scholarly journals Short Communication: Phylogenetic analysis and molecular identification of Canar (Smilax spp.) in Java, Indonesia Based on DNA Barcoding Analysis

2018 ◽  
Vol 19 (2) ◽  
pp. 364-368
Author(s):  
LULUT DWI SULISTYANINGSIH ◽  
MARLINA ARDIYANI ◽  
ABINAWANTO ABINAWANTO ◽  
ANDI SALAMAH
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Barcoding ◽  
Molecular Identification ◽  
Short Communication ◽  
Pharmacological Study ◽  
Dna Barcode ◽  
Phylogenetic Reconstruction ◽  
Steroidal Saponin ◽  
Morphological Variations ◽  
Molecular Approaches

Sulistyaningsih LD, Abinawanto, Ardiyani M, Salamah A. 2018. Short Communication: Phylogenetic analysis and molecular identification of Canar (Smilax spp.) in Java, Indonesia Based on DNA Barcoding Analysis. Biodiversitas 19: 364-368. Smilax spp. (Smilacaceae) has long been used as medicinal herbs especially in East Asia and North America as they were known to be rich in steroidal saponin. Pharmacological study has been carried out in Indonesia. This genus is widespread in Indonesia and fairly abundant in Java and has been known either as edible fruit or medicinal plants. Characteristics of Smilax as a dioecious plant with high morphological variations make it thorny in species identification. Various molecular approaches have been devised to overcome identification problems such as DNA barcoding. This study, therefore was conducted to analyze the DNA barcoding application for phylogenetic and identification of Smilax in Java. A total of 31 samples were used in this study including 19 accession numbers from NCBI GeneBank. The genus Ripogonum was used as the out-group in phylogenetic reconstruction. Samples were successfully extracted by CTAB method with some modifications. rbcL region was used as the DNA barcode showed sufficient variation and conserved flanks. Two unidentified specimens have high similarity with S. leucophyla and lies in the same clade. The phylogenetic tree constructed by Maximum Likelihood analysis. The result showed that the monophyletic of Smilacaceae consisted of four clades. The genus Heterosmilax nested with Smilax though with low bootstraps value. It supports the monogeneric status of Smilacaceae.

Research Paper DNA barcode identification of fish products from Guiyang markets in southwest China

2022 ◽  
Author(s):  
Qian Tang ◽  
Qi Luo ◽  
Qian Duan ◽  
Lei Deng ◽  
Renyi Zhang
Keyword(s):  
Dna Barcoding ◽  
Molecular Identification ◽  
Fish Consumption ◽  
Southwest China ◽  
Dna Barcode ◽  
Guizhou Province ◽  
Accurate Identification ◽  
Continuous Growth ◽  
Fish Products ◽  
Fresh Frozen

Nowadays, the global fish consumption continues to rise along with the continuous growth of the population, which has led to the dilemma of overfishing of fishery resources. Especially high-value fish that are overfished are often replaced by other fish. Therefore, the accurate identification of fish products in the market is a problem worthy of attention. In this study, full-DNA barcoding (FDB) and mini-DNA barcoding (MDB) used to detect the fraud of fish products in Guiyang, Guizhou province in China. The molecular identification results showed that 39 of the 191 samples were not consistent with the labels. The mislabelling of fish products for fresh, frozen, cooked and canned were 11.70%, 20.00%, 34.09% and 50.00%, respectively. The average kimura 2 parameter distances of MDB within species and genera were 0.27% and 5.41%, respectively; while average distances of FDB were 0.17% within species and 6.17% within genera. In this study, commercial fraud is noticeable, most of the high-priced fish were replaced of low-priced fish with a similar feature. Our study indicated that DNA barcoding is a valid tool for the identification of fish products and that it allows an idea of conservation and monitoring efforts, while confirming the MDB as a reliable tool for fish products.

scholarly journals DNA Barcoding of the Solanaceae Family in Puerto Rico Including Endangered and Endemic Species

2019 ◽  
Vol 144 (5) ◽  
pp. 363-374 ◽  
Author(s):  
Lumariz Hernandez Rosario ◽  
Juan O. Rodríguez Padilla ◽  
Desiree Ramos Martínez ◽  
Alejandra Morales Grajales ◽  
Joel A. Mercado Reyes ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Puerto Rico ◽  
Dna Barcoding ◽  
Endemic Species ◽  
Phylogenetic Trees ◽  
Dna Barcode ◽  
Pairwise Distance ◽  
Greater Antilles ◽  
Solanaceae Species ◽  
Solanaceae Family

