
Deep Understanding ◽  
Plastid Dna ◽  
Morphological Characters ◽  
Nuclear Ribosomal Dna ◽  
Nrdna Its ◽  
Relationship Of ◽  
The Relationship ◽  
Ribosomal Dna Sequence

Meeboldia H.Wolff, Sinodielsia H.Wolff and their relatives (Apiaceae: Apioideae) are similar in morphology, of which taxonomic treatments were controversial. In this study, the nuclear ribosomal DNA sequence (ITS) and two plastid DNA markers (rps16 and rpl16) were applied to reconstruct phylogenetic trees. The results demonstrated that Meeboldia and Sinodielsia formed a monophyletic group in phylogenetic trees and their highly similar morphological characteristics in taproot, basal leaves, calyx teeth, ribs, and vittae of fruits also confirmed their close relationships. Consequently, the following results were obtained: (1) Sinodielsia should be merged into Meeboldia; (2) Sinodielsia delavayi was confirmed conspecific with Meeboldia yunnanensis and renamed as Meeboldia delavayi (Franch.) W.Gou & X.J.He; (3) Sinodielsia thibetica was away from other Sinodielsia species; (4) Sinodielsia microloba was a member of Meeboldia and renamed as Meeboldia microloba (Kljuykov) W.Gou & X.J.He; (5) The name of Sinodielsia clade was suggested to be replaced by Hymenidium clade. We applied multiple approaches to explore the relationship of morphologically similar taxa, which will facilitate a deep understanding of taxonomy and species diversity of Apiaceae.

scholarly journals Exploring the relationship of Homalosilpha and Mimosilpha (Blattodea, Blattidae, Blattinae) from a morphological and molecular perspective, including a description of four new species

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10618
Author(s):  
Shuran Liao ◽  
Yishu Wang ◽  
Duting Jin ◽  
Rong Chen ◽  
Zongqing Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Close Relationship ◽  
Relationship Of ◽  
The Relationship ◽  
Six Genes

This study utilized six genes (12S, 16S, 18S, 28S, COII and H3) from a total of 40 samples to construct maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees in order to infer the relationships between the morphologically similar genera Homalosilpha Stål, 1874 and Mimosilpha Bey-Bienko, 1957. The phylogenetic analysis showed the two genera have a close relationship and were recovered as sister groups based on ML and BI analyses. Four new species are described among these samples, i.e., Homalosilpha obtusangula sp. nov., Homalosilpha recta sp. nov., Homalosilpha alba sp. nov. and Homalosilpha clavellata sp. nov. based on morphological and COI data. A key to the worldwide Homalosilpha is provided.

scholarly journals The first next-generation sequencing approach to the mitochondrial phylogeny of African monogenean parasites (Platyhelminthes: Gyrodactylidae and Dactylogyridae)

2018 ◽  
Author(s):  
Maarten P.M. Vanhove ◽  
Andrew G. Briscoe ◽  
Michiel W.P. Jorissen ◽  
D. Tim J. Littlewood ◽  
Tine Huyse
Keyword(s):  
Next Generation Sequencing ◽  
Gene Order ◽  
Stop Codon ◽  
Start Codon ◽  
Phylogenetic Position ◽  
Next Generation ◽  
Protein Coding ◽  
Complete Mitogenome ◽  
Generation Sequencing ◽  
Mitochondrial Phylogeny

