scholarly journals IDENTIFIKASI SPESIES MENGGUNAKAN DNA BARCODING DALAM MENUNJANG BUDIDAYA DAN KONSERVASI TERIPANG DI PERAIRAN LAMPUNG

2021 ◽  
Vol 16 (1) ◽  
pp. 31
Author(s):  
Anna Rejeki Simbolon ◽  
Masteria Yunovilsa Putra ◽  
Ismiliana Wirawati
Keyword(s):  
Dna Barcoding ◽  
Sea Cucumber ◽  
Phylogenetic Reconstruction ◽  
Scuba Diving ◽  
Coi Gene ◽  
Universal Primers ◽  
Neighbor Joining ◽  
Accurate Identification ◽  
Sea Cucumbers ◽  
The Right

Teripang merupakan komoditas perikanan yang saat ini dibudidayakan dan dieksploitasi di perairan Lampung. Namun terdapat kesulitan dalam mengidentifikasi teripang karena kemiripan morfologis di antara spesies yang ada. Identifikasi yang baik berguna agar proses pembudidayaan dan konservasi dapat tepat sasaran. Penggunaan DNA barcoding dapat digunakan untuk mengidentifikasi jenis-jenis teripang yang ada, jarak genetik, dan keragaman genetik intra/inter spesies. Penelitian ini bertujuan untuk mengidentifikasi teripang di perairan Lampung dengan menggunakan sekuen DNA gen COI. Teripang diambil dengan menggunakan metode jelajah pada saat surut dan dengan scuba diving. Pengamatan DNA menggunakan primer universal ceF, pengeditan dan diurutkan dengan program Geneious ver 9 dan program BLAST. Konstruksi pohon filogenetik dilakukan dengan metode neighbor joining (NJ) pada model Kimura-2. Penelitian ini menunjukkan spesies teripang yang teridentifikasi adalah Holothuria leucospilota, H. atra, Stichopus vastus, dan S. horrens dengan jarak kesamaan 99%-100%. S. vastus dan S. horrens memiliki jarak genetik terendah dengan pengurangan yang tinggi. Rekonstruksi filogenetik memperlihatkan pengelompokkan spesies-spesies ke dalam genus Holothuria dan Stichopus. Stichopus sp. memiliki kesamaan morfologi yang tinggi sehingga kesalahan identifikasi sering terjadi. DNA barcoding dapat mengidentifikasi teripang secara cepat dan akurat sehingga pengelolaan teripang baik secara budidaya maupun pengambilan langsung di alam dapat berkelanjutan. Identifikasi spesies yang tepat menjadi kunci utama dalam upaya pembudidayaan dan konservasi teripang yang tepat sasaran dan berkelanjutan.Sea cucumbers is a highly valued fishery commodity that is currently cultivated and exploited in Lampung waters. However, differentiating a sea cucumber species from another is sometimes difficult due the morphological similarities between the species. Developing an accurate identification method is then critical to ensure successfull farming activities and conservation efforts of sea cucumbers. DNA barcoding could be used to accurately identify sea cucumber species, genetic distance, and genetic diversity between species. This study aimed to identify sea cucumbers existed in Lampung waters using DNA barcoding of the COI gene with ceF and ceR universal primers. Sea cucumbers are taken using the cruising method at low tide and by scuba diving. The DNA sequence was then edited and aligmented using the Geneious ver.9 program and analyzed using the BLAST program. Phylogenetic tree construction was carried out using the neighbor joining (NJ) method on the Kimura-2 model. This study showed that the identified species of sea cucumbers were Holothuria leucospilota, H. atra, Stichopus vastus, and S. horrens with a similarity distance of 99%-100%. S. vastus and S. horrens have the lowest genetic range. Phylogenetic reconstruction shows the classification of species into the genus Holothuria and Stichopus. Stichopus sp. have high morphological similarities within the same genus which often lead to species misidentification. DNA barcoding can identify sea cucumbers quickly and accurately. This method allows the identification of the right sea cucumber species which is the main key in the effort to cultivate and conserve targeted and sustainable sea cucumbers.

