scholarly journals Phylogenomics and barcoding ofPanax: toward the identification of ginseng species

2018 ◽  
Author(s):  
V. Manzanilla ◽  
A. Kool ◽  
Nhat L. Nguyen ◽  
H. Nong Van ◽  
H. Le Thi Thu ◽  
...  
Keyword(s):  
Panax Ginseng ◽  
Molecular Identification ◽  
High Throughput Sequencing ◽  
Economic Value ◽  
Cost Effective ◽  
Morphological Characters ◽  
Species Discrimination ◽  
Sister Relationship ◽  
Plastid Genomes ◽  
Molecular Phylogenetic

AbstractBackgroundThe economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time, the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecular phylogenetic studies. In this study, we use a full plastome phylogenomic framework to resolve relationships inPanaxand to identify molecular markers for species discrimination.ResultsWe used high-throughput sequencing of MBD2-Fc fractionatedPanaxDNA to supplement publicly available plastid genomes to create a phylogeny based on fully assembled and annotated plastid genomes from 60 accessions of 8 species. The plastome phylogeny based on a 163 kbp matrix resolves the sister relationship ofPanax ginsengwithP. quinquefolius. The closely related speciesP. vietnamensisis supported as sister ofP. japonicus. The plastome matrix also shows that the markerstrnC-rps16, trnS-trnG, andtrnE-trnMcould be used for unambiguous molecular identification of all the represented species in the genus.ConclusionsMBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective alternative to Sanger sequencing based DNA barcoding for molecular identification. The plastome phylogeny provides a robust framework that can be used to study the evolution of morphological characters and biosynthesis pathways of ginsengosides for phylogenetic bioprospecting. Molecular identification of ginseng species is essential for authenticating ginseng in international trade and it provides an incentive for manufacturers to create authentic products with verified ingredients.

scholarly journals Identification of the Pathogen Causing Stem Blight Disease on Chili in Sindangjaya Village, Cipanas, Cianjur, West Java Based on Morphological and Molecular Analyses

2021 ◽  
Vol 17 (1) ◽  
pp. 35
Author(s):  
Wartono Wartono
Keyword(s):  
Molecular Identification ◽  
Phytophthora Capsici ◽  
Economic Value ◽  
Morphological Characters ◽  
Stem Rot ◽  
West Java ◽  
Molecular Analyses ◽  
Molecular Approaches ◽  
Rot Disease ◽  
Blight Disease

<p>Chili (Capsicum annuum L.) is a vegetable commodity with high economic value which is widely cultivated by farmers in Indonesia. One of the obstacles faced in chili cultivation is stem rot disease. This study aimed to identify the pathogens that caused stem rot in chili plants obtained from one location in Sindangjaya Village, Cipanas District, Cianjur Regency, West Java Province based on morphological and molecular analyses. Pathogen identification was performed with morphological and molecular approaches. The morphological characters observed included colony shape, sporangium diameter, and mating type. The pathogenicity of the isolates was assayed by inoculating chili stems aged 40 days. Molecular identification was carried out using two pairs of primers for ITS regions and TEF-1 gene. Based on the results of morphological and molecular identification, as well as pathogenicity tests, it was confirmed that Phytophthora capsici pathogen was the causal agent of stem rot in chili plants collected from Sindangjaya Village. Further study is needed to determine the spread of the disease, damage, and yield loss caused by stem rot disease, as well as how to prevent and control the disease.</p>

scholarly journals HiMAP: robust Phylogenomics from Highly Multiplexed Amplicon sequencing

2017 ◽  
Author(s):  
Julian R. Dupuis ◽  
Forest T. Bremer ◽  
Angela Kauwe ◽  
Michael San Jose ◽  
Luc Leblanc ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Insect Pests ◽  
Amplicon Sequencing ◽  
Read Mapping ◽  
Sister Relationship ◽  
New Approach ◽  
Hands On ◽  
Locus Selection ◽  
Molecular Phylogenetic ◽  
Tephritid Fruit Flies