AbstractBackgroundMonogenean flatworms are the main ectoparasites of fishes. Representatives of the species-rich families Gyrodactylidae and Dactylogyridae, especially those infecting cichlid fishes and clariid catfishes, are important parasites in African aquaculture, even more so due to the massive anthropogenic translocation of their hosts worldwide. Several questions on their evolution, such as the phylogenetic position of Macrogyrodactylus and the highly speciose Gyrodactylus, remain unresolved with available molecular markers. Also, diagnostics and population-level research would benefit from the development of higher-resolution genetic markers. We aim to advance genetic work on African monogeneans by providing mitogenomic data of four species (two each belonging to the Gyrodactylidae and Dactylogyridae), and analysing their gene sequences and gene order from a phylogenetic perspective.ResultsBased on Illumina technology, the first four mitochondrial genomes of African monogeneans were assembled and annotated for the cichlid parasites Gyrodactylus nyanzae, Cichlidogyrus halli, Cichlidogyrus mbirizei (near-complete mitogenome) and the catfish parasite Macrogyrodactylus karibae (near-complete mitogenome). The start codon TTG is new for Gyrodactylus and for the Dactylogyridae, as is the incomplete stop codon TA for the Dactylogyridae. The most variable markers are nad genes and these are under relaxed selection. Especially nad2 is promising for primer development. Gene order was identical for protein-coding genes and differed between the African representatives of these families only in a tRNA gene transposition. A mitochondrial phylogeny based on an alignment of nearly 12,500 bp including 12 protein-coding and two ribosomal RNA genes confirms that the Neotropical oviparous Aglaiogyrodactylus forficulatus takes a sister group position with respect to the other gyrodactylids, rather than the supposedly ‘primitive’ African Macrogyrodactylus. Inclusion of the African Gyrodactylus nyanzae confirms the paraphyly of Gyrodactylus. The position of the African dactylogyrid Cichlidogyrus is unresolved, although gene order suggests it is closely related to marine ancyrocephalines.ConclusionsThe amount of mitogenomic data available for gyrodactylids and dactylogyrids is increased by roughly one-third. Our study underscores the potential of mitochondrial genes and gene order in flatworm phylogenetics, and of next-generation sequencing for marker development for these non-model helminths for which few primers are available while they constitute a risk to tropical aquaculture.

MICROBIOMA: AMIGO O ENEMIGO EN PACIENTES CON COVID - 19

SCIENTIARVM ◽  
2015 ◽  
Vol 1 (1) ◽  
pp. 15-21
Author(s):  
Katherine Milagros Quispe Medina ◽  
◽  
Angel Sixto Mamani Ruelas ◽  
Brenda Jasmin Alvarez Vera ◽  
Yasmin Yessenia Silvestre Gutierrez ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Gastrointestinal Tract ◽  
Molecular Biology ◽  
Gut Microbiome ◽  
Next Generation ◽  
Multiple Factors ◽  
Lung Microbiome ◽  
The Relationship ◽  
Generation Sequencing ◽  
Clinical Cases

The research of the microbiome concerning various diseases has grown in the last ten years due to the advances in molecular biology and next-generation sequencing, finding interactions with various pathologies. The new coronavirus 19 (SARS-COV 2) pandemic has aroused interest in the study of multiple factors that could influence in the development of symptoms mainly due to the interaction of the microbiome whether of the respiratory or gastrointestinal tract finally in the prognosis. Therefore, in this study, we focus on reviewing and analyzing the current bibliography of research and clinical cases about the relationship between the lung and gut microbiome and COVID-19, highlighting its effect on infected patients, aiming to contribute to this new line of research. Keywords: Microbiome, COVID-19, SARS-COV 2, gut microbiome, lung microbiome.

scholarly journals Whole Chloroplast Genomes reveals the uniqueness of Bolivian native cacao (Theobroma cacao) from the northern part of Bolivia

2021 ◽  
Author(s):  
Marcia Gumiel ◽  
Oscar M Rollano-Penaloza ◽  
Carmelo Peralta-Rivero ◽  
Leslie Tejeda ◽  
Valeria D. Palma Encinas ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Theobroma Cacao ◽  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Next Generation ◽  
Center Of Origin ◽  
Chloroplast Genomes ◽  
Geographical Locations ◽  
Generation Sequencing

We report the complete chloroplast sequences of two varieties of Theobroma cacao collected in the Bolivian Amazonia using Next-Generation Sequencing. Comparisons made between these two chloroplast genomes and the Belizean reference plastid genome identified 19 and 22 nucleotide variants. The phylogenetic analysis reported three main T. cacao clades belonging to the Forastero, Criollo and Trinitario groups. The Bolivian Native Cacao varieties were located inside the Trinitario group forming their unique branch. The Bolivian Native Cacao branch reveals a possible new subpopulation different from the well-characterized T. cacao subpopulations. The phylogenetic trees showed that the relationships among the T. cacao varieties were consistent with their geographical locations placing the Cacao Center of Origin in Western Amazon. The data presented here will contribute to the usage of ultrabarcoding to distinguish different T. cacao varieties and to identify native cacaos from introduced cacaos. Thus helping in the conservation of local native varieties of T. cacao.

