scholarly journals FILOGENI POPULASI Haliotis squamata REEVE, 1846 DARI PANTAI SELATAN PULAU JAWA DAN BALI BERDASARKAN SEKUEN CYTOCHROME B DNA MITOKONDRIA

2020 ◽  
Vol 12 (2) ◽  
pp. 585-595
Author(s):  
Syamsul Bachry ◽  
Dedy D. Solihin ◽  
Rudhy Gustiano ◽  
Kadarwan Soewardi ◽  
Nurlisa A. Butet
Keyword(s):  
Genetic Distance ◽  
Cytochrome B ◽  
Phylogenetic Trees ◽  
Parameter Method ◽  
Neighbor Joining ◽  
Southern Coast ◽  
Nucleotide Difference ◽  
Tree Construction ◽  
Relationship Of ◽  
Two Populations

Abalone Haliotis squamata Reeve 1846 is an abalone that has distribution on the southern coast of Java and Bali in Indonesia. The purpose of this study was to analyze the phylogenetic relationship of H. squamata from the southern coast of Java and Bali based on the cytochrome b (Cyt b) mitochondrial DNA sequence. A total of 38 samples were collected from Java (Binuangeun, Pangandaran, Banyuwangi, and Bali (Buleleng). Samples were extracted, applied using method PCR, and sequencing the method Sanger sequencing di 1st BASE Malaysia. Using primary sequences to applied namely forward primers forward AB-Cytb DivF (5'-TAAGCCAATTCGTAAGGTTC-3') dan primer reverse AB-Cytb DivR (5'-AAAATACCACTCTGGCTGAA-3'). Genetic distance was analyzed using the Kimura 2-parameter method and phylogenetic tree construction was carried out by Neighbor-Joining using the MEGA 7. The result showed that a specific nucleotide difference of 81 bp to 820 bp. The genetic distance between H. squamata intraspecies from the southern coast of Java and Bali is 0.96%-1.06%. This genetic distance is high enough to separate the two populations and form their clusters based on phylogenetic trees. The population of Bali seems to form new subpopulations. The data obtained in this study will be very useful for the management of H. squamata abalone genetic resources related to their sustainability and utilization.

scholarly journals GENETIC DIFFERENTIATION AMONG POPULATIONS OF Chromobotia macracanthus BLEEKER FROM SUMATRA AND KALIMANTAN BASED ON SEQUENCING GENE OF MTDNA CYTOCHROME B AND NUCLEUS DNA RAG2

2008 ◽  
Vol 3 (2) ◽  
pp. 107 ◽  
Author(s):  
Sudarto Sudarto ◽  
Kafi Hidonis ◽  
Emmanuel Paradis
Keyword(s):  
Genetic Differentiation ◽  
Genetic Distance ◽  
Cytochrome B ◽  
Nucleotide Diversity ◽  
Population Group ◽  
Fish Population ◽  
Neighbor Joining ◽  
R Language ◽  
Estimation Of Time ◽  
Two Populations

Research on genetic differentiation among populations of Chromobotia macracanthus Bleeker from Sumatra, based on sequencing gene of mtDNA Cytochrome b and nucleus DNA RAG2 has been done. The objectives of the study were to obtain the representation of genetic differentiation among population of clown loach fishes or botia (Chromobotia macracanthus) from Sumatra and Kalimantan and to estimate the time divergence of both population group of botia. Samples of botia population were taken from 3 rivers in Sumatra namely Batanghari, Musi, and Tulang Bawang and one river from Kalimantan namely Kapuas. The genetic analysis was based on the sequencing of mtDNA Cytochrome b and nucleus DNA RAG2. The statistical analysis was done by using APE package on R language. The parameters observed were: nucleotide diversity, genetic distance, and neighbor-joining tree. The result showed that the highest nucleotide diversity was fish population of Musi, while the other two populations, Tulang Bawang (Sumatra) and Kapuas (Kalimantan), were considered as the lowest genetic diversity especially based on nucleus DNA RAG2 sequencing. Based on mtDNA Cytochrome-b sequencing, the most distinct population among those populations based on genetic distance were fish populations of Musi and Kapuas. According to the result of neighbor-joining tree analysis, the populations of botia were classified into two groups namely group of Sumatra and group of Kalimantan. The estimation of time divergence among group of population of Sumatra and Kalimantan based on mtDNA Cytochrome b was about 9.25—9.46 million years (Miocene era). The high genetic differences between groups of Sumatra and Kalimantan suggested that the effort of restocking botia from Sumatra into Kalimantan has to be done carefully, because it may disturb the gene originality of both botia populations.