A test of DNA barcoding in crayfish of the upper James River basin, Virginia

2015 ◽  
Vol 21 (1) ◽  
pp. 179-183
Author(s):  
Paul R. Cabe ◽  
Bradleigh E. Navalsky ◽  
Ainsley K. Bloomer ◽  
Ryan Doherty ◽  
Jordan Edgren ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
River Basin ◽  
Native Species ◽  
Biological Diversity ◽  
Coi Gene ◽  
Test Case ◽  
Accurate Identification ◽  
James River ◽  
Coi Sequences ◽  
Current Sequence

Abstract Crayfish populations in North America face many conservation threats, including habitat loss, degradation, and the introduction of non-native species. The management of biological diversity requires accurate identification of species, and for crayfish, many species are difficult to identify using standard morphological approaches. We investigated DNA barcoding using cytochrome oxidase I (COI) gene sequences to determine if this widely used method is useful in the identification of crayfish. As a test case, we sampled crayfish from the middle and upper James River basin in Virginia. This area had been recently surveyed by experienced crayfish biologists, and hosts a moderate number of species. We collected nearly 300 COI sequences, which clustered clearly into seven groups, mirroring the seven species reported for this watershed. Despite the unambiguous clustering, the range of sequence variation within species overlapped the range of variation between species; we detected no clear "barcode gap." Although this method holds promise as an aid to crayfish identification, current sequence databases (GenBank, BOLD) do not contain enough appropriate COI sequences to allow unequivocal identification in this unique and understudies fauna.

scholarly journals The DNA Barcoding of Several Commercial Fish from Simeulue Islands Coast of Aceh Using Cytochrome Oxidase Sub Unit I (COI) Gene Marker

2019 ◽  
Vol 1 (1) ◽  
pp. 62-70
Author(s):  
Edwarsyah Edwarsyah ◽  
Muhammad Nasir ◽  
Muhammad Banda Selamat
Keyword(s):  
Dna Barcoding ◽  
Species Level ◽  
Dna Bases ◽  
Coi Gene ◽  
Gene Marker ◽  
Base Pairs ◽  
Commercial Fish ◽  
Morphological Approach ◽  
Mitochodrial Dna ◽  
The Right

Simeulue is a cluster of islands that rich of commercial fisheries in Aceh waters. Management of the fisheries products is highly related to species identification in order to ascertain the appropriate steps to manage the resources sustainably. Identification using DNA barcoding tools is the right answer for the problem that have not been able to be resolved even by morphological approach. Some of 11 individual samples were taken from 6 sampling points based on lobster’s catchment and cultivation areas. All of the samples were identified using COI mitochodrial DNA resulting 6 species including Scomber scombus, Scomberomorus plurilineatus, Octopus cyanea, Taeniura Lymna, Sympterygia bonapartii and Panulirus versicolor. The DNA bases were aligned using MEGA application and Neigbour- Joining method, Kimura 2 parameters resulting a 690 base pairs nucleotides. Reconstruction of philogenetic tree shows that the species of Simeulue were conjoined into one clade with the sequences downloaded from genebank. It shows that those species were closely related genetically indicating by the bootstrap value of Scomber scombus (100), Scomberomorus plurilineatus (100), Octopus cyanea (100). The results of the study shows that the DNA barcoding tools can explicate not only the identification up to the species level but also the genetic relationship that can be seen from the interspecies bases composition.

scholarly journals DNA barcoding to resolve the confusion in identifying Tribolium confusum and Tribolium castaneum

2019 ◽  
Vol 47 (2) ◽  
pp. 333-342
Author(s):  
Abu Faiz Md Aslam ◽  
Sharmin Sultana ◽  
Sumita Rani Das ◽  
Abdul Jabber Howlader
Keyword(s):  
Dna Barcoding ◽  
Tribolium Castaneum ◽  
Life Stage ◽  
Dna Barcode ◽  
Tribolium Confusum ◽  
Likelihood Method ◽  
Coi Gene ◽  
Pest Species ◽  
Stored Grain ◽  
Accurate Identification

Tribolium confusum and Tribolium castaneum (Coleoptera: Tenebrionidae) are two very confusing pest species while identification is done on the basis of morphology only. Such pests are discovered in stored grain as immature stages, which further complicates the identification process. Accurate identification of these pests is urgently required for integrated pest management. In this research, DNA barcoding was used to identify these pests accurately at any life stage. A 658 bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene was analyzed. DNA barcode dataset of T. confusum (GeneBank Acc. no. MK120453.1) and T. castaneum (Acc. no. MK411585.1) were constructed. The nucleotide composition reveals that average AT contents (59.9%) were higher than the GC contents (38.6%). Phylogenetic analysis by maximum likelihood method showed that both the species were originated from a common major clade. About 17.13% nucleotide differences were noted between the CO1 sequences by multiple sequence alignment. The interspecies nucleotide genetic distance (0.200) was calculated using Kimura 2 parameter. Haplotype analysis showed high genetic diversity (112 mutaional steps) among them. Bangladesh J. Zool. 47(2): 333-342, 2019

scholarly journals DNA Barcoding: A Study of Guppy Fish (Poecilia reticulata) in East Java, Indonesia

