Plant Taxonomy Research Articles

Structural characterization of Platanthera ussuriensis chloroplast genome and comparative analyses with other species of Orchidaceae

BackgroundThe genus Tulotis has been classified into the genus Platanthera in the present taxonomic studies since the morphological characteristics of this genus is very similar to that of Platanthera. Platanthera ussuriensis, formerly named as Tulotis ussuriensis, is a small terrestrial orchid species and has been listed as wild plant under State protection (category II) in China. An improved understanding of the genomic information will enable future applications of conservation strategy as well as phylogenetic studies for this rare orchid species. The objective of this research was to characterize and compare the chloroplast genome of P. ussuriensis with other closely related species of Orchidaceae.ResultsThe chloroplast genome sequence of P. ussuriensis is 155,016 bp in length, which included a pair of inverted repeats (IRs) of 26,548 bp that separated a large single copy (LSC) region of 83,984 bp and a small single copy (SSC) region of 17,936 bp. The annotation contained a total of 132 genes, including 86 protein-coding genes, 38 tRNA genes and 8 rRNA genes. The simple sequence repeat (SSR) analysis showed that there were 104 SSRs in the chloroplast genome of P. ussuriensis. RNA editing sites recognition indicated 72 RNA editing events occurred, and all codon changes were C to T conversions. Comparative genomics showed that the chloroplast sequence of Platanthera related species were relatively conserved, while there were still some high variation regions that could be used as molecular markers. Moreover, Platanthera related species showed similar IR/SSC and IR/LSC borders. The phylogenetic analysis suggested that P. ussuriensis had a closer evolutionary relationship with P. japonica followed by the remaining Platanthera species.ConclusionOrchidaceae is a key group of biodiversity protection and also a hot spot group in the plant taxonomy and evolution studies due to their characteristics of high specialization and rapid evolution. This research determined the complete chloroplast genome of P. ussuriensis for the first time, and compared the sequence with other closely related orchid species. These results provide a foundation for future genomic and molecular evolution of the Orchidaceae species, and provide insights into the development of conservation strategy for Platanthera species.

Does clustering of DNA barcodes agree with botanical classification directly at high taxonomic levels? Trees in French Guiana as a case study.

Characterizing biodiversity is one of the main challenges for the coming decades. Most diversity has not been morphologically described, and barcoding is now complementing morphological-based taxonomy to further develop inventories. Both approaches have been cross-validated at the level of species and OTUs. However, many known species are not listed in reference databases. One path to speed up inventories using barcoding is to directly identify individuals at coarser taxonomic levels. We therefore studied in barcoding of plants whether morphological-based and molecular-based approaches are in agreement at genus, family and order levels. We used Agglomerative Hierarchical Clustering (with Ward, Complete and Single Linkage) and Stochastic Block Models (SBM), with two dissimilarity measures (Smith-Waterman scores, kmers). The agreement between morphological-based and molecular-based classifications ranges in most of the cases from good to very good at taxonomic levels above species, even though it decreases when taxonomic levels increase, or when using the tetramer-based distance. Agreement is correlated with the entropy of morphological-based classification and with the ratio of the mean within- and mean between-groups dissimilarities. The Ward method globally leads to the best agreement, whereas Single Linkage can show poor behaviours. SBM provides a useful tool to test whether or not the dissimilarities are structured by the botanical groups. These results suggest that automatic clustering and group identification at taxonomic levels above species are possible in barcoding.

Plant Taxonomy and Biosystematics in PGR Collecting and Conservation

A sound understanding of the principles and practices of plant taxonomy is essential for plant genetic resources (PGR) conservation. Identification of new crop wild relatives (CWR) taxa, designating appropriate taxon status for discontinuous variants representing a geographical area, developing descriptors for new crops, and recruiting wild economic plants and semi-domesticates into cultivation, all require a good taxonomic base. The taxonomy of cultivated plants is essentially governed by a different set of guidelines under International Code of Nomenclature for Cultivated Plants (ICNCP). Biosystematic analysis helps to elucidate the genepool relationship of wild relatives with the crop, thereby promoting its utilization in crop improvement.