scholarly journals Filogenetik Kutu Penghisap Darah (Haematopinus sp.) pada Beberapa Jenis Sapi berdasarkan Gen 18S rRNA

2020 ◽  
Vol 3 (2) ◽  
pp. 31-37
Author(s):  
Aan Awaludin ◽  
Yudhi Ratna Nugraheni ◽  
Mira Andriani ◽  
Niswatin Hasanah ◽  
Agus Hadi Prayitno
Keyword(s):  
Phylogenetic Tree ◽  
Genetic Distance ◽  
Phylogenetic Relationship ◽  
Maximum Parsimony ◽  
18S Rrna ◽  
Universal Primers ◽  
Neighbor Joining ◽  
Phylogenetic Tree Construction ◽  
Tree Construction ◽  
Relationship Of

The purpose of this study was to determine the phylogenetic relationship of Haematopinus sp. which became parasites in several types of cattle, namely Simmental, Limousin, PO (Peranakan Ongole), and FH (Friesian Holstein) from Jember Regency and Simmental and PO cattle from Karanganyar Regency. The method used was to isolate DNA from 6 samples of Haematopinus sp. and amplified using 18S rRNA universal primers with 18S (5'-TCATTACGAGCTCTGCAAT-3) reverse primers and 18S (5'-TTCAAAGTAAACGTGTCGGC-3) sequential PCR sequencing. Sequencing results were analyzed using MEGA 6 software for phylogenetic tree construction using the Neighbor-Joining and Maximum Parsimony Methods. The results showed that the sample Haematopinus sp. originating from Simmental, Limousin, and PO cattle from Jember, and Simmental and PO from Karanganyar were included in one cluster by Haematopinus quadripertusus. Haematopinus sp. sample from Jember FH cattle had a considerable genetic distance from Haematopinus quadripertusus which was possible because the sequence that could be analyzed was only 236 nt.

scholarly journals Kajian Variasi Sekuens Interspesies dan Filogeni Kelelawar Pteropus sp. Menggunakan Gen COI

Jurnal MIPA ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 71
Author(s):  
Era Monalisa ◽  
Feky Recky Mantiri ◽  
Hanry Jefri Lengkong
Keyword(s):  
Genetic Distance ◽  
Phylogenetic Relationship ◽  
Coi Gene ◽  
Gene Sequences ◽  
Base Pairs ◽  
Probable Explanation ◽  
Nucleotide Base ◽  
Tree Construction ◽  
Most Probable Explanation ◽  
Relationship Of