ABSTRACTHigh-throughput sequencing has fundamentally changed how molecular phylogenetic datasets are assembled, and phylogenomic datasets commonly contain 50-100-fold more loci than those generated using traditional Sanger-based approaches. Here, we demonstrate a new approach for building phylogenomic datasets using single tube, highly multiplexed amplicon sequencing, which we name HiMAP (Highly Multiplexed Amplicon-based Phylogenomics), and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and post-sequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously, requires minimal hands-on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically-important agricultural insect pests. The resulting dataset (>150,000 bp concatenated alignment) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status ofZeugodacusand the sister relationship betweenDacusandZeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting dataset provides into relationships of this diverse insect group.

scholarly journals Revision of the genus Dichaetophora Duda (Diptera: Drosophilidae), part I: DNA bar-coding and molecular phylogenetic reconstruction

2021 ◽  
Author(s):  
Takehiro K Katoh ◽  
Ji-Min Chen ◽  
Jin-Hua Yang ◽  
Guang Zhang ◽  
Lu Wang ◽  
...  
Keyword(s):  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Morphological Data ◽  
Sister Relationship ◽  
Mitochondrial Coi ◽  
Adaptive Diversification ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Cladistic Analyses ◽  
Species Groups

The genus Dichaetophora Duda is of 69 formally described, Old World species assigned into five species groups, i.e., agbo, tenuicauda, acutissima, sinensis and trilobita. Most of these species were delimitated morphologically, with the within-genus relationship established largely via cladistic analyses of morphological characters. In the present study, we first conducted species-delimitation with aids of morphological data as well DNA barcodes (nucleotide sequences of the mitochondrial COI, i.e., cytochrome c oxidase subunit I, gene), for a huge sample of Dichaetophora and allied taxa (genus Mulgravea and subgenus Dudaica of Drosophila) collected from a wide geographical range. Then, multiple-locus phylogenetic reconstruction was conducted based on elaborate taxon sampling from the known and newly recognized species in the above taxa, with the maximum likelihood (ML) and Bayesian inference (BI) methods. As a result, 189 species (186 of Dichaetophora, 2 of Mulgravea, and 1 for Dudaica) were newly recognized. In our ML and BI trees, several well-supported species clusters equivalent to the species groups agbo (excluding of neocirricauda), tenuicauda, sinensis (inclusive of neocirricauda) and trilobita of Dichaetophora, were recovered, with the sister-relationship between the third and fourth proved. Other well-supported clusters include 1) a clade comprising of Di. acutissima group and Dudaica, with the former proved to be paraphyletic to the latter; 2) genus Mulgravea; 3) a clade comprising exclusively of newly recognized Dichaetophora species, and was placed as sister to Mulgravea. Three of the remaining five representatives of Dichaetophora species form a solid cluster, leaving the positions of the last two unresolved. The present study greatly renewed out knowledge about the species diversity in a pan-Dichaetophora clade, providing us with an unprecedented historical framework for further taxonomy revision of this clade, and valuable baseline knowledge for future reconstruction of the history of its adaptive diversification in the particular microhabitats.

scholarly journals Molecular and Morphological Variation among Populations of Pediomelum tenuiflorum (Pursh) A.N. Egan (Fabaceae) in Nebraska, USA

2019 ◽  
pp. 17-37
Author(s):  
Chauncey Kellar ◽  
P. Roxanne Kellar
Keyword(s):  
Growth Habit ◽  
Morphological Characters ◽  
Illumina Platform ◽  
Plastid Genomes ◽  
Disjunct Populations ◽  
Molecular Phylogenetic ◽  
Outgroup Taxon ◽  
Morphological Variants ◽  
The Many ◽  
Genomic Regions