2019 ◽  
Vol 11 (2) ◽  
pp. 272-278
Author(s):  
Sucipto Hariyanto ◽  
Hasan Adro’i ◽  
Mahrus Ali ◽  
Bambang Irawan
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
Dna Sequences ◽  
Poecilia Reticulata ◽  
Phylogenetic Reconstruction ◽  
Coi Gene ◽  
West Java ◽  
Advance Research ◽  
Phylogeny And Evolution ◽  
Guppy Fish

Poecilia reticulata is a freshwater fish from the northeastern part of South America and spread widely to various countries in Asia and other continents. However, research about P. reticulate is limited even though it is a well-known fish species in Indonesia. The purpose of study was to identify the fish species of P. reticulata through DNA barcoding using the COI gene to determine the phylogenetic relationships among fish populations in East Java, Indonesia. In a present study, there were eight samples of P. reticulata from four different freshwater locations in East Java. Extraction, amplification, and sequencing of DNA samples were conducted to obtain the genetic data and construct a phylogenetic tree based on DNA sequences. The COI gene is the most popular markers to study genetic populations and phylogeography among the animal kingdom. Our phylogenetic reconstruction showed a clear that there were two groups of P. reticulata. The first group was obtain through species from East Java, Sukabumi, West Java (KU692776.1), Dominican Republic, Pandeglang, Banten and Myanmar. The second group was P. reticulata from southern Africa, Brazil, and Sukabumi, West Java (KU692775.1). The result of this study indicate that the guppy fish in East Java identic with P. reticulata from West Java (KU692776.1), which a widely used in classification based on evolutionary relationships. The findings of this study have important implication for the development of advance research about adaptation, phylogeny, and evolution of fish, especially of guppy fish.

scholarly journals DNA Barcoding and CITES-Listed Wedgefish (Rhynchobatidae, Rhinidae) from South Bangka, Indonesia

2021 ◽  
Vol 24 (2) ◽  
pp. 232-236
Author(s):  
Siti Aisyah ◽  
Novi Santia ◽  
Okto Supratman ◽  
Ahmad Fahrul Syarif ◽  
Anggraeni Anggraeni
Keyword(s):  
Dna Barcoding ◽  
Conservation Status ◽  
Marine Ecosystem ◽  
Iucn Red List ◽  
Coi Gene ◽  
Accurate Identification ◽  
Tissue Samples ◽  
Wild Fauna ◽  
The Status ◽  
Elasmobranch Species

Overfishing of wedgefish greatly affects its population and the balance of the marine ecosystem. This is exacerbated by their relatively low fecundity, slow growth, and late maturity results in one of the lowest population growth rate within elasmobranch species. However, lacking database information results in insufficient regulations and surveillance of wedgefish fishing. The current situation is feared to the risk of wedgefish’s survival, especially in Bangka Belitung Islands, Indonesia. Fundamental to a database is the accurate identification of wedgefish species based on mitochondrial DNA (mtDNA) analysis. This study aimed to use DNA barcodes to identify, determine the conservation status, and the status according to the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). We collected samples including unidentified fin samples from confiscated illegal fishing catches, the traditional markets and fishing docks, South Bangka. In this research, we used DNA Barcoding (mitocondrial DNA, COI gene) to identify and examine of wedgefish samples. The tissue samples used in this study were identified as species listed in CITES Appendix II, they are Rhynchobatus australiae, Rhynchobatus springeri and Rhina ancylostoma. According to the IUCN Red List, 100% of the wedgefish species found are Critical Endangered at the global level.

scholarly journals Molecular Phylogenetic of Cerithidea anticipata (Iredale, 1929) (Mollusk: Gastropod)

2021 ◽  
Vol 9 (1) ◽  
pp. 9
Author(s):  
Dandi Saleky ◽  
Sendy Lely Merly
Keyword(s):  
Dna Barcoding ◽  
Phylogenetic Reconstruction ◽  
Dna Amplification ◽  
Mangrove Ecosystem ◽  
Coi Gene ◽  
Sequence Length ◽  
Local Alignment ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Degree Of Similarity