Stylosanthes (Leguminosae-Papilionoideae-Dalbergieae) in Northeast Brazil

Abstract Stylosanthes, with approximately 50 species, is a pantropical, economically important genus of Leguminosae, with several species having forage potential and soil improvement potential. Thirty-two species have been recorded in Brazil, with the Northeast region being one of the main centers of diversity of the genus in the country. Despite this, no taxonomic work focusing on Stylosanthes has been done for the region. This study presents a taxonomic treatment of Stylosanthes species occurring in the Northeast region of Brazil. Botanical specimens were collected in the field together with visits to the main herbaria in the Northeast (ALCB, HUEFS, HUNEB, HVASF) for specimen analysis. Online consultation of databases in virtual herbaria, analysis of regional flora accounts, assessment of types and discussions with legume experts were also undertaken. Twenty-three taxa were confirmed as occurring in NE Brazil, with six new occurrences recorded for the states of Ceará, Paraíba, Piauí, and Rio Grande do Norte. Species in the studied area are mainly differentiated by their fruit and bract morphology. Key words: campos rupestres, Cerrado, Fabaceae, flora, plant taxonomy, semiarid.

Bioprospecção como estratégia para a conservação e uso sustentável da Flora Brasileira

Abstract In Brazil, research with natural products had a strong impulse when FAPESP supported the creation of the Laboratory of Chemistry of Natural Products of the Institute of Chemistry of USP (1966). In 1999, FAPESP launched the Research Program in the Characterization, Conservation, Restoration and Sustainable Use of Biodiversity (BIOTA-FAPESP), which intensified the sustainable exploitation of biodiversity, and which evolved to form the Biota Network for Bioprospection and Bioassays (BIOprospecTA), which integrates groups from all over the country, optimizing the use of the skills already installed for the bioprospecting of microorganisms, plants, invertebrates, vertebrates and marine organisms. Of the 104 projects related to plant sciences, 35 carried out bioprospection of Brazilian flora, belonging to the areas of Chemistry, Botany, Genetics, Plant Physiology, Plant Morphology, Plant (Chemo)taxonomy, Ecosystem Ecology, Plant Genetics. Physical Sciences, Forest Resources, Forestry Engineering, Agronomy, leading to thousands of publications, engagement of hundreds of students and a deeper understanding of natural products in different biological models through macromolecules analysis aided by computational and spectrometric strategies, in addition to pharmacological evaluations. The development of omics approaches led to a more comprehensive view of the chemical profile of an organism, and enabled integrated and concomitant studies of several samples, and faster annotation of known molecules, through the use of hyphenated and chemometric techniques, and molecular networking. This also helped to overcome the lack of information on the safety and efficacy of herbal preparations, in projects dealing with the standardization of herbal products, according to international standards. The BIOTA-FAPESP program has also focused on environmental aspects, in accordance with the principles of Green Chemistry and has had positive effects on international collaboration, on the number and impact of scientific publications and on partnership with companies, a crucial step to add value and expand the production chain of bioproducts. Also, the compilation, systematization and sharing of data were contemplated with the creation of the NUBBEDB database, of free access, and that integrates with international databases (ACD/labs, American Chemical Society – ACS), helping researchers and companies in the development from different areas of science, technology, strengthening the bioeconomy and subsidizing public policies.

Challenges and opportunities to improve tropical fruits in Hainan, China

Tropical fruits play a major role in the economic and social development of Hainan. Despite favorable climatic conditions, the yield of tropical fruits in Hainan remains low, in part due to the low genetic potential of currently grown tropical fruit varieties. Consequently, there is a need to improve yield potential by exploiting the genome and germplasm resources of tropical fruit species, minimizing post-harvest losses, and improving transportation standards. In this study, we intend to collect germplasm resources from a wide range of domestic and exotic sources to evaluate the genetic yield potential and nutritional quality of fruit using plant morphology, taxonomy and physiological parameters. In this review, we aim to identify current bottlenecks in the Hainan tropical fruit industry and propose solutions through the use of conventional breeding and new biotechnological tools, including the use of omics and CRISPR to enhance yield and tackle biotic and abiotic stresses of tropical fruit species. Producing new fruit cultivars in Hainan, either through conventional strategies or the use of genome editing technology such as CRISPR, could help improve the socioeconomic status of this region. Furthermore, increasing the genetic potential and production of new cultivars can help in meeting the demands of new trade agreements with various nations under the “One Belt, One Road” initiative, Boao Forum for Asia, ASEAN agreements, and the Shanghai Cooperation Organization.