Individuals of Pediomelum tenuiflorum, “wild alfalfa”, from disjunct populations in Nebraska vary extensively in their overall gestalt. Those in the western and central part of the state have a very slender growth habit, with thin stems and few, small flowers; whereas, those in the southeast have a very robust growth habit with heavy-looking stems and many tightly clustered flowers. For nearly 200 years, taxonomists have alternated between splitting P. tenuiflorum into two species, with the many-flowered morphotype named P. floribundum, and lumping all the morphological variants into one species as they are now. In this study, we investigated morphological and molecular characters that could be used to clarify taxonomic classifications of these morphotypes. We measured 10 morphological characters on 51 specimens and sequenced nearly 300,000 nucleotide characters on the Illumina platform from three cellular genomes in seven samples of Pediomelum plus an outgroup taxon. Results revealed six significantly different morphological characters but ambiguous evolutionary histories of the plastid and mitochondrial genomes in P. tenuiflorum. Our complete plastid genomes and genes and noncoding regions of the mitochondrial genome may be used as a foundation for studying the evolutionary histories of these genomes. Additionally, we identified seven highly variable genomic regions in the chloroplast genome upon which a molecular phylogenetic investigation on an expanded set of samples from across the species’ geographic distribution can be conducted to further define the taxonomic placements of P. tenuiflorum and P. floribundum.

Transfer of the Kobresia taxa of the flora of Russia and adjacent countries to the genus Carex (Cyperaceae)

2020 ◽  
pp. 125-129
Author(s):  
D. G. Melnikov ◽  
L. I. Krupkina
Keyword(s):  
International Collaboration ◽  
Morphological Characters ◽  
Published Data ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
New Nomenclatural Combinations

Based on the published data of molecular phylogenetic studies of the tribe Cariceae Dumort. genera (Cyperaceae), obtained by an international collaboration (The Global Carex Group, 2016; et al.), and morphological characters of the genera (Kukkonen, 1990; and others), new nomenclatural combinations and replacement names in the genus Carex L. are published for 11 species, one subspecies and two sections previously included in the genus Kobresia Willd.

Worldview-2 and Landsat 8 Satellite Data for Seaweed Mapping along Karachi Coast

2016 ◽  
Vol 5 (2) ◽  
Author(s):  
Muhammad Danish Siddiqui ◽  
Arjumand Z Zaidi
Keyword(s):  
Satellite Data ◽  
Spatial Scales ◽  
Economic Value ◽  
Vegetation Indices ◽  
Cost Effective ◽  
Geographical Information ◽  
Landsat 8 ◽  
Coverage Area ◽  
Breeding Sites ◽  
Marine Plant

<span>Seaweed is a marine plant or algae which has economic value in many parts of the world. The purpose of <span>this study is to evaluate different satellite sensors such as high-resolution WorldView-2 (WV2) satellite <span>data and Landsat 8 30-meter resolution satellite data for mapping seaweed resources along the coastal<br /><span>waters of Karachi. The continuous monitoring and mapping of this precious marine plant and their <span>breeding sites may not be very efficient and cost effective using traditional survey techniques. Remote <span>Sensing (RS) and Geographical Information System (GIS) can provide economical and more efficient <span>solutions for mapping and monitoring coastal resources quantitatively as well as qualitatively at both <span>temporal and spatial scales. Normalized Difference Vegetation Indices (NDVI) along with the image <span>enhancement techniques were used to delineate seaweed patches in the study area. The coverage area of <span>seaweed estimated with WV-2 and Landsat 8 are presented as GIS maps. A more precise area estimation <span>wasachieved with WV-2 data that shows 15.5Ha (0.155 Km<span>2<span>)of seaweed cover along Karachi coast that is <span>more representative of the field observed data. A much larger area wasestimated with Landsat 8 image <span>(71.28Ha or 0.7128 Km<span>2<span>) that was mainly due to the mixing of seaweed pixels with water pixels. The <span>WV-2 data, due to its better spatial resolution than Landsat 8, have proven to be more useful than Landsat<br /><span>8 in mapping seaweed patches</span></span></span></span></span></span></span></span></span></span></span></span></span></span><br /><br class="Apple-interchange-newline" /></span></span></span></span></span>

scholarly journals Disentangling relationships among eastern Mediterranean Cymbalaria including description of a novel species from the southern Peloponnese (Greece)

2021 ◽  
Vol 307 (2) ◽  
Author(s):  
Pau Carnicero ◽  
Núria Garcia-Jacas ◽  
Llorenç Sáez ◽  
Theophanis Constantinidis ◽  
Mercè Galbany-Casals
Keyword(s):  
Eastern Mediterranean ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Distribution Patterns ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Long Distance ◽  
Aegean Islands ◽  
Molecular Phylogenetic

