Chloroplast genome sequencing based on genome skimming for identification of Eriobotryae Folium

Abstract Background Whole chloroplast genome (cpDNA) sequence is becoming widely used in the phylogenetic studies of plant and species identification, but in most cases the cpDNA were acquired from silica gel dried fresh leaves. So far few reports have been available to describe cpDNA acquisition from crude drugs derived from plant materials, the DNA of which usually was seriously damaged during their processing. In this study, we retrieved cpDNA from the commonly used crude drug Eriobotryae Folium (Pipaye in Chinese, which is the dried leaves of Eriobotrya japonica, PPY) using genome skimming technique. Results We successfully recovered cpDNA sequences and rDNA sequences from the crude drug PPY, and bioinformatics analysis showed a high overall consistency between the cpDNA obtained from the crude drugs and fresh samples. In the ML tree, each species formed distinct monophyletic clades based on cpDNA sequence data, while the phylogenetic relationships between Eriobotrya species were poorly resolved based on ITS and ITS2. Conclusion Our results demonstrate that both cpDNA and ITS/ITS2 are effective for identifying PPY and its counterfeits derived from distantly related species (i.e. Dillenia turbinata and Magnolia grandiflora), but cpDNA is more effective for distinguishing the counterfeits derived from the close relatives of Eriobotrya japonica, suggesting the potential of genome skimming for retrieving cpDNA from crude drugs used in Traditional Chinese Medicine for their identification.

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Verification of Thai ethnobotanical medicine “Kamlang Suea Khrong” driven by multiplex PCR and powerful TLC techniques

PLoS ONE ◽

10.1371/journal.pone.0257243 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0257243

Author(s):

Suthira Yanaso ◽

Ampai Phrutivorapongkul ◽

Darunee Hongwiset ◽

Sirivipa Piyamongkol ◽

Aekkhaluck Intharuksa

Keyword(s):

Chemical Analysis ◽

Multiplex Pcr ◽

Plant Species ◽

Specific Primers ◽

Discrimination Power ◽

Plant Materials ◽

Identification Methods ◽

Crude Drug ◽

Crude Drugs ◽

Species Specific

Kamlang Suea Khrong (KSK) crude drug, a traditional Thai medicine used for oral tonic and analgesic purposes, is obtained from three origins: the inner stem bark of Betula alnoides (BA) or the stems of Strychnos axillaris (SA) or Ziziphus attopensis (ZA). According to the previous reports, SA contains strychnine-type alkaloids that probably cause poisoning; however, only organoleptic approaches are insufficient to differentiate SA from the other plant materials. To ensure the botanical origin of KSK crude drug, powerful and reliable tools are desperately needed. Therefore, molecular and chemical identification methods, DNA barcoding and thin-layer chromatography (TLC), were investigated. Reference databases, i.e., the ITS region and phytochemical profile of the authentic plant species, were conducted. In case of molecular analysis, multiplex polymerase chain reaction (PCR) based on species-specific primers was applied. Regarding species-specific primers designation, the suitability of three candidate barcode regions (ITS, ITS1, and ITS2) was evaluated by genetic distance using K2P model. ITS2 presented the highest interspecific variability was verified its discrimination power by tree topology. Accordingly, ITS2 was used to create primers that successfully specified plant species of authentic samples. For chemical analysis, TLC with toluene:ethyl acetate:ammonia (1:9:0.025) and hierarchical clustering were operated to identify the authentic crude drugs. The developed multiplex PCR and TLC methods were then applied to identify five commercial KSK crude drugs (CK1-CK5). Both methods correspondingly indicated that CK1-CK2 and CK3-CK5 were originated from BA and ZA, respectively. Molecular and chemical approaches are convenient and effective identification methods that can be performed for the routine quality-control of the KSK crude drugs for consumer reliance. According to chemical analysis, the results indicated BA, SA, and ZA have distinct chemical profiles, leading to differences in pharmacological activities. Consequently, further scientific investigations are required to ensure the quality and safety of Thai ethnobotanical medicine known as KSK.