Toward a terrestrial biogeographical regionalisation of the world: historical notes, characterisation and area nomenclature

An interim hierarchical classification (i.e. biogeographical regionalisation or area taxonomy) of the world’s terrestrial regions is provided, following the work of Morrone published in Australian Systematic Botany in 2015. Area names are listed according to the International Code of Area Nomenclature so as to synonymise redundant names. The interim global terrestrial regionalisation to the subregion level recognises 3 kingdoms, 2 subkingdoms, 8 regions, 21 subregions and 5 transition zones. No new names are proposed for the regions; however, Lydekker’s Line is renamed Illiger’s Line. We note that some regions still require area classification at the subregion level, particularly the Palearctic, Ethiopian and Oriental regions. Henceforth, the following interim global regionalisation may be used as a template for further revisions and additions of new areas in the future.

A current and historical situation report of Chinese plant taxonomists

A current and historical situation report of Chinese plant taxonomists

Spontaneous poisoning by Baccharis vulneraria Backer in cattle

ABSTRACT: Baccharis vulneraria Backer is a sub-shrub frequently found in southern Brazil, which leads to gastrointestinal tract intoxication. The objective of this study is to describe epidemiological, clinical and anatomopathological aspects of two cases of B. vulneraria poisoning in cattle. Two bovines from two different municipalities in the Itajaí Valley, Santa Catarina, Brazil were necropsied and performed the histopathological evaluation and botanical classification of the plant found in the pasture. Bovine 1 had dehydration, ruminal atony, diarrhea, congested mucous membranes and hypothermia for 20 hours, and died during clinical care. At necropsy, there was moderate multifocal detachment and reddening of the forestomachs mucosa. Bovine 2 presented anorexia, dry feces, ruminal atony, vocalization and muscle tremors for ten days, unresponsive to treatments, evolving to death. At necropsy were seen loosening of the mucosa with marked diffuse reddening and transmural edema. The microscopic exam revealed degeneration, necrosis, vesiculation, and detachment of the forestomachs’ mucosa, associated with moderate multifocal neutrophilic infiltrate (Bovine 1); marked diffuse transmural necrosis, edema, hemorrhage, and marked fibrinous exudation (Bovine 2). A large amount of B. vulneraria was found in the pastures, with signs of consumption. In this report, a case of subacute evolution of B. vulneraria poisoning was observed, since the poisoning by this plant is usually acute. More knowledge about poisoning by this plant is necessary for the prevention and control, avoiding new mortality cases.

Biometry in plant systematic of European and Mediterranean Gymnosperms, a review

The morphological features of plants, which were the basis of taxonomic solutions in the past, are now sometimes less appreciated due to the intensive development of genetic methods. The present review looks at the results of the research on the taxonomy of plants carried out by the team led by A. Boratyński. The team characterized the taxonomic and geographical differentiation of some species of the genera Abies, Juniperus, Pinus, Cupressus, Cedrus, as well as several others. Many of these studies were carried out in the Mediterranean area due to its importance for biodiversity. The results allowed unravelling taxonomic ambiguities, emphasizing the importance of geographic barriers in shaping variability, e.g., the Strait of Gibraltar or the Aegean Sea, and highlighting the role of mountain ranges as refuges, e.g., the Taurus and Anti-Taurus Mountains. All of the results obtained with biometrics were confirmed by genetic methods by different authors. Detailed research allowed the publication of a new name, Juniperus thurifera subsp. africana (Maire) Romo & Boratyński, stat. nov., and restoration of species status for the dubious taxon Juniperus canariensis. The review shows that relying on the research of a large number of correctly sampled populations and correctly selected differentiated characteristics of plants allows the generation of reliable results.

