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 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 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 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.

scholarly journals Inventory of some Tulipa species from Uzbekistan using DNA barcoding

2021 ◽  
Vol 38 ◽  
pp. 00086
Author(s):  
Elena V. Nikitina ◽  
Farkhod I. Karimov ◽  
Natalja V. Savina ◽  
Svetlana V. Kubrak ◽  
Aleksandr V. Kilchevsky
Keyword(s):  
Dna Barcoding ◽  
Phenotypic Diversity ◽  
Climatic Conditions ◽  
Quaternary Period ◽  
Climate Fluctuations ◽  
Phylogenetic Studies ◽  
Early Diversification ◽  
Molecular Phylogenetic ◽  
Nuclear Its ◽  
Sequence Encoding

Climate fluctuations in the Quaternary period in significantly influenced the evolution and distribution of plants, which caused to a serious genetic effects and speciation activity [1]. Thus, Central Asia is distinguished by a wide variety of flora, including 9520 species, while 20% are endemics [2]. Great phenotypic diversity of the wild flora in Uzbekistan, numbering about 4400 species of vascular plants is determined by the peculiar climatic conditions, a variety of zoning, altitudinal zones [3]. At the same time, being one of the centers of early diversification of monocotyledonous geophytes, taxonomically complex representatives of this group are not sufficiently involved in phylogenetic studies. This study is a pilot study of the flora of Uzbekistan using DNA barcoding method, that based on sequencing of phylogenetically significant sequences. Four plastid (rbcL, psbA-trnH, matK, trnL-F) and one nuclear (ITS) markers were used for species identification of the genus Tulipa. The results of molecular phylogenetic analysis for 15 species of Tulipa (Liliaceae) using the marker sequence encoding ITS fragment are presented. The successful usefulness of DNA technology for genetic inventory has been demonstrated.

scholarly journals Endorsement and Phylogenetic Analysis of some Fabaceae Plants based on DNA Barcoding gene MatK

2021 ◽  
Author(s):  
Nader R. Abdelsalam ◽  
Mohamed E. Hasan ◽  
Samar M.A. Rabie ◽  
Houssam El-Din M.F. El-wakeel ◽  
Amera F. Zaitoun ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Dna Barcoding ◽  
Dna Sequences ◽  
Phylogenetic Reconstruction ◽  
Sequence Length ◽  
Morphological Identification ◽  
Phylogenetic Tree Analysis ◽  
Parkinsonia Aculeata ◽  
Link Type ◽  
Matk Gene

DNA barcodes have been considered as a tool to facilitate species identification based on their simplicity and high-level accuracy compression to the complexity and subjective biases linked to morphological identification of taxa. MaturaseK gene “ MatK” of the chloroplast is very crucial in the plant system which is involved in the group II intron splicing. The main objective of this current study is determining the relative utility of the “ MatK” chloroplast gene for barcoding in fifteen legume trees by both single region and multiregional approaches. The chloroplast “ MatK” gene sequences were submitted to GenBank and accession numbers (GenBank: LC602060, LC602154, LC602263, LC603347, LC603655, LC603845, LC603846, LC603847, LC604717, LC604718, LC605994, LC604799, LC605995, LC606468, LC606469) were obtained with sequence length ranging from 730 to 1545 nucleotides. These DNA sequences were aligned with database sequence using PROMALS server , Clustal Omega server and Bioedit program. Also,  the maximum likelihood and neighbor-joining algorithms for phylogenetic reconstruction using the MEGA-X program were employed. Overall, these results indicated that the phylogenetic tree analysis and the evolutionary distances of an individual dataset of each species were agreed with a phylogenetic tree of all each other consisting of two clades, the first clade comprising (Enterolobium contortisiliquum, Albizia lebbek), Acacia saligna , Leucaena leucocephala, Dichrostachys Cinerea, (Delonix regia, Parkinsonia aculeata), (Senna surattensis, Cassia fistula, Cassia javanica) and Schotia brachypetala were more closely to each other, respectively. The remaining four species of Erythrina humeana, (Sophora secundiflora, Dalbergia Sissoo, Tipuana Tipu) constituted the second clade. Therefore, MatK gene is considered promising a candidate for DNA barcoding in plant family Fabaceae and providing a clear relationship between the families. Moreover, their sequences could be successfully utilized in single nucleotide polymorphism (SNP) or part of the sequence as DNA fragment analysis utilizing polymerase chain reaction (PCR) in plant systematic.

