scholarly journals Species delimitation of Melia dubia Cav. from Melia azedarach L. complex based on DNA barcoding

Botany ◽  
2018 ◽  
Vol 96 (5) ◽  
pp. 329-336 ◽  
Author(s):  
Irusappan Sivaraj ◽  
Stalin Nithaniyal ◽  
Varadharajan Bhooma ◽  
Umapathy Senthilkumar ◽  
Madasamy Parani
Keyword(s):  
Dna Barcoding ◽  
Distinct Species ◽  
Melia Azedarach ◽  
Nuclear Marker ◽  
Intraspecific Divergence ◽  
Interspecific Divergence ◽  
Medicinal Properties ◽  
Melia Dubia ◽  
Chloroplast Dna Markers ◽  
Suitable Marker

The genus Melia L., which belongs to the “Mahogany” family Meliaceae, is a source of important phytochemicals with marked medicinal properties. Species identification in Melia is complex due to the existence of overlapping morphological features. Although Melia dubia Cav. is listed as a synonym of Melia azedarach L., it is not clear from the available literature whether they are the same species or different, and the species complexity still remains unresolved. In the present study, 10 accessions of M. dubia and M. azedarach were analysed by DNA barcoding using three chloroplast DNA markers (rbcL, matK, and trnH–psbA), and one nuclear marker (ITS2). Intraspecific divergence was not found in any of the four markers. However, the interspecific divergence between M. azedarach and M. dubia ranged between 0.3% (rbcL) and 4.7% (ITS2) for individual markers, and for the combined dataset, it was 8.5%. Among the four markers, ITS2 was found to be the most suitable marker for differentiating M. azedarach and M. dubia. Parsimony analysis of the DNA barcoding data showed a clear segregation between M. azedarach and M. dubia as distinct monophyletic clades in all the markers, except the rbcL marker. Our results based on Bayesian analysis of the concatenated dataset strongly support the view that M. dubia be considered a distinct species; not a synonym of M. azedarach.

Morphology and DNA barcodes reveal the presence of the non-native land planarian Obama marmorata (Platyhelminthes : Geoplanidae) in Europe

2015 ◽  
Vol 29 (1) ◽  
pp. 12 ◽  
Author(s):  
Domingo Lago-Barcia ◽  
Fernando A. Fernández-Álvarez ◽  
Lisandro Negrete ◽  
Francisco Brusa ◽  
Cristina Damborenea ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Geographic Origin ◽  
Original Description ◽  
Neotropical Region ◽  
Morphological Evidence ◽  
Intraspecific Divergence ◽  
Interspecific Divergence ◽  
Allochthonous Species ◽  
First Time ◽  
Land Planarian

We report for the first time the occurrence of Obama marmorata in the Iberian Peninsula as an introduced species from the Neotropical Region. The species is also reported for the first time in Argentina. The identification was made on the basis of morphological evidence. The divergence levels of a fragment of the mitochondrial cytochromec oxidaseI gene from Argentinean and Iberian samples were studied. The morphology of samples from the two regions was the same and matched the original description of the species. A DNA barcoding matrix was constructed using new sequences from O. marmorata and sequences of related species taken from GenBank. Among the Geoplanidae, interspecific divergence ranged between 3.3 and 14.4%, while intraspecific divergence percentages were 0–1.2%, signalling the presence of a DNA barcoding gap. All O. marmorata sequences, irrespective of their geographic origin, form a well supported clade with an intraspecific divergence of 0–0.9 (average = 0.4%). These results indicate the utility of DNA barcoding to discover allochthonous species in this group of organisms.

scholarly journals Challenging species delimitation in Collembola: cryptic diversity among common springtails unveiled by DNA barcoding

2012 ◽  
Vol 26 (6) ◽  
pp. 470 ◽  
Author(s):  
D. Porco ◽  
A. Bedos ◽  
Penelope Greenslade ◽  
C. Janion ◽  
D. Skarżyński ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Functional Groups ◽  
Species Delimitation ◽  
Sequence Divergence ◽  
Cryptic Diversity ◽  
Congeneric Species ◽  
Nuclear Marker ◽  
Accurate Identification ◽  
Intraspecific Divergence