Penelitian ini bertujuan untuk menganalisis variasi interspesies kelelawar Pteropus sp. dan menjelaskan hubungan filogeni Pteropus sp. dengan spesies Pteropus lain yang terdata di GenBank berdasarkan Gen COI. Analisis sekuens menggunakan Geneious v5.6.4 dan menunjukkan adanya variasi interspesies sekuens gen COI pada ketiga sampel Pteropus sp. yang ditunjukkan oleh adanya perbedaan 5 pasang basa nukleotida pada urutan sekuens sampel nomor 157, 160, 421, 427 dan 652 dengan jarak genetik 0,006. Filogeni Ke-3 sampel kelelawar Pteropus sp. dengan spesies Pteropus lain dilakukan menggunakan MEGAX. Hasil filogeni menunjukkan bahwa sampel yang diteliti merupakan kelelawar dari genus Pteropus tetapi belum dapat dipastikan spesiesnya, karena ketika pohon filogeni dikonstruksikan membentuk satu klaster sendiri. Penjelasan dari proses tersebut adalah penyortiran garis keturunan yang tidak lengkap dan terjadinya hibridisasi, serta diduga bahwa primer yang digunakan kurang mampu dalam membedakan variasi intrespesies terhadap kelelawar genus PteropusThis study aimed to analyze the interspecificvariations of bats from Pteropus sp. and describethe phylogenetic relationship of Pteropus sp. with other Pteropus species recorded inGenBank based on the COI gene. Sequenceanalysis by Geneious v5.6.4 showed interspecificvariations of COI gene sequences in all threesamples of Pteropus sp. which was indicated byvariations in 5 nucleotide base pairs in thesequences number 157, 160, 421, 427 and 652with 0.006 of genetic distance value. Phylogeneticof the 3 bat samples of Pteropus sp. with otherPteropus species was carried out by MEGAX.Phylogenetic analyses showed that the samplesstudied are bats of the genus Pteropus, but theexact species cannot be determined because thesamples were grouped in the same cluster duringphylogenetic tree construction. The most probable explanation for this observation is hybridization between two different Pteropus spesies and also it is assumed that the primersused are not capable to distinguish interspecificvariations of the bats from the Pteropus genusPenelitian ini bertujuan untuk menganalisis variasi interspesies kelelawar Pteropus sp. dan menjelaskan hubungan filogeni Pteropus sp. dengan spesies Pteropus lain yang terdata di GenBank berdasarkan Gen COI. Analisis sekuens menggunakan Geneious v5.6.4 dan menunjukkan adanya variasi interspesies sekuens gen COI pada ketiga sampel Pteropus sp. yang ditunjukkan oleh adanya perbedaan 5 pasang basa nukleotida pada urutan sekuens sampel nomor 157, 160, 421, 427 dan 652 dengan jarak genetik 0,006. Filogeni Ke-3 sampel kelelawar Pteropus sp. dengan spesies Pteropus lain dilakukan menggunakan MEGAX. Hasil filogeni menunjukkan bahwa sampel yang diteliti merupakan kelelawar dari genus Pteropus tetapi belum dapat dipastikan spesiesnya, karena ketika pohon filogeni dikonstruksikan membentuk satu klaster sendiri. Penjelasan dari proses tersebut adalah penyortiran garis keturunan yang tidak lengkap dan terjadinya hibridisasi, serta diduga bahwa primer yang digunakan kurang mampu dalam membedakan variasi intrespesies terhadap kelelawar genus Pteropus

scholarly journals Short Communication: Molecular study on mt-DNA COX2 gene of Sumatran elephant (Elephas maximus sumatranus)

2021 ◽  
Vol 22 (2) ◽  
Author(s):  
Deny Setyo Wibowo ◽  
Rini Widiyanti ◽  
Machmud Asvan ◽  
Prista Dwi Restanti ◽  
Hery Wijayanto
Keyword(s):  
Genetic Distance ◽  
Phylogenetic Trees ◽  
Short Communication ◽  
Molecular Study ◽  
Elephas Maximus ◽  
Individual Species ◽  
Parameter Method ◽  
Exploratory Research ◽  
Mt Dna ◽  
Asian Elephants