Species identification is very important and an important part of bioecological studies, so phylogenetic studies of Cerithidea anticipata (Iredale, 1929) was conducted in September 2020 to identify C. anticipata (Iredale, 1929) based on DNA barcoding techniques. Samples of C. anticipata (Iredale, 1929) were collected from the mangrove ecosystem of Payum Merauke Beach Papua (Indonesia), where the genes used were primary COI Gene forward LCO1490 and reverse HCO2198. The result of DNA amplification obtained DNA sequence length of 660 bp, then based on the identification of Basic Local Alignment Search Tools (BLAST) obtained a similarity level of 98.42% and phylogenetic reconstruction showed the existence of grouping based on the degree of similarity and genetic distance between populations.Keywords: Cerithidea anticipata; COI genes; DNA barcoding; phylogeneticsAbstrakIdentifikasi spesies sangat penting dilakukan dan menjadi bagian penting dalam studi bioekologi, sehingga kajian filogenetik Cerithidea anticipata (Iredale, 1929) telah dilakukan pada bulan September 2020 dengan tujuan untuk mengidentifikasi C. anticipata (Iredale, 1929) berdasarkan teknik DNA barcoding. Sampel C. anticipata (Iredale, 1929) dikoleksi dari ekosistem mangrove Pantai Payum Merauke Papua (Indonesia), dimana gen yang digunakan adalah Gen COI primer forward LCO1490 dan reverse HCO2198. Hasil dari amplifikasi DNA diperoleh panjang sekuen DNA 660 bp, kemudian berdasarkan identifikasi Basic Local Alignment Search Tools (BLAST) diperoleh tingkat kemiripannya 98.42% dan rekonstruksi filogenetiknya memperlihatkan adanya pengelompokan berdasarkan tingkat kemiripan maupun jarak genetik antar populasi.Kata kunci: Cerithidea anticipata; Gen COI; DNA barcoding; filogenetik

scholarly journals DNA Barcoding in Selected Species and Subspecies of Rye (Secale) Using Three Chloroplast Loci (matK, rbcL, trnH-psbA)

2018 ◽  
Vol 47 (1) ◽  
pp. 54-62 ◽  
Author(s):  
Lidia SKUZA ◽  
Izabela SZUĆKO ◽  
Ewa FILIP ◽  
Anastazja ADAMCZYK
Keyword(s):  
Chloroplast Dna ◽  
Dna Barcoding ◽  
Plant Species ◽  
Plant Material ◽  
High Variability ◽  
Universal Primers ◽  
Neighbor Joining ◽  
Cultivated Species ◽  
Chloroplast Dna Regions

DNA barcoding is a relatively new method of identifying plant species using short sequences of chloroplast DNA. Although there is a large number of studies using barcoding on various plant species, there are no such studies in the genus Secale. In this study the plant material consisted of 10 cultivated and non-cultivated species and subspecies of rye genus. Three chloroplast DNA regions (rbcL, matK, trnH-psbA) were tested for their suitability as DNA barcoding regions. Universal primers were used, and sequenced products were analyzed using Neighbor Joining and the Maximum Likelihood in the MEGA 7.1 program. We did not observe high variability in nucleotide sequences within the matK and rbcL regions. Only 2.2% of the sequences showed polymorphism in the rbcL region, while 6.5% in the matK region. The most variable trnH-psbA (15.6%) intergenic region was the most useful for rye barcoding. Individual application of the studied regions did not provide the expected results. None of the regions used in the study allowed the division of rye species and subspecies according to the adopted classification of the genus Secale. The results confirm that the use of matK and rbcL is insufficient for DNA barcoding in rye species, and better discrimination within the genus Secale can be obtained only in combination with the non-coding trnH-psbA sequence. Our results also indicate the necessity of using a different region. All of the new sequences have been deposited in Genbank.

scholarly journals Research on Phylogenetic Relationship of Lotus Populations Collected in Thua Thien Hue Province, Vietnam based on the Chloroplast Genome by DNA Barcode

2021 ◽  
Author(s):  
Dang Thanh Long ◽  
Hoang Thi Kim Hong ◽  
Le Ly Thuy Tram ◽  
Nguyen Thi Quynh Trang
Keyword(s):  
Chloroplast Genome ◽  
Dna Barcoding ◽  
Phylogenetic Analyses ◽  
Dna Barcode ◽  
Haplotype Diversity ◽  
Universal Primers ◽  
Nucleotide Position ◽  
Accurate Identification ◽  
Low Levels ◽  
Relationship Of

