scholarly journals psbE-psbL and ndhA Intron, the Promising Plastid DNA Barcode of Fagopyrum

2019 ◽  
Vol 20 (14) ◽  
pp. 3455 ◽  
Author(s):  
Yue Huang ◽  
Zhiqiang Li ◽  
Chenglong Wang ◽  
Chenyan Zou ◽  
Wen Wen ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Phylogenetic Relationship ◽  
Dna Barcode ◽  
Plastid Dna ◽  
Food Material ◽  
Wild Buckwheat ◽  
Phylogenetic Studies ◽  
Related Wild Species ◽  
The Relationship ◽  
Species Hybridization

Buckwheat is an important functional food material with high nutritional value. However, it is still a difficult task for the taxonomy studies of wild buckwheat that are only based on morphology. In order to demonstrate the most efficient DNA barcode in the phylogenetic research of buckwheat, promote the investigation of wild buckwheat, and also reveal the phylogenetic relationship between Fagopyrum species, psbE-psbL and ndhA intron were validated here, which previously have been proved to be promising DNA barcode candidates for phylogenetic studies in genera Fagopyrum. Meanwhile, ndhA intron + psbE-psbL and matK + psbE-psbL could distinguish the relationship between species clearly. Combining the results of morphology and molecular markers, we suggested the buckwheat species should be divided into two subgroups, one subgroup consisted of F. tataricum, F. esculentum, F. cymosum and its related wild species, and the other subgroup included other wild buckwheat species. Our results could fulfill molecular markers of taxonomy research in genera Fagopyrum, promote wild buckwheat species identification, and assist in the use of wild buckwheat resources in the future. Additionally, the phylogenetic relationship revealed here could provide valuable information for molecular breeding of buckwheat and provide reference for inter-species hybridization.

DNA barcodes provide evidence for the independent origin of the cultivated silkworms Samia ricini and Samia cynthia

2021 ◽  
pp. 1-8
Author(s):  
J.-C. Huang ◽  
X.-Y. Li ◽  
Y.-P. Li ◽  
R.-S. Zhang ◽  
D.-B. Chen ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Phylogenetic Relationship ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Molecular Evidence ◽  
Dna Barcodes ◽  
Close Relationship ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework

Samia ricini (Wm. Jones) and Samia cynthia (Drury) (Lepidoptera: Saturniidae) have been used as traditional sources of food as well as silk-producing insects. However, the phylogenetic relationship between the two silkworms remains to be addressed. In this study, the mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences corresponding to DNA barcodes from 13 Samia species were analysed, and a DNA barcode-based phylogenetic framework for these Samia species was provided. Phylogenetic analysis showed that multiple individuals of a species could be clustered together. Our analysis revealed a close relationship among Samia yayukae Paukstadt, Peigler and Paukstadt, Samia abrerai Naumann and Peigler, Samia kohlli Naumann and Peigler, Samia naessigi Naumann and Peigler, Samia naumanni Paukstadt, Peigler and Paukstadt, and Samia kalimantanensis Paukstadt and Paukstadt. The mixed clustering relationship and low Kimura-2-parameter (K2P) genetic distance (0.006) between individuals of S. ricini and Samia canningi (Hutton) indicated that the cultivated silkworm S. ricini was derived from the non-cultivated silkworm S. canningi. The remote phylogenetic relationship and high K2P genetic distance (0.039) indicated that S. ricini and S. cynthia are distinct species, thus providing solid molecular evidence that they had entirely independent origins. The relationships between S. kalimantanensis and S. naumanni and between S. cynthia and Samia wangi Naumann and Peigler, as well as the potential cryptic species within S. abrerai were also discussed. This is the first study to assess the DNA barcodes of the genus Samia, which supplements the knowledge of species identification and provides the first molecular phylogenetic framework for Samia species.

The relationship among freezing tolerance, vernalization requirement, Ppd alleles and winter hardiness in European wheat cultivars

2017 ◽  
Vol 155 (9) ◽  
pp. 1353-1370 ◽  
Author(s):  
A. GORASH ◽  
R. ARMONIENĖ ◽  
Ž. LIATUKAS ◽  
G. BRAZAUSKAS
Keyword(s):  
Molecular Markers ◽  
Western Europe ◽  
Complex Trait ◽  
Winter Hardiness ◽  
Photoperiod Sensitivity ◽  
The Other ◽  
Wheat Cultivars ◽  
Crucial Component ◽  
Per Se ◽  
The Relationship