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Studies on Crude Drugs originated from Gentianaceous Plants. III. The Bitter Principle of the Chinese Crude Drug Qinjiao and Its Content

YAKUGAKU ZASSHI ◽

10.1248/yakushi1947.96.3_362 ◽

1976 ◽

Vol 96 (3) ◽

pp. 362-365 ◽

Cited By ~ 5

Author(s):

TERUAKI HAYASHI ◽

MASAYUKI HIGASHINO

Keyword(s):

Crude Drug ◽

Bitter Principle ◽

Crude Drugs

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Phylogenetic Relations of Rhizoplaca Zopf. from Anatolia Inferred from ITS Sequence Data

Zeitschrift für Naturforschung C ◽

10.1515/znc-2006-5-617 ◽

2006 ◽

Vol 61 (5-6) ◽

pp. 405-412 ◽

Cited By ~ 4

Author(s):

Demet Cansaran ◽

Sümer Aras ◽

İrfan Kandemir ◽

Gökhan Halıcı

Keyword(s):

Genetic Variability ◽

Phylogenetic Tree ◽

Sequence Data ◽

Volcanic Rocks ◽

Morphological Characteristics ◽

Its Rdna ◽

Its Sequence ◽

Phylogenetic Relations ◽

Rdna Sequences

Like many lichen-forming fungi, species of the genus Rhizoplaca have wide geographical distributions, but studies of their genetic variability are limited. The information about the ITS rDNA sequences of three species of Rhizoplaca from Anatolia was generated and aligned with other species from other countries and also with the data belonging to Lecanora species. The examined species were collected from the volcanic rocks of Mount Erciyes which is located in the middle of Anatolia (Turkey). The sequence data aligned with eight other samples of Rhizoplaca and six different species of Lecanora were obtained from GenBank. The results support the concept maintained by Arup and Grube (2000) that Rhizoplaca may not be a genus separate from Lecanora. According to the phylogenetic tree, Rhizoplaca melanopthalma from Turkey with two different samples of R. melanopthalma from Arizona (AF159929, AF159934) and a sample from Austria formed a group under the same branch. R. peltata and R. chrysoleuca samples from Anatolia located in two other branches of the tree formed sister groups with the samples of the same species from different countries. Although R. peltata remained on the same branch with other samples of the same species from other countries it was placed in a different branch within the group. When the three species from Anatolia were considered alone, it was noticed that Rhizoplaca melanopthalma and Rhizoplaca peltata are phylogenetically closer to each other than Rhizoplaca chrysoleuca; the morphological characteristics also support this result.

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Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1423790112 ◽

2015 ◽

Vol 112 (33) ◽

pp. 10200-10207 ◽

Cited By ~ 117

Author(s):

Jan Janouškovec ◽

Denis V. Tikhonenkov ◽

Fabien Burki ◽

Alexis T. Howe ◽

Martin Kolísko ◽

...

Keyword(s):

Plastid Genome ◽

Sequence Data ◽

Sister Group ◽

Molecular Characteristics ◽

Phylogenomic Analysis ◽

Free Living ◽

Plastid Genomes ◽

Monophyletic Lineage ◽

Causative Agents ◽

Close Relatives

Apicomplexans are a major lineage of parasites, including causative agents of malaria and toxoplasmosis. How such highly adapted parasites evolved from free-living ancestors is poorly understood, particularly because they contain nonphotosynthetic plastids with which they have a complex metabolic dependency. Here, we examine the origin of apicomplexan parasitism by resolving the evolutionary distribution of several key characteristics in their closest free-living relatives, photosynthetic chromerids and predatory colpodellids. Using environmental sequence data, we describe the diversity of these apicomplexan-related lineages and select five species that represent this diversity for transcriptome sequencing. Phylogenomic analysis recovered a monophyletic lineage of chromerids and colpodellids as the sister group to apicomplexans, and a complex distribution of retention versus loss for photosynthesis, plastid genomes, and plastid organelles. Reconstructing the evolution of all plastid and cytosolic metabolic pathways related to apicomplexan plastid function revealed an ancient dependency on plastid isoprenoid biosynthesis, predating the divergence of apicomplexan and dinoflagellates. Similarly, plastid genome retention is strongly linked to the retention of two genes in the plastid genome, sufB and clpC, altogether suggesting a relatively simple model for plastid retention and loss. Lastly, we examine the broader distribution of a suite of molecular characteristics previously linked to the origins of apicomplexan parasitism and find that virtually all are present in their free-living relatives. The emergence of parasitism may not be driven by acquisition of novel components, but rather by loss and modification of the existing, conserved traits.