Background: The DNA barcoding is currently an effective and widely used tool that enables rapid and accurate identification of plant species. Methods: DNA barcoding of 9 chloroplast genes (rbcL, matK, trnH-psbA, accD-psaI, ndhA, psbE-petL, Rpl32-trnL, trnW-psaJ, trnSGCU-trnGGCC) were used to provide the theoretical basis for species identification, genetic diversity analysis of lotus population collected in Thua Thien Hue province, Vietnam. Universal primers were used and sequence products were analyzed using the MEGA X program. Result: The results showed that high levels of haplotype diversity (Hd), ranging from 0.618-0.869 and low levels of nucleotide diversity (Pi), ranging from 0.180 × 10-3-3.280 × 10-3 base on a total of nine gene regions of chloroplast genome. The neutrality tests show an excess of rare nucleotide position variations in individuals’ white lotus and derived haplotypes recent expansion. While the evolution of the individuals in the pink lotus may have to decrease. The phylogenetic analyses indicated that combined sequences were not insufficient to make a difference to the DNA barcoding in the individual’s lotus of the N. nucifera species this is in the study. The standardized and accurate barcode information of lotus is provided for researchers. It lays the foundation for the conservation, evaluation, innovative utilization and protection of Nelumbonaceae germplasm resources.

scholarly journals DNA barcoding approach to identification of Cassidula angulifera (Petit, 1841) (Mollusca: Gastropoda)

2021 ◽  
Vol 5 (1) ◽  
pp. 55
Author(s):  
Dandi Saleky ◽  
Sendy L Merly
Keyword(s):  
Genetic Distance ◽  
Dna Barcoding ◽  
Dna Sequence ◽  
Phylogenetic Reconstruction ◽  
Coi Gene ◽  
Sequence Length ◽  
Gastropod Species ◽  
Gene Markers ◽  
Entire Sequence ◽  
High Bootstrap

A large number of gastropod species have similarities in morphology (cryptic) makes misidentification probably happen/occurred. Accurate species identification is needed in studying bioecology of species. This research aims to identify the species of Cassidulla sp. Which was collected from Peyum Beach Merauke with DNA barcoding techniques using COI gene markers. The primers used in this study are forward primers (LCO1490) and reverse primers (HCO2198). The result of identification with DNA barcoding showed that the species analyzed was Cassidula angulifera with a 99.53% similarity level with a DNA sequence length of 650 bp. Phylogenetic reconstruction showing the entire sequence of Cassidula sp. which were analyzed separately based on the type and genetic distance with high bootstrap value. Phylogenetic reconstruction of Cassidula sp. form a monophyletic group, which means that the species come from the same ancestors. DNA barcoding is very good and accurate in identifying species.

scholarly journals A Beetle in a Haystack: Are There Alternate Hosts of the Coffee Berry Borer (Hypothenemus hampei) in Puerto Rico?

Agronomy ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 228 ◽  
Author(s):  
Victor J. Vega ◽  
Yobana A. Mariño ◽  
Daymara Deynes ◽  
Elsie B. Greco ◽  
Donald E. Bright ◽  
...  
Keyword(s):  
Puerto Rico ◽  
Dna Barcoding ◽  
Management Strategies ◽  
Coi Gene ◽  
Hypothenemus Hampei ◽  
Coffee Berry ◽  
Coffee Berry Borer ◽  
Accurate Identification ◽  
Alternate Hosts ◽  
Preference Tests

Can the coffee berry borer (Hypothenemus hampei, or CBB) use host plants other than coffee for food and shelter? The use of fruits other than coffee has been reported. However, the validity of these reports depends on accurate identification of CBB, which is sometimes uncertain. In this study we sampled potential alternate hosts in coffee farms in Puerto Rico. Fruits with perforations were collected and examined for the presence of scolytid beetles (Coleoptera: Curculionidae: Scolytinae). Scolytids were identified by morphology and DNA barcoding of the COI gene. Association between the presence of Inga vera and Guarea guidonia trees and infestation rate of CBB in coffee fruits was evaluated. Food preference tests were performed in the laboratory. A total of 3563 beetles were found and 587 were identified as Hypothenemus spp.; of these, 85 identifications were confirmed by DNA barcoding. Twenty-seven of the beetles identified were H. hampei, mostly in I. vera fruits in periods between coffee crops. Most scolytids identified were H. obscurus. In preference tests, some CBB initially penetrated G. guidonia fruits, but eventually chose coffee. There was no evidence of feeding or reproduction in fruits of G. guidonia or Cajanus cajan. The results show that in Puerto Rico it is rare to find CBB in fruits of alternate hosts. The scarcity of coffee fruits in the off-season might cause some CBBs to take refuge in other fruits, but they did not feed or reproduce in them in laboratory tests. Understanding the refugia of CBB in the off-season may be useful for designing effective management strategies.

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