SUMMARYWinter hardiness of wheat is a complex trait involving a system of structural, regulatory and developmental genes, which interact in a complex pathway. The objective of the present work was to study the relationship among the main traits determining the level of adaptation and the possibility for target manipulation of breeding material by using molecular markers and phenological parameters. Wheat cultivars from different ecoclimatic environments of Europe were included for analysis. Gene-specific assay showed that photoperiod sensitivity of the studied cultivars was determined by polymorphism in the Ppd-D1 allele. The study established the relationship among winter hardiness, LT50 (the temperature at which 50% of plants are killed), photoperiod sensitivity, vernalization duration and earliness per se genes in the environment of Lithuania. The cultivars from Northern and Western Europe exhibited stronger requirement for vernalization and photoperiod. Although the group of cultivars from the southern latitudes were characterized by earliness, they possessed a stronger level of LT50. The level of LT50 was found to be the most crucial component of winter hardiness, the other traits served as supplementary components.

scholarly journals Optimal markers for the identification ofColletotrichumspecies

2019 ◽  
Author(s):  
Willie Anderson dos Santos Vieira ◽  
Priscila Alves Bezerra ◽  
Anthony Carlos da Silva ◽  
Josiene Silva Veloso ◽  
Marcos Paz Saraiva Câmara ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Species Complex ◽  
Plant Pathogens ◽  
Phylogenetic Signal ◽  
Intergenic Spacer ◽  
Internal Transcribed Spacers ◽  
Type Locus ◽  
Phylogenetic Studies ◽  
Fungal Plant Pathogens ◽  
Species Complexes

ABSTRACTColletotrichumis among the most important genera of fungal plant pathogens. Molecular phylogenetic studies over the last decade have resulted in a much better understanding of the evolutionary relationships and species boundaries within the genus. There are now approximately 200 species accepted, most of which are distributed among 13 species complexes. Given their prominence on agricultural crops around the world, rapid identification of a large collection ofColletotrichumisolates is routinely needed by plant pathologists, regulatory officials, and fungal biologists. However, there is no agreement on the best molecular markers to discriminate species in each species complex. Here we calculate the barcode gap distance and intra/inter-specific distance overlap to evaluate each of the most commonly applied molecular markers for their utility as a barcode for species identification. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone-3 (HIS3), DNA lyase (APN2), intergenic spacer between DNA lyase and the mating-type locusMAT1-2-1 (APN2/MAT-IGS), and intergenic spacer between GAPDH and a hypothetical protein (GAP2-IGS) have the properties of good barcodes, whereas sequences of actin (ACT), chitin synthase (CHS-1) and nuclear rDNA internal transcribed spacers (nrITS) are not able to distinguish most species. Finally, we assessed the utility of these markers for phylogenetic studies using phylogenetic informativeness profiling, the genealogical sorting index (GSI), and Bayesian concordance analyses (BCA). Although GAPDH, HIS3 and β-tubulin (TUB2) were frequently among the best markers, there was not a single set of markers that were best for all species complexes. Eliminating markers with low phylogenetic signal tends to decrease uncertainty in the topology, regardless of species complex, and leads to a larger proportion of markers that support each lineage in the Bayesian concordance analyses. Finally, we reconstruct the phylogeny of each species complex using a minimal set of phylogenetic markers with the strongest phylogenetic signal and find the majority of species are strongly supported as monophyletic.

scholarly journals Development of Molecular Markers for the authentication of Zanthoxyli Pericarpium by the analysis of rDNA-ITS DNA barcode regions

2015 ◽  
Vol 30 (3) ◽  
pp. 41-47 ◽  
Author(s):  
Wook Jin Kim ◽  
Yunui Ji ◽  
Young Mi Lee ◽  
Young Min Kang ◽  
Goya Choi ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Dna Barcode ◽  
Rdna Its

scholarly journals Fungi of entomopathogenic potential in Chytridiomycota and Blastocladiomycota, and in fungal allies of the Oomycota and Microsporidia

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Agata Kaczmarek ◽  
Mieczysława I. Boguś
Keyword(s):  
Biological Control Agent ◽  
Sister Group ◽  
Control Agent ◽  
Scale Insects ◽  
Black Flies ◽  
Larval Stages ◽  
Phylogenetic Studies ◽  
Lady Beetles ◽  
Molecular Phylogenetic ◽  
The Relationship