Molecular organization of 5S ribosomal DNA of Apis mellifera ligustica

Aim. 5S rDNA belongs to the moderately repeated, tandemly arranged sequences composed of coding regions and intergenic spacers (IGS). The IGS comparison is successfully used for the study of microevolution and in the molecular taxonomy of plants, vertebrates and some invertebrates. However, 5S rDNA of insects still remains insufficiently characterized. In this article, we analyze the molecular organization and polymorphism of 5S rDNA IGS of Apis mellifera ligustica. Methods. DNA extraction, PCR amplification, cloning of 5S rDNA, sequencing, bioinformatics analysis. Results. The 5S rDNA IGS of A. m. ligustica was cloned into the plasmid vector and sequenced. The obtained sequences were compared with the same genomic region of A. m. carnica. It was found that the genome of A. m. ligustica contains one class of IGS, which is represented by structural subclasses 1A, 1B, 1G and 1F. Two of these subclasses, 1G and 1F, which are identified here for the first time, are specific for A. m. ligustica. Conclusions. The obtained results show a high intra- and intergenomic polymorphism of 5S rDNA within the subspecies of Apis mellifera.Keywords: 5S rDNA, intergenic spacer, repeated sequences, Apis mellifera, Apidae.

Pharmacological Efficacy of Tamarix aphylla: A Comprehensive Review.

Tamarix aphylla is a well-known species of the genus Tamarix. T. aphylla (Tamaricaceae) is a perennial tree in Asia, the Middle East, and Central Africa. It is used as a carminative diuretic in tuberculosis, leprosy, and hepatitis. Various pharmacological properties have been shown by T. aphylla, such as antidiabetic, anti-inflammatory, antibacterial, antifungal, anticholinesterase, and wound-healing activity. However, T. aphylla has not received much attention for its secondary metabolites and bioactive constituents. Research has shown that this plant has hidden potential that needs to be explored. This review aims to cover botanical classification, geographical distribution, taxonomy, ethnobotanical uses, and the phytochemical compounds found in T. aphylla. The toxicology and pharmacological effects of T. aphylla are also discussed. We examined various scholarly resources to gather information on T. aphylla, including Google Scholar, Scopus, Science Direct, Springer Link, PubMed, and Web of Science. The finding of this work validates a connection between T. aphylla in conventional medicine and its antidiabetic, antibacterial, anti-inflammatory, wound-healing, antifungal, anticholinesterase, and other biological effects. T. aphylla’s entire plant (such as bark, leaves, fruits) and root extracts have been used to treat hypertension, stomach discomfort, hair loss, cough and asthma, abscesses, wounds, rheumatism, jaundice, fever, tuberculosis, and gum and tooth infection. The phytochemical screening revealed that noticeably all extracts were devoid of alkaloids, followed by the presence of tannins. In addition, different parts have revealed the existence of steroids, flavonoids, cardiac glycosides, and byproducts of gallic acid and ellagic acid. T. aphylla has shown many valuable activities against different diseases and supports its traditional uses. Therefore, high-quality preclinical research and well-designated clinical trials are needed to establish the efficacy and safety of this plant in humans.

The Healing Analysis of II Degree Burn from Surgery Essential Oil Ointment (Curcuma Longa) in Wistar Rats (Rattus Norvegicus)

Data in Indonesia the death rate from burns is still high at around 40%, mainly caused by severe burns. The most potential medicinal turmeric plant is its rhizome, which contains the phenolic compound curcumin and essential oils. Some of the benefits of turmeric antioxidants, anti-inflammatory, anti-cancer, acetylcholinesterase activity inhibitors, anti-fungal, and anti-bacterial. This study aims to find out the phytochemical content and effects of Turmeric Essential Oil Ointment (Curcuma longa Linn) in curing grade II burns in Wistar rats (Rattus norvegicus). This type of research is experimental with a pre-post approach and post-test control group design. The study was conducted at Riwandi Pet Shop and Animal House March-May 2021. The research sample is turmeric (Curcuma longa) obtained from a traditional market in the city of Medan and identified in herbarium Medanese (MEDA), Laboratoirum Taxonomy of Plants, Department of Biology, Faculty of Mathematics and Natural Sciences (FMIPA), University of North Sumatra, Medan. The test animal is a Wistar strain rat with as many as 20 tails divided into 4 treatment groups, so each group consists of 5 rats. The results of the study contained significant differences in the epithelial period of the standard group, 10% turmeric ointment and 15% against the control group. However, in the turmeric ointment group and the standard group, there was no difference in epithelialization periods. This is evident from the value P < 0.05 (Value P = 0.029). The healing effects of burns possessed by Turmeric ointment are both 10% and 15% and nebacetin ointment as standard shows significant differences. Where the wound contraction rate of turmeric ointment is 15% better than nebacetin ointment as standard. But in both turmeric ointments, both 10% and 15% and nebacetin ointment as standard did not show significant differences in the parameters of the epithelial period.