AbstractThe eastern Mediterranean basin hosts a remarkably high plant diversity. Historical connections between currently isolated areas across the Aegean region and long-distance dispersal events have been invoked to explain current distribution patterns of species. According to most recent treatments, at least two Cymbalaria species occur in this area, Cymbalaria microcalyx and C. longipes. The former comprises several intraspecific taxa, treated at different ranks by different authors based on morphological data, evidencing the need of a taxonomic revision. Additionally, some populations of C. microcalyx show exclusive morphological characters that do not match any described taxon. Here, we aim to shed light on the systematics of eastern Mediterranean Cymbalaria and to propose a classification informed by various sources of evidence. We performed molecular phylogenetic analyses using ITS, 3’ETS, ndhF and rpl32-trnL sequences and estimated the ploidy level of some taxa performing relative genome size measures. Molecular data combined with morphology support the division of traditionally delimited C. microcalyx into C. acutiloba, C. microcalyx and C. minor, corresponding to well-delimited nrDNA lineages. Furthermore, we propose to combine C. microcalyx subsp. paradoxa at the species level. A group of specimens previously thought to belong to Cymbalaria microcalyx constitute a well-defined phylogenetic and morphological entity and are described here as a new species, Cymbalaria spetae. Cymbalaria longipes is non-monophyletic, but characterized by being glabrous and diploid, unlike other eastern species. The nrDNA data suggest at least two dispersals from the mainland to the Aegean Islands, potentially facilitated by marine regressions.

Integrative taxonomic and geographic variation analyses in Cyrtodactylus aequalis (Squamata: Gekkonidae) from southern Myanmar (Burma): one species, two different stories

2020 ◽  
Vol 66 (3-4) ◽  
pp. 151-179
Author(s):  
L. Lee Grismer ◽  
L. Wood Perry ◽  
Marta S. Grismer ◽  
Evan S.H. Quah ◽  
Myint Kyaw Thura ◽  
...  
Keyword(s):  
Geographic Variation ◽  
Evolutionary History ◽  
Phylogenetic Inference ◽  
Morphological Characters ◽  
Molecular Data ◽  
Biodiversity Crisis ◽  
Allopatric Populations ◽  
Compelling Argument ◽  
Historical Accuracy ◽  
Molecular Phylogenetic

The historical accuracy of building taxonomies is improved when they are based on phylogenetic inference (i.e., the resultant classifications are less apt to misrepresent evolutionary history). In fact, taxonomies inferred from statistically significant diagnostic morphological characters in the absence of phylogenetic considerations, can contain non-monophyletic lineages. This is especially true at the species level where small amounts of gene flow may not preclude the evolution of localized adaptions in different geographic areas while underpinning the paraphyletic nature of each population with respect to the other. We illustrate this point by examining genetic and morphological variation among three putatively allopatric populations of the granite-dwelling Bent-toed Gecko Cyrtodactylus aequalis from hilly regions in southeastern Myanmar. In the absence of molecular phylogenetic inference, a compelling argument for three morphologically diagnosable species could be marshaled. However, when basing the morphological analyses of geographic variation on a molecular phylogeny, there is a more compelling argument that only one species should be recognized. We are cognizant of the fact however, that when dealing with rare species or specimens for which no molecular data are possible, judicious morphological analyses are the only option—and the desired option given the current worldwide biodiversity crisis.

scholarly journals The relative taxonomic value of morphological characters in the genus <i>Nummulites</i> (Foraminiferida)

1992 ◽  
Vol 11 (2) ◽  
pp. 197-209 ◽  
Author(s):  
Andrew Racey
Keyword(s):  
Morphological Character ◽  
Morphological Characters ◽  
Species Discrimination ◽  
Evolutionary Trends ◽  
Ontogenetic Effects

Abstract. The main evolutionary trends in the nummulites are briefly summarised and the value of certain morphological characters in species discrimination are summarised. The degree of interdependence of each morphological character on all other characters is assessed and the characters are weighted in order of importance. Environmental and ontogenetic effects on each character are then reviewed and the characters reweighted in order of importance.

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