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Phylogenetic relationships and chloroplast capture in the Amelanchier-Malacomeles-Peraphyllum clade (Maleae, Rosaceae): Evidence from chloroplast genome and nuclear ribosomal DNA data using genome skimming

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2020.106784 ◽

2020 ◽

Vol 147 ◽

pp. 106784 ◽

Cited By ~ 6

Author(s):

Bin-Bin Liu ◽

Christopher S. Campbell ◽

De-Yuan Hong ◽

Jun Wen

Keyword(s):

Chloroplast Genome ◽

Ribosomal Dna ◽

Phylogenetic Relationships ◽

Nuclear Ribosomal Dna ◽

Chloroplast Capture ◽

Genome Skimming

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The tribal position of Fockea and Cibirhiza (Apocynaceae: Asclepiadoideae): evidence from pollinium structure and cpDNA sequence data

Grana ◽

10.1080/00173130310012549 ◽

2003 ◽

Vol 42 (2) ◽

pp. 70-81 ◽

Cited By ~ 3

Author(s):

Rudolf L Verhoeven ◽

Sigrid Liede ◽

Mary E Endress

Keyword(s):

Sequence Data ◽

Cpdna Sequence

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Molecular analysis of selected paramphistome isolates from cattle in southern Africa

Journal of Helminthology ◽

10.1017/s0022149x15000905 ◽

2015 ◽

Vol 90 (6) ◽

pp. 784-788 ◽

Cited By ~ 3

Author(s):

S. Dube ◽

M.S. Sibula ◽

Z. Dhlamini

Keyword(s):

Sequence Data ◽

Animal Health ◽

Phylogenetic Reconstruction ◽

Morphological Characterization ◽

Its2 Sequence ◽

Molecular Techniques ◽

Its2 Rdna ◽

African Countries ◽

Rdna Sequences ◽

The Individual

AbstractParamphistomes are parasites of domestic and wild ruminants, the effects of which in animal health remain underestimated. Very few studies in Africa have been done using molecular techniques to resolve situations associated with taxonomical groupings and epidemiology of these parasites. In this study, the genetic variability of nine representative paramphistome isolates collected from southern African countries, namely Botswana, South Africa, Zambia and Zimbabwe, was assessed using both morphological and internal transcribed spacer 2 (ITS2) rDNA sequence data. Morphological characterization and identification were carried out using median sagittal sections of the paramphistomes. DNA of the individual paramphistomes was isolated, the ITS2 rDNA was amplified, purified and sequenced. The sequences were submitted to GenBank, which assigned them the following accession numbers: KP639631, KP639630, KP639632, KP639633, KP639634, KP639635, KP639636, KP639637 and KP639638. These sequences were used for phylogenetic analysis using MEGA 6. Morphological characterization revealed three species of paramphistomes belonging to three different sub-families: one Stephanopharynx compactus isolate, a member of the Stephanopharyngidae sub-family; one Carmyerius dollfusi isolate, a member of the Gastrothylacidae sub-family; and seven Calicophoron microbothrium isolates belonging to the Paramphistomidae sub-family. ITS2 sequence analysis using BlastN results indicated that this is the first report of S. compactus (KP639630) and C. dollfusi (KP639636). Phylogenetic reconstruction of the paramphistome isolates revealed three separate clades representing the three species. However, the clade with all the C. microbothrium isolates was the only one that was supported by a higher bootstrap value of 92%, although there was no differentiation of the isolates according to geographical locations. The low divergence values on the ITS2 sequences of the C. microbothrium isolates indicate that ITS rDNA sequences can be used as a molecular tool to infer knowledge for resolving taxonomic groupings.

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On the phylogeny of Ophiostoma, Ceratocystis s.s., and Microascus, and relationships within Ophiostoma based on partial ribosomal DNA sequences

Canadian Journal of Botany ◽

10.1139/b93-148 ◽

1993 ◽

Vol 71 (9) ◽

pp. 1249-1265 ◽

Cited By ~ 54

Author(s):

G. Hausner ◽

J. Reid ◽

G. R. Klassen

Keyword(s):

Dna Sequences ◽

Sequence Data ◽

Large Subunit ◽

Small Subunit ◽

Data Set ◽

Rdna Sequences ◽

Morphological Criteria ◽

Small Subunit Rdna ◽

Rdna Sequence Data ◽

Large Subunit Rdna

Phylogenetic analysis of partial rDNA sequences suggests that Ophiostoma should remain the sole genus of the Ophiostomataceae, and this should be the sole family within the Ophiostomatales, whereas Ceratocystis s.s. would be best disposed within the Microascales. Although morphological criteria suggest that the genus Ophiostoma is heterogeneous, analysis of partial small subunit rDNA sequence data shows that Ophiostoma (excluding O. roraimense) represents a monophyletic taxon. Analysis of a partial large subunit rDNA data set, which included sequences from 55 species assignable to Ophiostoma, failed to support the strict subdivision of the genus based on either ascospore characters or the nature of the anamorph. Key words: Ceratocystis, Microascus, Ophiostoma, partial rDNA sequences, phylogeny.

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