psbA-trnH Spacer Regions Research Articles

The efficacy of machine learning algorithm for raw drug authentication in Coscinium fenestratum (Gaertn.) Colebr. employing a DNA barcode database.

Medicinal plants are a valuable resource for traditional as well as modern medicine. Consequently huge demand has exerted a heavy strain on the existing natural resources. Due to over exploitation and unscientific collection most of the commercially traded ayurvedic plants are in the phase of depletion. Adulteration of expensive raw drugs with inferior taxa has become a common practice to meet the annual demand of the ayurvedic industry. Although there are several recommended methods for proper identification varying from the traditional taxonomic to organoleptic and physiochemical, it is difficult to authenticate ayurvedic raw drugs available in extremely dried, powdered or shredded forms. In this regard, the study addresses proper authentication and illicit trade in Coscinium fenestratum (Gaertn.) Colebr. using CBOL recommended standard barcode regions viz. nuclear ribosomal-Internally Transcribed Spacer (nrDNA- ITS), maturase K (matK), ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL), and psbA-trnH spacer regions. Further, an integrated analytical approach employing Maximum Likelihood phylogenetic tree and Machine Learning Approach, Waikato Environment for Knowledge Analysis was employed to prove efficacy of the method. The automated species identification technique, Artificial Intelligence uses the ability of computers to build models that can receive the input data and then conduct statistical analyses which significantly reduces the human labour. Concurrently, scientific management, restoration, cultivation and conservation measures should be given utmost priority to reduce the depletion of wild resources as well as to meet the rapidly increasing demand of the herbal industries.

Barcoding assessment of the Citrus species cultivated in the eastern Afghanistan

The establishment of a modern fruit culture in developing countries requests an accurate evaluation of the preexisting germplasm and its health status. This to prevent the possibility to introduce new germplasm which can be easily prey of the endemic diseases carried by asymptomathic host plants. Therefore, after the identification of cases of citrus plants affected by Tristeza virus, a survey of the germplasm cultivated in the Nangarhar valley and some nearby regions was run. The survey was focussed on the identification of the main Citrus species widely cultivated using barcoding analysis of conserved sequences located in the plastid DNA. The sequences of matK and rbcl genes did not show any discriminatory ability while the analysis of the the non-coding psbA-trnH intergenic spacer (psbA-trnH) showed a robust single nucleotide polymorphism (sNP) discriminating C. aurantium from C. sinensis in all analysed samples. These non-coding regions have no known function; thus, much of the variation may result from the spread of mutations unconstrained by selection. Because nucleotide variation in the psbA-trnH spacer region is high, mutational hot spots may be useful to detect species-level variations. According to our study, the afghan citrus germplasm belong to the C. aurantium species which is commonly used in citrus culture as a rootstock. In Afghanistan it is widely cultivated for fresh consumption, without topworking with selected varieties and this may be the reason why symptoms are often mild and cultivation can be anyhow carried on.

DNA profiles to identify Dillenia species (Dilleniaceae) in Thailand

Surveying of the species throughout Thailand revealed 13 identified and one unidentified species including D. aurea, D. excelsa, D. grandifolia, D. hookeri, D. indica, D. obovata, D. ovata, D. parviflora, D. pentagyna, D. philippinensis, D. pulchella, D. reticulata, D. suffruticosa and Dillenia sp. They were phylogenetically examined based on RAPD profiles of 2,290 discrete characters including a monomorphic and 226 polymorphic characteristics. The phylogenetic relationships calculated from theses banding data show that the intraspecific genetic similarity (S) values ranged from 0.990 to 1.000, and the interspecific S values ranged from 0.520 to 0.790. The RAPD method can be effectively used in Dillenia study. However, its quality of unreproducible method, it cannot be reasonable used in any study on specific genes or areas. In additions, sequences from two molecular regions, rbcL gene and psbA-trnH spacer, were analyzed and determined for genetic distances. The rbcL gene sequences were rather ineffective, as all of the paired species displayed no or low genetic distance values. The psbA-trnH spacer sequences were rather effective, with only one pair (D. reticulata and D. parviflora) showing low genetic distance values. The other species pairs indicated rather far genetic distances, ranging from 0.006 (D. parviflora and D. grandifolia) to 0.376 (Dillenia specie and D. indica). Intraspecific genetic distance values ranged from 0–0.003 and 0–0.013 for rbcL and psbA-trnH spacer regions, respectively. Based on the results from both nucleotide variations and DNA fingerprinting, D. grandifolia and D. ovata were distinct Dillenia species.