AbstractThe relationship between entomopathogenic fungi and their insect hosts is a classic example of the co-evolutionary arms race between pathogen and target host. The present review describes the entomopathogenic potential of Chytridiomycota and Blastocladiomycota fungi, and two groups of fungal allies: Oomycota and Microsporidia. The Oomycota (water moulds) are considered as a model biological control agent of mosquito larvae. Due to their shared ecological and morphological similarities, they had long been considered a part of the fungal kingdom; however, phylogenetic studies have since placed this group within the Straminipila. The Microsporidia are parasites of economically-important insects, including grasshoppers, lady beetles, bumblebees, colorado potato beetles and honeybees. They have been found to display some fungal characteristics, and phylogenetic studies suggest that they are related to fungi, either as a basal branch or sister group. The Blastocladiomycota and Chytridiomycota, named the lower fungi, historically were described together; however, molecular phylogenetic and ultrastructural research has classified them in their own phylum. They are considered parasites of ants, and of the larval stages of black flies, mosquitoes and scale insects.

scholarly journals A phylogenetic analysis of the genus Pleurothallis, with emphasis on Pleurothallis subsection Macrophyllae-Fasciculatae, using nuclear ITS and chloroplast DNA sequencing

Lankesteriana ◽  
2011 ◽  
Vol 11 (3) ◽  
Author(s):  
M. Wilson ◽  
C. Belle ◽  
A. Dang ◽  
P. Hannan ◽  
C. Kenyon ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Preliminary Data ◽  
Plastid Dna ◽  
Maximum Parsimony Tree ◽  
Its Sequencing ◽  
Phylogenetic Studies ◽  
Parsimony Tree ◽  
Molecular Phylogenetic ◽  
Nuclear Its ◽  
Expanded Concept

Several revisions of the genus Pleurothallis have been proposed. Luer has proposed that Pleurothallis species in subgenus Scopula be segregated into the genera Colombiana and Ancipitia. Szlachetko and Margonska (2001) proposed the genus Zosterophyllanthos for Pleurothallis subsection Macrophyllae-Fasciculatae. As an alternative, Luer (2005) proposed the genus Acronia by uniting Pleurothallis subsection Macrophyllae-Fasciculatae with subsections Acroniae and Amphygiae. The molecular phylogenetic studies by Pridgeon and Chase (2001), however, suggested that these taxonomic revisions might not be justified. We report here a more detailed phylogenetic analysis of the genus Pleurothallis, with emphasis on subsection Macrophyllae-Fasciculatae, with data primarily from nuclear ITS sequencing, supplemented with preliminary data from plastid DNA (rpoB2, rpoC1, and ycf1) sequencing. Some initial, tentative conclusions can be drawn. In the strict consensus maximum-parsimony tree of ITS data, many of the clades collapse, leaving a polytomy with a single, highly supported node that tentatively could be used to delimit the genus Pleurothallis. Such a tree would argue for an expanded concept of the genus Pleurothallis, in which the groups Ancipitia, Colombiana, and Acronia/Zosterophyllanthos, if shown to be monophyletic, are relegated to subgenera. 

Phylogeny of Echiura updated, with a revised taxonomy to reflect their placement in Annelida as sister group to Capitellidae

2020 ◽  
Vol 34 (1) ◽  
pp. 101 ◽  
Author(s):  
Ryutaro Goto ◽  
James Monnington ◽  
Marija Sciberras ◽  
Isao Hirabayashi ◽  
Greg W. Rouse
Keyword(s):  
Molecular Phylogeny ◽  
Deep Sea ◽  
Sister Group ◽  
Molecular Data ◽  
Monterey Bay ◽  
Phylogenetic Studies ◽  
Littoral Zones ◽  
Family Level ◽  
Relationship Of ◽  
The Relationship

Echiura (commonly called spoon worms) are derived annelids that have an unsegmented sausage-shaped body with a highly extensible anterior end (i.e. a proboscis). Echiura currently contains two superfamilies: Echiurioidea (with Echiuridae, Urechidae and Thalassematidae) and Bonellioidea (with Bonelliidae, and Ikedidae). Ikedidae contains only Ikeda, which is distinctive in having a huge trunk, a highly elongate proboscis with stripes or dots, and numerous gonoducts. A recent molecular phylogeny of Echiura recovered Ikedidae as the sister group to Bonelliidae. However, due to relatively low support values for the monophyly of Bonelliidae, this relationship remains problematic. In this study, we reinvestigated the relationship of Bonelliidae and Ikedidae using an expanded dataset with more taxa and genes. In contrast to the previous results, our analyses strongly support that Ikeda is nested within Bonelliidae due to the placement of Maxmuelleria. On the basis of this result, we synonymise Ikedidae with Bonelliidae and transfer Ikeda to the latter, the diagnosis of which is amended. In addition, we synonymise Urechidae with its sister group Echiuridae because they share the synapomorphy of having anal chaetae rings. Furthermore, considering that recent phylogenetic studies have consistently recovered Echiura as the sister group to Capitelliidae within Annelida, we drop the rank of the echiuran clade to family-level and propose a revised classification: Thalassematidae with two subfamilies, Thalassematinae (with two tribes Echiurini and Thalassematini) and Bonelliinae. In addition, we identified a sample collected from the deep sea (~1820 m) of Monterey Bay, California, based on its molecular data. This terminal unexpectedly formed the sister group to the eight genera of Thalassematini, most members of which are inhabitants of littoral zones.