Investigation of anatomical signs of canadian goldenrod herbs, introduced in Ukraine

The monograph «Goldenrod» SPhU 2.0 describes the general morphological and anatomical features of two species – Solidago gigantea Ait and Solidago canadensis L., which are similar. Not all diagnostic signs can be identified in powdered raw materials. It was important to investigate domestic series of сanadian goldenrod and to identify additional diagnostic signs.
 The aim of the work was to study the series of domestic raw materials of сanadian goldenrod by anatomical features and to determine the totality of individual features of the species to establish the identity of raw materials.
 The object of the study were samples of сanadian goldenrod grass, which were harvested in August 2020 in the regions of Ukraine. We used an iPhone XR camera, Item PB-2610 V microscope.
 Important features of the anatomical structure of the raw material of сanadian goldenrod include: the cells of the stem epidermis are parenchymal, ortho-walled, porous, the leaves – sinuous- and ortho-walled. The presence in the pubescence of stems and leaves 3 types of hairs: simple long, 5–8-celled (up to 20), with thickened walls and pointed cell; short, 2–3-celled, with a dormant apical cell; short and headed with a 2–3-celled stalk and a rounded unicellular head; on the surface and edge of the leaves of the involucre – simple short and 3–4-cell hairs, corollas of flowers – multicellular double-row hairs; stem vessels are spiral, ladder, porous and reticulate; schizogenous structures in the stems, leaves and leaves of the involucre; sphenocrystals of inulin in the parenchyma and vessels of the stem, the cells of the corollas of flowers.
 A series of domestic raw materials of сanadian goldenrod has been studied according to anatomical features, a set of individual features of the species has been determined. The obtained results can be used in plant taxonomy for comparative analysis of morphologically similar species of the genus Zolotushnik, as well as to supplement the section «Identification B» of the monograph SPhU 2.0 «Zolotushnik».

Origin Identification of Hungarian Honey Using Melissopalynology, Physicochemical Analysis, and Near Infrared Spectroscopy

The objective of the study was to check the authenticity of Hungarian honey using physicochemical analysis, near infrared spectroscopy, and melissopalynology. In the study, 87 samples from different botanical origins such as acacia, bastard indigo, rape, sunflower, linden, honeydew, milkweed, and sweet chestnut were collected. The samples were analyzed by physicochemical methods (pH, electrical conductivity, and moisture), melissopalynology (300 pollen grains counted), and near infrared spectroscopy (NIRS:740–1700 nm). During the evaluation of the data PCA-LDA models were built for the classification of different botanical and geographical origins, using the methods separately, and in combination (low-level data fusion). PC number optimization and external validation were applied for all the models. Botanical origin classification models were >90% and >55% accurate in the case of the pollen and NIR methods. Improved results were obtained with the combination of the physicochemical, melissopalynology, and NIRS techniques, which provided >99% and >81% accuracy for botanical and geographical origin classification models, respectively. The combination of these methods could be a promising tool for origin identification of honey.

Morphological characteristics of Zingiberaceae in Serang District, Banten, Indonesia