Collembola is one of the major functional groups in soil as well as a model taxon in numerous disciplines. Therefore the accurate identification of specimens is critical, but could be jeopardised by cases of cryptic diversity. Several populations of six well characterised species of springtails were sequenced using the COI barcode fragment as a contribution to the global Collembola barcoding campaign. Each species showed high intraspecific divergence, comparable to interspecific sequence divergence values observed in previous studies and in 10 congeneric species barcoded here as a reference. The nuclear marker, 28S, confirmed all the intraspecific lineages found with COI, supporting the potential specific status of these entities. The implications of this finding for taxonomy and for disciplines relying on species names, such as evolution and ecology, are discussed.

scholarly journals Identifying Chinese species of Gammarus (Crustacea: Amphipoda) using DNA barcoding

2009 ◽  
Vol 55 (2) ◽  
pp. 158-164 ◽  
Author(s):  
Zhong-e Hou ◽  
Zhu Li ◽  
Shu-qiang Li
Keyword(s):  
Cryptic Species ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Neighbor Joining ◽  
Cytochrome C Oxidase I ◽  
Widespread Species ◽  
Intraspecific Divergence ◽  
Gammarus Lacustris ◽  
Interspecific Divergence ◽  
Identification Of Species

Abstract Using a standard cytochrome c oxidase I sequence, DNA barcoding has been shown to be effective to distinguish known species and to discover cryptic species. Here we assessed the efficiency of DNA barcoding for the amphipod genus Gammarus from China. The maximum intraspecific divergence for widespread species, Gammarus lacustris, was 3.5%, and mean interspecific divergence reached 21. 9%. We presented a conservative benchmark for determining provisional species using maximum intraspecific divergence of Gammarus lacustris. Thirty-one species possessed distinct barcode clusters. Two species were comprised of highly divergent clades with strong neighbor-joining bootstrap values, and likely indicated the presence of cryptic species. Although DNA barcoding is effective, future identification of species of Gammarus should incorporate DNA barcoding and morphological detection.

DNA barcoding of forensically important flies in the Western Cape, South Africa

Genome ◽  
2018 ◽  
Vol 61 (12) ◽  
pp. 823-828 ◽  
Author(s):  
Tenielle Cooke ◽  
Kyle Kulenkampff ◽  
Marise Heyns ◽  
Laura Jane Heathfield
Keyword(s):  
South Africa ◽  
Dna Barcoding ◽  
Dna Sequences ◽  
The Body ◽  
Western Cape ◽  
Accurate Identification ◽  
Intraspecific Divergence ◽  
Post Mortem Interval ◽  
Interspecific Divergence

Forensic entomology aids the determination of post mortem interval based on arthropods associated with a deceased body. This relies on the accurate identification of insects that visit the body, particularly first colonisers such as Calliphoridae (Diptera). Traditional species identification though morphological keys can be challenging as immature or closely related specimens can look similar. Some of these challenges have been overcome through “DNA barcoding”, which involves the sequencing of informative regions within a species’ DNA and comparison to a database of reference sequences. However, reference DNA sequences of blow fly species in South Africa is currently limited. In this study, adult blow flies representing four species common to the Western Cape, South Africa (Chrysomya chloropyga, Chrysomya albiceps, Chrysomya marginalis, Lucilia sericata) were examined using morphological keys and DNA barcoding of two regions: COI and ITS2. These DNA sequences were then used as references for the successful identification of seven unknown immature specimens. Intraspecific divergence showed a maximum of 0.36% and 2.25% for COI and ITS2, respectively; interspecific divergence showed a minimum of 6.14% and 64.6% for COI and ITS2, respectively. According to these results, COI and ITS2 have sufficient discriminatory power for species-level identification for the four species studied.

scholarly journals ddRAD Sequencing Sheds Light on Low Interspecific and High Intraspecific mtDNA Divergences in Two Groups of Caddisflies