An updated phylogeny and morphological study of the Phymaturus vociferator clade (Iguania: Liolaemidae)

Zootaxa ◽  
2018 ◽  
Vol 4441 (3) ◽  
pp. 447 ◽  
Author(s):  
JAIME TRONCOSO-PALACIOS ◽  
FRANCISCO FERRI-YÁÑEZ ◽  
ALEJANDRO LASPIUR ◽  
CÉSAR AGUILAR
Keyword(s):  
Species Delimitation ◽  
Morphological Study ◽  
Phylogenetic Reconstruction ◽  
Integrative Approach ◽  
Phylogenetic Studies ◽  
Ecological Features ◽  
Molecular Phylogenetic ◽  
Almost All ◽  
A New Species ◽  
Lines Of Evidence

Species delimitation in Phymaturus has been a difficult task due to the highly conserved morphological and ecological features present in this genus. Almost all species of Phymaturus have been described without DNA data or lacking statistical analyses which makes even more difficult to compare species. Although two molecular phylogenetic studies have been recently published, here we provide the first multilocus phylogenetic reconstruction including all Chilean species, with samples from all type localities and some previously unsampled populations. We also estimate pairwise distances among the Chilean species of Phymaturus (P. vociferator and P. mallimaccii clades) and compare our results with the P. payuniae clade, where previous studies have used multiple lines of evidence. Additionally, we performed univariate and multivariate morphological analyses and skeletal comparisons (clavicle) for the species of the P. vociferator clade. As a result of this integrative approach, we describe a new species. 

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.

Transfer of the Kobresia taxa of the flora of Russia and adjacent countries to the genus Carex (Cyperaceae)

2020 ◽  
pp. 125-129
Author(s):  
D. G. Melnikov ◽  
L. I. Krupkina
Keyword(s):  
International Collaboration ◽  
Morphological Characters ◽  
Published Data ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
New Nomenclatural Combinations

Based on the published data of molecular phylogenetic studies of the tribe Cariceae Dumort. genera (Cyperaceae), obtained by an international collaboration (The Global Carex Group, 2016; et al.), and morphological characters of the genera (Kukkonen, 1990; and others), new nomenclatural combinations and replacement names in the genus Carex L. are published for 11 species, one subspecies and two sections previously included in the genus Kobresia Willd.

Systematics and evolution of Lentibulariaceae: III. Utricularia

2018 ◽  
Author(s):  
Richard W. Jobson ◽  
Paulo C. Baleeiro ◽  
Cástor Guisande
Keyword(s):  
Gene Flow ◽  
Species Diversity ◽  
Population Level ◽  
Oceanic Islands ◽  
Vulnerable Species ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic

Utricularia is a morphologically and ecologically diverse genus currently comprising more than 230 species divided into three subgenera—Polypompholyx, Utricularia, and Bivalvaria—and 35 sections. The genus is distributed worldwide except on the poles and most oceanic islands. The Neotropics has the highest species diversity, followed by Australia. Compared to its sister genera, Utricularia has undergone greater rates of speciation, which are linked to its extreme morphological flexibility that has resulted in the evolution of habitat-specific forms: terrestrial, rheophytic, aquatic, lithophytic, and epiphytic. Molecular phylogenetic studies have resolved relationships for 44% of the species across 80% of the sections. Scant data are available for phylogeography or population-level processes such as gene flow, hybridization, or pollination. Because nearly 90% of the species are endemics, data are urgently needed to determine how to protect vulnerable species and their habitats.

scholarly journals Endangered Uyghur Medicinal PlantFerulaIdentification through the Second Internal Transcribed Spacer

2015 ◽  
Vol 2015 ◽  
pp. 1-6 ◽  
Author(s):  
Congzhao Fan ◽  
Xiaojin Li ◽  
Jun Zhu ◽  
Jingyuan Song ◽  
Hui Yao
Keyword(s):  
Medicinal Plant ◽  
Related Species ◽  
Internal Transcribed Spacer ◽  
Morphological Characteristics ◽  
Its2 Sequence ◽  
Sequence Length ◽  
Local Alignment ◽  
Accurate Identification ◽  
Distance Method ◽  
Closely Related Species

The medicinal plantFerulahas been widely used in Asian medicine, especially in Uyghur medicine in Xinjiang, China. Given that various substitutes and closely related species have similar morphological characteristics,Ferulais difficult to distinguish based on morphology alone, thereby causing confusion and threatening the safe use ofFerula. In this study, internal transcribed spacer 2 (ITS2) sequences were analyzed and assessed for the accurate identification of two salableFerulaspecies (Ferula sinkiangensisandFerula fukangensis) and eight substitutes or closely related species. Results showed that the sequence length of ITS2 ranged from 451 bp to 45 bp, whereas guanine and cytosine contents (GC) were from 53.6% to 56.2%. A total of 77 variation sites were detected, including 63 base mutations and 14 insertion/deletion mutations. The ITS2 sequence correctly identified 100% of the samples at the species level using the basic local alignment search tool 1 and nearest-distance method. Furthermore, neighbor-joining tree successfully identified the genuine plantsF. sinkiangensisandF. fukangensisfrom their succedaneum and closely related species. These results indicated that ITS2 sequence could be used as a valuable barcode to distinguish Uyghur medicineFerulafrom counterfeits and closely related species. This study may broaden DNA barcoding application in the Uyghur medicinal plant field.

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