scholarly journals ESTIMATION OF EFFICIENCY OF CONSTRUCTION OF AGRO-PHYTOCENOSES AND FERTILIZER OF THE OIL RADISH ON THE BASIS OF THE MODULAR-VITALITY METHOD

2019 ◽  
pp. 54-78
Author(s):  
Yaroslav Tsytsiura
Keyword(s):  
Plant Density ◽  
Morphological Characters ◽  
Climatic Conditions ◽  
Morphological Integration ◽  
Plant Oil ◽  
Long Term Study ◽  
Relationship Of ◽  
The Relationship ◽  
Fertilizer Rates

The article presents the results of a long-term study of the features of the phytocenology of agrophytocenoses of oil radish using different methods for assessing their condition and studying the tactics of the plant vitality strategy. A comprehensive assessment was made of the effect of changes in row spacing, seeding rates and fertilizer rates on the formation of various plant morphotypes, the variability of morphological characters and the general characteristics of plant viability. Three idiotypes of the plant oil radish were identified in a vertical study of agrophytocenosis, on the basis of which a detailed analysis of the variability of each group and a statistical assessment of the reliability of its existence were carried out. The features of the morphological integration of each tier are analyzed and its impact on the formation of the overall field productivity is evaluated. Based on the modular and vitality grouping, the effectiveness and feasibility of combining various options for plant density and fertilizer in the range of 30-90 kg of active substance per 1 ha were evaluated. Conclusions are drawn about the desired model of agrophytocenosis of oil radish based on the characteristics of its vital tactics and the goals of its growing. Grouping was carried out according to a variety of morphological traits of plants in the population and the possibilities of applying the basic patterns of phytocenology in their application to radish oilseed plants were evaluated. Through the use of regression analysis, the influence of climatic conditions on the formation of various morphological types of plants and the nature of the relationship of plants of oil radish in cenoses of various densities against the background of various fertilizer options has been evaluated. The main promising areas for further research on the peculiarities of creating highly productive and highly adaptable agrophytocenoses of oil radish have been outlined.

scholarly journals Metagenomic Next-Generation Sequencing Reveal Presence of a Novel Ungulate Bocaparvovirus in Alpacas

Viruses ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 701 ◽  
Author(s):  
Kumar ◽  
Chaudhary ◽  
Lu ◽  
Duff ◽  
Heffel ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Amino Acid ◽  
Phylogenetic Trees ◽  
Neurological Diseases ◽  
Virus Infectivity ◽  
Whole Genome ◽  
Ns1 Protein ◽  
Next Generation ◽  
Percent Identity ◽  
Generation Sequencing

Viruses belonging to the genus Bocaparvovirus (BoV) are a genetically diverse group of DNA viruses known to cause respiratory, enteric, and neurological diseases in animals, including humans. An intestinal sample from an alpaca (Vicugna pacos) herd with reoccurring diarrhea and respiratory disease was submitted for next-generation sequencing, revealing the presence of a BoV strain. The alpaca BoV strain (AlBoV) had a 58.58% whole genome nucleotide percent identity to a camel BoV from Dubai, belonging to a tentative ungulate BoV 8 species (UBoV8). Recombination events were lacking with other UBoV strains. The AlBoV genome was comprised of the NS1, NP1, and VP1 proteins. The NS1 protein had the highest amino acid percent identity range (57.89–67.85%) to the members of UBoV8, which was below the 85% cut-off set by the International Committee on Taxonomy of Viruses. The low NS1 amino acid identity suggests that AlBoV is a tentative new species. The whole genome, NS1, NP1, and VP1 phylogenetic trees illustrated distinct branching of AlBoV, sharing a common ancestor with UBoV8. Walker loop and Phospholipase A2 (PLA2) motifs that are vital for virus infectivity were identified in NS1 and VP1 proteins, respectively. Our study reports a novel BoV strain in an alpaca intestinal sample and highlights the need for additional BoV research.

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