A molecular marker for in situ genetic resource conservation of Capsicum annuum var. acuminatum (Solanaceae)

The Thailand cultivar pepper 'phrik man bangchang' (Capsicum annuum var. acuminatum, Solanaceae) was originally cultivated in the Bangchang Subdistrict, Amphawa District in Samut Songkhram Province. The cultivated areas are limited; we verified its distribution in Thailand for in situ 'phrik man bangchang' genetic resource conservation. Samples were collected from the original cultivation area of Bangchang Subdistrict (Or) and were randomly explored in Ratchaburi Province (RB), Khon Kaen Province (KK), and Sakon Nakhon Province (SN). A pure line from The Tropical Vegetable Research Center at Kasetsart University was used as the standard indicator. Two more Capsicum species, C. chinensis and C. frutescens, and a species from another genus in the family, Solanum melongena, were included. A dendrogram constructed from random amplified polymorphic DNA fingerprints indicated that the Or, RB, KK, and SN samples were C. annuum var. acuminatum with supportive similarity coefficients of 0.79 to 0.98. Finally, DNA barcodes, from psbA-trnH spacer region, were provided for the 3 wild species, C. annuum var. acuminatum, C. chinensis, and C. frutescens under GenBank accession Nos. JQ087869-JQ087871. The nucleotide variations between species were 0.23 to 0.26. In summary, 'phrik man bangchang' is still being planted in Bangchang Subdistrict, but only in small areas. The distribution of planting areas is expected to be throughout Thailand.

Medicinal parasitic plants on diverse hosts with their usages and barcodes

Medicinal properties of parasitic plants were investigated by means of ethnobotanical study in some areas of northeastern Thailand. Important traditional usages are: Scurrula atropurpurea nourishes blood, Dendrophthoe pentandra decreases high blood pressure, and Helixanthera parasitica treats liver disease. Their systematics were also determined. The research is based on findings obtained from 100 parasite-host pairs. Of these, eight parasitic species were recorded; they are members of two families, viz. family Loranthaceae, namely D. lanosa, D. pentandra, H. parasitica, Macrosolen brandisianus, M. cochinchinensis and S. atropurpurea, and family Viscaceae, namely Viscum articulatum and V. ovalifolium. In addition, each parasitic species is found on diverse hosts, indicating non-host-parasitic specificity. Species-specific tagging of all species studied was carried out using the rbcL and psbA-trnH chloroplast regions. These tag sequences are submitted to GenBank databases under accession numbers JN687563-JN687578. Genetic distances calculated from nucleotide variations in a couple of species of each genus, Dendrophthoe, Macrosolen, and Viscum, were 0.032, 0.067 and 0.036 in the rbcL region, and 0.269, 0.073 and 0.264 in the psbA-trnH spacer region, respectively. These variations will be used for further identification of incomplete plant parts or other forms such as capsule, powder, dried or chopped pieces.

Identification ofDendrobiumSpecies by a Candidate DNA Barcode Sequence: The ChloroplastpsbA-trnHIntergenic Region

DNA barcoding is a novel technology that uses a standard DNA sequence to facilitate species identification. Although a consensus has not been reached regarding which DNA sequences can be used as the best plant barcodes, the psbA-trnH spacer region has been tested extensively in recent years. In this study, we hypothesize that the psbA-trnH spacer regions are also effective barcodes for Dendrobium species. We have sequenced the chloroplast psbA-trnH intergenic spacers of 17 Dendrobium species to test this hypothesis. The sequences were found to be significantly different from those of other species, with percentages of variation ranging from 0.3 % to 2.3 % and an average of 1.2 %. In contrast, the intraspecific variation among the Dendrobium species studied ranged from 0 % to 0.1 %. The sequence difference between the psbA-trnH sequences of 17 Dendrobium species and one Bulbophyllum odoratissimum ranged from 2.0 % to 3.1 %, with an average of 2.5 %. Our results support the notion that the psbA-trnH intergenic spacer region could be used as a barcode to distinguish various Dendrobium species and to differentiate Dendrobium species from other adulterating species.

Phylogenetics and Evolution of the Macaronesian Clade of Crassulaceae Inferred from Nuclear and Chloroplast Sequence Data

Abstract The Macaronesian clade of Crassulaceae comprises four genera (Aichryson, Aeonium, Greenovia, and Monanthes) that are largely endemic to Macaronesia, a region encompassing the Azores, Madeira, and the Cape Verde, Canary, and Salvage Islands. The monophyly of this clade has been supported by recent family-level phylogenetic analyses; however, the relationships within the clade remain uncertain. To resolve relationships within the Macaronesian clade, we sequenced several chloroplast DNA regions (matK and the trnL-trnF and psbA-trnH spacer regions) and the nuclear rDNA ITS region. Parsimony analyses of separate ITS and cpDNA data sets recover three major clades, corresponding to Aichryson, the perennial species of Monanthes, and Aeonium (including Greenovia). Congruence tests revealed significant heterogeneity between the ITS and cpDNA data sets. Comparison of the topologies resulting from analyses of these separate data sets indicated five instances of incongruence between the ITS and cpDNA that may...