scholarly journals Breakdown of coevolution between symbiotic bacteriaWolbachiaand their filarial hosts

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1840 ◽  
Author(s):  
Emilie Lefoulon ◽  
Odile Bain ◽  
Benjamin L. Makepeace ◽  
Cyrille d’Haese ◽  
Shigehiko Uni ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Horizontal Transmission ◽  
Parasitic Nematodes ◽  
Global Pattern ◽  
Host Group ◽  
Reproductive Parasitism ◽  
Phylogenetic Studies ◽  
The Relationship

Wolbachiais an alpha-proteobacterial symbiont widely distributed in arthropods. Since the identification ofWolbachiain certain animal-parasitic nematodes (the Onchocercidae or filariae), the relationship between arthropod and nematodeWolbachiahas attracted great interest. The obligate symbiosis in filariae, which renders infected species susceptible to antibiotic chemotherapy, was held to be distinct from theWolbachia-arthropod relationship, typified by reproductive parasitism. While co-evolutionary signatures inWolbachia-arthropod symbioses are generally weak, reflecting horizontal transmission events, strict co-evolution between filariae andWolbachiahas been reported previously. However, the absence of close outgroups for phylogenetic studies prevented the determination of which host group originally acquiredWolbachia. Here, we present the largest co-phylogenetic analysis ofWolbachiain filariae performed to date including: (i) a screening and an updated phylogeny ofWolbachia; (ii) a co-phylogenetic analysis; and (iii) a hypothesis on the acquisition ofWolbachiainfection. First, our results show a general overestimation ofWolbachiaoccurrence and support the hypothesis of an ancestral absence of infection in the nematode phylum. The accuracy of supergroup J is also underlined. Second, although a global pattern of coevolution remains, the signal is derived predominantly from filarial clades associated withWolbachiain supergroups C and J. In other filarial clades, harbouringWolbachiasupergroups D and F, horizontal acquisitions and secondary losses are common. Finally, our results suggest that supergroup C is the basalWolbachiaclade within the Ecdysozoa. This hypothesis on the origin ofWolbachiawould change drastically our understanding ofWolbachiaevolution.

scholarly journals THE RELATIONSHIP OF THE COMMUNITY KNOWLEDGE LEVEL AMONG BEHAVIOR OF HANDLING NONCOROSIVE AGENT FOOD POINTING IN SINDANG BARANG BOGOR

2020 ◽  
Vol 11 (1) ◽  
pp. 73-81
Author(s):  
Tety Tety Novianty ◽  
Mulyani Siti Mulyani
Keyword(s):  
Human Life ◽  
Food Poisoning ◽  
P Value ◽  
Knowledge Level ◽  
Food Material ◽  
Cross Sectional ◽  
Corrosive Agent ◽  
Level Of Knowledge ◽  
Relationship Of ◽  
The Relationship

Food includes for the most important and very essential basic needs in human life. Called food poisoning if someone experiences health problems after consuming food which contaminated with bacteria or poison which produced by bacteria diseases. These microorganisms can enter to our bodies through the food with people mediators who process food or indeed come from the food itself by poor processing result. Non-corrosive food poisoning is a food material that is not derived from chemicals containing corrosive substances. The purpose of the research was to determine the connection between the knowledge level of the society with the behavior of handling non corrosive food poisoning agent in Sindang Barang Bogor. The type of the research used is quantitative analysis with the research design using descriptive analytical method through cross sectional approach. The population in this study was 140 citizens in Sindang Bogor. The amount of sampling used in the assessment was using the Slovin formula. So the sample in this research was 60 respondents. The results showed that from the total of 60 respondents, 24 people (40.0%) had a good level of knowledge. The Non-Corrosive Food Poisoning Behavior results stated that of 60 respondents, 34 people (56.7%) had negative Non-corrosive food poisoning behavior. There is a significant connection between the knowledge level of the society with the behavior of handling non corrosive agent food poisoning in Sindang Barang Bogor with value p= 0,002(p value > α). It was expected that the society in Sindang Barang Bogor can handle food poisoning Non- corrosive agent from factors so that the incidence of Non-corrosive food poisoning can be overcome.

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