2021 ◽  
Vol 5 (5) ◽  
Author(s):  
Juha Salokannel ◽  
Kyung Min Lee ◽  
Aki Rinne ◽  
Marko Mutanen
Keyword(s):  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Nuclear Genome ◽  
Distinct Species ◽  
Present Species ◽  
Cryptic Diversity ◽  
Weak Support ◽  
Genomic Scale ◽  
Group Species

Abstract Large-scale global efforts on DNA barcoding have repeatedly revealed unexpected patterns of variability in mtDNA, including deep intraspecific divergences and haplotype sharing between species. Understanding the evolutionary causes behind these patterns calls for insights from the nuclear genome. While building a near-complete DNA barcode library of Finnish caddisflies, a case of barcode-sharing and some cases of deep intraspecific divergences were observed. In this study, the Apatania zonella (Zetterstedt, 1840) group and three Limnephilus Leach, 1815 species were studied using double digest RAD sequencing (ddRAD-seq), morphology, and DNA barcoding. The results support the present species boundaries in the A. zonella group species. A morphologically distinct but mitogenetically nondistinct taxon related to parthenogenetic Apatania hispida (Forsslund, 1930) got only weak support for its validity as a distinct species. The morphology and genomic-scale data do not indicate cryptic diversity in any of the three Limnephilus species despite the observed deep intraspecific divergences in DNA barcodes. This demonstrates that polymorphism in mtDNA may not reflect cryptic diversity, but mitonuclear discordance due to other evolutionary causes.

scholarly journals A Review of Recent Phytomedicinal Investigations and the Need for DNA Barcoding of Endemic Plants of Northern Cyprus

2020 ◽  
pp. 61-70
Author(s):  
Dudu Özkum Yavuz ◽  
Mustapha Bulama- Modu
Keyword(s):  
Quality Control ◽  
Dna Barcoding ◽  
Dna Sequences ◽  
Pharmacological Properties ◽  
Endemic Plants ◽  
Dna Barcodes ◽  
Inclusion Criteria ◽  
Ovid Medline ◽  
Northern Cyprus ◽  
Medicinal Properties

Aims: To review the phytomedicinal researches on endemic plants of Northern Cyprus and to assess the plants of their DNA barcoding status. Study Design: A review. Methodology: This work reviewed available and accessible original articles in EBSCO, Ovid MEDLINE®, PubMed®, ScienceDirectTM, Scopus® and Web of ScienceTM databases on phytomedicinal investigations and BOLD System, MMDBD version 1.5 and GenBank® on DNA barcodes of the endemic plants of Northern Cyprus until May, 2020. Using keywords searches related to phytochemistry, biological activity and DNA barcoding, DNA Sequences and the data obtain evaluated and the information that does not meet the inclusion criteria were excluded. We believe that this information would tentatively help researchers to ethically explore these plants for their Medicinal and Aromatic potentials. Results: Only 6 of the 20 endemic plants of Northern Cyprus were phytopharmaceutically investigated, while DNA sequences of 5 were found to be deposited in the publicly accessible databases accounting for 30% and 25% of the total plants respectively. Conclusion: Endemism is related to uniqueness in features including the phytomedicinal features, thus Northern Cyprus endemic plants hold ample of such. However the results of this review showed that only few were harnessed for their medicinal properties and hence the need for their pharmacological properties and comprehensive barcoding for proper authentication, detection of adulteration, and quality control.

scholarly journals COI-based barcoding of Chinese vipers (Reptilia: Squamata: Viperidae)

2015 ◽  
Vol 36 (4) ◽  
pp. 361-372 ◽  
Author(s):  
Qin Liu ◽  
Fei Zhu ◽  
Guanghui Zhong ◽  
Yunyu Wang ◽  
Min Fang ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Intraspecific Variability ◽  
Gene Fragment ◽  
Reference Library ◽  
Threshold Method ◽  
Cytochrome Oxidase Subunit ◽  
Barcoding Gap ◽  
Putative Species ◽  
Interspecific Divergence ◽  
Identification Of Species