Abstract. Windarsih G, Utami DW, Yuriyah S. 2021. Morphological characteristics of Zingiberaceae in Serang District, Banten, Indonesia. Biodiversitas 22: 5507-5529. Zingiberaceae, known as ginger family, is a family of monocotyledon belonging to the Zingiberales order. This family is widely used its rhizome for various purposes, especially as medicinal plant. The morphological characters can be used to help the identification of species in the field of plant taxonomy. The aim of study was to characterize the morphological traits, both vegetative and generative organs, of Zingiberaceae from Serang District, Banten. Plant specimens were collected from Serang District, Banten, including in Pabuaran, Gunungsari, and Ciomas sub-district using purposive sampling. The examination of morphological characters data was conducted through observation and documentation. There were 13 species/varieties of Zingiberaceae collected from the studied area, i.e. Amomum compactum, Alpinia purpurata, Curcuma xanthorrhiza, C. longa, C. heyneana, C. mangga, C. aeruginosa, Kaempferia rotunda, Etlingera elatior, Zingiber zerumbet, Z. officinale, Zingiber officinale var. rubrum, and Z. cassumunar, in which the generative organs were found only in eight species/cultivars of them. Based on the morphological characters of vegetative organs, thirteen species/cultivars had a similarity distance coefficient from 37% to 94%; while based on the morphological characters of both vegetative and generative organs, the eight species/cultivars had a similarity distance coefficient from 31% to 94%. The results showed that using the characters of vegetative organs data were still able to provide consistent grouping results with the generative organs.

Phyto-Pharmacological Profile of Wrightia tinctoria

Wrightia tinctoria is a medium sized ever green tree grows up to 18 m tall and to 20 cm which produces milky white latex from the leaves which is directly applied on inflammation. Since from ancient period this plant constantly been used as a source of medicine. This plant shows a very important component of the health care system in India. In ayurvedic system the drug activity of W.tinctoria is defined as titka, kashaya, rooksha, sita and katu. Various parts of this plant such as stem bark, leaves, flowers also seed have been known to have medicinal assets. Phytochemical studies have shown that it contains alkaloids, triterpenoids, steroids, flavonoids, phenolics, carbohydrates, lipids etc. Wrightia tinctoria has been allotted to have good analgesic, anti-inflammatory, anthelmintic, antiulcer, antidysentric, antidiabetic, anticancer, antipyretic activities as well as active in the treatment of psoriasis. The present review primed to describe the botanical classification, vernacular names, species, Pharmacognostical and Phytochemical Properties and pharmacological activities of the plant Wrightia tinctoria.

Cynodondactylon: A Review of Pharmacological Activities

The annual weedy grass Cynodondactylon (L.) Pers. Belonging to the family Poaceae is one of the tenth fortunate plants in ayurveda’s ‘Dasapushpam’ and ‘Navgaraha’ groups. Cynodondactylon (L.) Pers. has a wide range of therapeutic uses. The species is a natural resource because it grows as a weed. An overview on Cynodondactylon (L.) Pers. is undertaken with the goal of providing all the relevant information regarding this grass. The review includes botanical classification, various other species of this grass, chemical classification, pharmacological activities, various dosage forms, ethnobotanical uses, patent registered, vernacular names around the world, cultivators around the world, macroscopy, microscopy of the grass.

Controlled transitions between phyllotactic states of repulsive particles confined on the surface of a cylinder

Phyllotaxis is a botanical classification scheme that can describe regular lattice-like structures on cylinders, often as a set of helical chains. In this letter, we study the general properties of repulsive particles on cylindrical geometries and demonstrate that this leads to a model which allows one to predict the minimum energy configuration for any given combination of system parameters. We are able to predict a sequence of transitions between phyllotactic ground states at zero temperature. Our results are understood in terms of a newly identified global scale invariant, α, dependent on circumference and density, which alone determines the ground-state structure. This representation provides a framework within which to understand and create lattice structures on more complex curved surfaces, which occur in both biological and nanoscale experimental settings.

Collections Education: The Extended Specimen and Data Acumen.

Biodiversity scientists must be fluent across disciplines; they must possess the quantitative, computational, and data skills necessary for working with large, complex data sets, and they must have foundational skills and content knowledge from ecology, evolution, taxonomy, and systematics. To effectively train the emerging workforce, we must teach science as we conduct science and embrace emerging concepts of data acumen alongside the knowledge, tools, and techniques foundational to organismal biology. We present an open education resource that updates the traditional plant collection exercise to incorporate best practices in twenty-first century collecting and to contextualize the activities that build data acumen. Students exposed to this resource gained skills and content knowledge in plant taxonomy and systematics, as well as a nuanced understanding of collections-based data resources. We discuss the importance of the extended specimen in fostering scientific discovery and reinforcing foundational concepts in biodiversity science, taxonomy, and systematics.