The Solanaceae family is one of the largest and well-distributed plant families in the world. It contains species of agricultural and economical importance, such as Solanum tuberosum, Solanum melongena, Solanum lycopersicum, Nicotiana tabacum, and Capsicum annuum. In Puerto Rico, there are ≈46 species of Solanaceae of which six are endemic: Brunfelsia densifolia, Brunfelsia lactea, Brunfelsia portoricensis, Goetzea elegans, Solanum ensifolium, and Solanum woodburyi. Our objective was to use DNA barcoding to identify the Solanaceae species in Puerto Rico, including the endemics, and to assess the species relationships between them. To accomplish our objective, two chloroplast regions (psbA-trnH and matK) and a nuclear region [internal transcribed spacer (ITS)] were assessed. Pairwise distance and phylogenetic analysis demonstrate that DNA barcoding can be used to discriminate at the species level among these taxa in Puerto Rico. For all three markers, the genus that showed the highest pairwise distance between represented species was Solanum, whereas the genus that displayed the least was Capsicum. Phylogenetic trees of single and concatenated regions were generated from sequences obtained in this study and from data downloaded from the National Center for Biotechnology Information database. Our results show that this technique can be used to identify species with one, two, or three combinations of DNA barcode markers depending on the taxon. In addition, this is the first study to include the endemic species S. woodburyi in a molecular phylogenetic analysis, and it was found to have a close relationship with S. ensifolium, also endemic to Puerto Rico, and to Solanum bahamense from the Bahamas and Greater Antilles. Therefore, we suggest that S. woodburyi might be part of the Bahamense clade.

scholarly journals DNA Barcoding Analysis and Phylogenetic Relation of Mangroves in Guangdong Province, China

Forests ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 56 ◽  
Author(s):  
Feng Wu ◽  
Mei Li ◽  
Baowen Liao ◽  
Xin Shi ◽  
Yong Xu
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Barcode ◽  
Phylogenetic Reconstruction ◽  
Pcr Amplification ◽  
Guangdong Province ◽  
Nuclear Ribosomal Dna ◽  
Success Rates ◽  
Mangrove Species ◽  
Identification Rate

Mangroves are distributed in the transition zone between sea and land, mostly in tropical and subtropical areas. They provide important ecosystem services and are therefore economically valuable. DNA barcoding is a useful tool for species identification and phylogenetic reconstruction. To evaluate the effectiveness of DNA barcoding in identifying mangrove species, we sampled 135 individuals representing 23 species, 22 genera, and 17 families from Zhanjiang, Shenzhen, Huizhou, and Shantou in the Guangdong province, China. We tested the universality of four DNA barcodes, namely rbcL, matK, trnH-psbA, and the internal transcribed spacer of nuclear ribosomal DNA (ITS), and examined their efficacy for species identification and the phylogenetic reconstruction of mangroves. The success rates for PCR amplification of rbcL, matK, trnH-psbA, and ITS were 100%, 80.29% ± 8.48%, 99.38% ± 1.25%, and 97.18% ± 3.25%, respectively, and the rates of DNA sequencing were 100%, 75.04% ± 6.26%, 94.57% ± 5.06%, and 83.35% ± 4.05%, respectively. These results suggest that both rbcL and trnH–psbA are universal in mangrove species from the Guangdong province. The highest success rate for species identification was 84.48% ± 12.09% with trnH-psbA, followed by rbcL (82.16% ± 9.68%), ITS (66.48% ± 5.97%), and matK (65.09% ± 6.00%), which increased to 91.25% ± 9.78% with the addition of rbcL. Additionally, the identification rate of mangroves was not significantly different between rbcL + trnH-psbA and other random fragment combinations. In conclusion, rbcL and trnH-psbA were the most suitable DNA barcode fragments for species identification in mangrove plants. When the phylogenetic relationships were constructed with random fragment combinations, the optimal evolutionary tree with high supporting values (86.33% ± 4.16%) was established using the combination of matK + rbcL + trnH-psbA + ITS in mangroves. In total, the 476 newly acquired sequences in this study lay the foundation for a DNA barcode database of mangroves.

scholarly journals DNA Barcode for the Parthenogenetic Surinam Cockroach Pycnoscelus surinamensis (Linnaeus, 1758) (Blattodea: Blaberidae) from India

2022 ◽  
Vol 7 (1) ◽  
pp. 1-7
Author(s):  
A Shabnam ◽  
K P Dinesh
Keyword(s):  
Dna Barcoding ◽  
Molecular Identification ◽  
Western Ghats ◽  
Dna Barcode ◽  
Insect Fauna ◽  
Mt Dna ◽  
Faunal Diversity ◽  
Southern Western Ghats

DNA Barcoding is one of the emerging tools in molecular identification of faunal diversity, specifically insect fauna. The Surinam cockroach, Pycnoscelus surinamensis is the only known roach to be obligatorily parthenogenetic, with reported haplotypes. P. surinamensis is well established in Indomalayan, tropical and subtropical regions and substantially documented from India with a phenetic approach. Herewith we report the first set of mt DNA barcode from a vouchered collection for the species from southern Western Ghats India. Discussions are made on the identity of two sequences each of Blatteria species and Pycnoscelus species reported from USA.

scholarly journals DNA barcoding of razor clam Solen spp. (Solinidae, Bivalva) in Indonesian beaches