DNA barcoding seeks to assemble a standardized reference library for rapid and unambiguous identification of species, and can be used to screen for potentially cryptic species. The 5′ region of cytochrome oxidase subunit I (COI), which is a mitochondrial DNA (mtDNA) gene fragment, has been proposed as a universal marker for this purpose among animals. However, DNA barcoding of reptiles is still supported only by few datasets compared with other groups. We investigated the utilization of COI to discriminate 34 putative species of vipers, representing almost 92% of the recorded species in China. Based on a total of 241 sequences, our results indicated that the average degree of intraspecific variability (0.0198) tends to be one-sixth the average of interspecific divergence (0.0931), but no barcoding gap was detected between them. The threshold method, BLOG analyses and tree-based methods all can identify species with a high success rate. These results consistently suggested the usefulness and reliability of the DNA barcoding approach in Chinese vipers.

scholarly journals Multi-locus DNA barcoding identifies matK as a suitable marker for species identification in Hibiscus L.

Genome ◽  
2016 ◽  
Vol 59 (12) ◽  
pp. 1150-1156 ◽  
Author(s):  
Sundar Poovitha ◽  
Nithaniyal Stalin ◽  
Raju Balaji ◽  
Madasamy Parani
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Barcode ◽  
Species Differentiation ◽  
Molecular Method ◽  
Peninsular India ◽  
Plant Materials ◽  
Medicinal Value ◽  
Formed Part ◽  
Suitable Marker

The genus Hibiscus L. includes several taxa of medicinal value and species used for the extraction of natural dyes. These applications require the use of authentic plant materials. DNA barcoding is a molecular method for species identification, which helps in reliable authentication by using one or more DNA barcode marker. In this study, we have collected 44 accessions, representing 16 species of Hibiscus, distributed in the southern peninsular India, to evaluate the discriminatory power of the two core barcodes rbcLa and matK together with the suggested additional regions trnH-psbA and ITS2. No intraspecies divergence was observed among the accessions studied. Interspecies divergence was 0%–9.6% with individual markers, which increased to 0%–12.5% and 0.8%–20.3% when using two- and three-marker combinations, respectively. Differentiation of all the species of Hibiscus was possible with the matK DNA barcode marker. Also, in two-marker combinations, only those combinations with matK differentiated all the species. Though all the three-marker combinations showed 100% species differentiation, species resolution was consistently better when the matK marker formed part of the combination. These results clearly showed that matK is more suitable when compared to rbcLa, trnH-psbA, and ITS2 for species identification in Hibiscus.

Plant DNA barcoding necessitates marker-specific efforts to establish more comprehensive reference databases

Genome ◽  
2020 ◽  
pp. 1-34
Author(s):  
Andreas Kolter ◽  
Birgit Gemeinholzer
Keyword(s):  
Dna Barcoding ◽  
Machine Learning Algorithms ◽  
Reference Database ◽  
Sampling Effort ◽  
Identification Rate ◽  
Established Plant ◽  
Reference Databases ◽  
Suitable Marker ◽  
The Impact ◽  
Comprehensive Reference

The problem of low species-level identification rates in plants by DNA barcoding is exacerbated by the fact that reference databases are far from being comprehensive. We investigate the impact of increased sampling depth on identification success by analyzing the efficacy of established plant barcode marker sequences (rbcL, matK, trnL-trnF, psbA-trnH, ITS). Adding sequences of the same species to the reference database led to an increase in correct species assignment of +10.9% for rbcL and +19.0% for ITS. Simultaneously, erroneous identification dropped from ∼40% to ∼12.5%. Despite its evolutionary constraints, ITS showed the highest identification rate and identification gain by increased sampling effort, which makes it a very suitable marker in the planning phase of a barcode study. The limited sequence availability of trnL-trnF is problematic for an otherwise very promising plastid plant barcoding marker. Future developments in machine learning algorithms have the potential to give new impetus to plant barcoding, but are dependent on extensive reference databases. We expect that our results will be incorporated into future plans for the development of DNA barcoding reference databases and will lead to these being developed with greater depth and taxonomic coverage.

Sign in / Sign up

Export Citation Format

Share Document