2020 ◽  
Vol 21 (2) ◽  
Author(s):  
Ninis trisyani Margono ◽  
DWI ANGGOROWATI RAHAYU
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Distance ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Morphological Characteristics ◽  
Wide Distribution ◽  
Coi Gene ◽  
Razor Clam ◽  
Molecular Phylogenetic ◽  
Solen Grandis

Abstract. Trisyani N, Rahayu DA. 2020. DNA barcoding of razor clam Solen spp. (Solinidae, Bivalva) in Indonesian beaches. Biodiversitas 21: 478-484. Solen spp. are shells with various morphological characteristics with a wide distribution of tropical and subtropical beaches, including Indonesia. The identification of Solen spp. is generally based on its morphological characteristics. This method is very problematic due to specimens share similarity in morphology and color. This study was using DNA barcode as a molecular identification tool. The bivalve COI sequence was amplified using PCR and molecular phylogenetic analysis using the Neighbor-Joining method. The amplified COI gene has a length of about 665 bp. The purpose of this study was to evaluate genetic variation and compare the phylogenetic Solen spp. in Indonesian waters. The composition of the nucleotide bases of Solen spp. the comparative species are A = 26.79%, C = 23.16%, G = 19.17% and T = 30.93%. The total nucleotide base A + T was 57.72%, while G + C was 42.33%. The results of phylogenetic analysis showed that Solen spp. Cirebon and Jambi are in one clade with Solen regularis with genetic distance 0.000 - 0.002. Solen spp. Surabaya, Bangkalan, Pamekasan, and Sumenep are in separate clades and are related to Solen grandis, Solen stricus and Solen lamarckii with genetic distance from 0.146 - 0.156. The diversity of nucleotide was 0.9780 and was divided into 12 haplotypes.

DNA barcoding unravels three new species and a subspecies of Olepa Watson, 1980 (Lepidoptera, Erebidae, Arctiinae) from India, with morphotypes

2020 ◽  
Vol 19 (2) ◽  
pp. 44-60
Author(s):  
APARNA SURESHCHANDRA KALAWATE ◽  
K. P. DINESH ◽  
A. SHABNAM
Keyword(s):  
New Species ◽  
Dna Barcoding ◽  
Dna Sequences ◽  
Dna Barcode ◽  
Coi Gene ◽  
Male And Female ◽  
Morphological Variations ◽  
Three New Species ◽  
First Time ◽  
Respective Species

The genus Olepa is distributed in Palearctic and Oriental regions with more species in India and Sri Lanka. In the recent studies, morphological variations within the group were well established, with couple of first set of mt COI DNA barcodes for at least three species. In the present account, three new species and a new subspecies are described from the northern Western Ghats region of Maharashtra based on mt COI DNA barcode studies. Due to high morphological divergence and complete genetic homogeneity on the mt COI DNA, four morphotypes under two species are reported. Morphological and genital characters of male and female are provided along with their respective species morphotypes for the first time under this genus from India. The genitalia and the habitus of male and female are illustrated. Preliminary phylogenetic tree based on the mt COI DNA sequences available in the GenBank for the genus with the sequences for the new species also provided and discussed. Key words: new taxa, morphotype, Maharashtra, DNA barcoding, mt COI gene

scholarly journals DNA barcode reveals the occurrence of Palearctic Olepa schleini Witt et al., 2005 (Lepidoptera: Erebidae: Arctiinae) from peninsular India with morphological variations and a new subspecies

2020 ◽  
Vol 12 (9) ◽  
pp. 16143-16152
Author(s):  
Aparna Sureshchandra Kalawate ◽  
Shital Pawara ◽  
A. Shabnam ◽  
K.P. Dinesh
Keyword(s):  
Dna Barcoding ◽  
New Record ◽  
Dna Barcode ◽  
Mt Dna ◽  
Peninsular India ◽  
New Subspecies ◽  
Morphological Variations ◽  
Morphological Studies ◽  
Tiger Moth ◽  
Species Groups

The present study was taken up to report a new record of the tiger moth genus, Olepa Watson, 1980 from India along with the discovery of a new subspecies.  Earlier  the genus was thought to have restricted distribution range in South and South-East Asia until the report of O. schleini Witt, Müller, Kravchenko, Miller, Hausmann & Speidel from the Mediterranean Coastal Plain of Israel in 2005. The species identification and the new subspecies is proposed based on the combination of morphological studies, available literature comparisons, geographical distribution,  DNA barcoding and its phylogeny. Morphological character crypticity and genital structure variations are well documented in the genus with ‘bio-species’ groups. DNA Barcoding data of mt COI has provided some resolution in sorting the problems of ‘bio-species’ groups of the genus in the past studies. In the present study, with the available  mt DNA COI barcodes and newly generated barcodes genetic identity is confirmed for the species O. ricini, O. schleini, O. toulgoeti and Olepa schleini chandrai ssp. nov., with their phylogenetic relationships. Morphological variations within the O. schleini species complex are discussed with a new record of the species for India and a new subspecies description. With the first mt COI barcode phylogeny for the genus, comments are made on the taxonomic identity of the mt COI DNA barcodes available in the GenBank for the Olepa species from India.  

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