Abstract. Wibowo DS, Widiyanti R, Asvan M, Restanti PD, Wijayanto H. 2021. Short Communication: Molecular study on mt-DNA COX2 gene of Sumatran elephant (Elephas maximus sumatranus). Biodiversitas 22: 1063-1068. Sumatran elephant is the only subspecies of Asian elephants that receives a critically endangered status from the International Union for Conservation and Nature Resources (IUCN). Identifying the genetic marker of Sumatran elephants is, therefore, important for their conservation. This study aimed to identify the Sumatran elephant based on specific mitochondrial DNA markers of the Cytochrome c oxidase subunit II (COX2) gene. It is an exploratory research considering the limited data and research about the genetic, especially the COX2 of Sumatran elephant (Elephas maximus sumatranus). Forward and reverse sequencing of PCR products was conducted using the primary COX2 from Sumatran elephant samples. The results of the subsequent gene sequencing were aligned with the sequences of other Asian elephants from Genbank using Clustal W software and analyzed using the MEGA program version 6.06. The analysis of genetic distance based on COX2 constituent nucleotides calculated with Kimura’s two-parameter method showed that the genetic distance between Elephas maximus sumatranus and Elephas maximus outside of Sumatra was 0.25%. The phylogenetic trees analyzed using the maximum-likelihood based on nucleotide sequences showed a high homogeneity. The ratio of Elephas maximus sumatranus with Elephas maximus shows levels of nucleotide mutations which are nine nucleotides and four nucleotides. These results indicated that the COX2 gene could not identify the individual species of Sumatran elephant because of the high intraspecies homogeneity, but it detected the interspecies divergence clustered in Asian elephant clade.

scholarly journals Phylogeny of certain members of Hyrcanus group (Diptera: Culicidae) in China based on mitochondrial genome fragments

2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Hui-Min Zhu ◽  
Shu-Han Luo ◽  
Man Gao ◽  
Feng Tao ◽  
Jing-Peng Gao ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Trees ◽  
Genetic Distances ◽  
Malaria Vectors ◽  
Mitochondrial Genomes ◽  
Neighbor Joining ◽  
Minimum Evolution ◽  
Data Sequence ◽  
Rdna Its2 ◽  
Relationship Of

Abstract Background Species of the Anopheles hyrcanus group are widely distributed in Palearctic and Oriental regions and some of them are important malaria vectors. The cryptic species of An. hyrcanus group was almost impossible to identify based only on their morphology. The phylogenetic relationship of An. hyrcanus group was also not clear. Methods Five members of An. hyrcanus group were identified by rDNA ITS2 sequencing as An. yatsushiroensis, An. belenrae, An. kleini, An. lesteri and An. sineroides. The mitochondrial genome fragments were sequenced and annotated using the mitochondrial genome of An. sinensis as reference. Based on the four segments and Joint Data sequences of these species, and other four anopheline species downloaded from GenBank, intraspecific as well as interspecific genetic distances were calculated and the phylogenetic trees were reconstructed by the methods of neighbor joining, maximum parsimony, minimum evolution and maximum likelihood. Findings Four parts of mitochondrial genomes, which were partial fragments COI + tRNA + COII (F5), ATP6 + COIII(F7 + F8), ND1(F19) and lrRNA (F21), were obtained. All fragments were connected as one sequence (referred as Joint Data), which had a total length of 3393 bp. All fragment sequences were highly conservative within species, with the maximum p distance (0.026) calculated by F19 of An. belenrae. The pairwise interspecific p distance calculated by each fragment showed minor or even no difference among An. sinensis, An. kleini and An. belenrae. However, interspecific p distances calculated by the Joint Data sequence ranged from 0.004 (An. belenrae vs An. kleini) to 0.089 (An. sineroides vs An. minimus), and the p distances of the six members of An. hyrcanus group were all less than 0.029. The phylogenetic tree showed two major clades: all subgenus Anopheles species (including six members of An. hyrcanus group, An. atroparvus and An. quadrimaculatus A) and subgenus Cellia (including An. dirus and An. minimus). The An. hyrcanus group was divided into two clusters as ((An. lesteri, An. sineroides) An. yatsushiroensis) and ((An. belenrae, An. sinensis) An. kleini)). Conclusions The An. hyrcanus group in this study could be divided into two clusters, in one of which An. belenrae, An. sinensis and An. kleini were most closely related. More molecular markers would make greater contribution to phylogenetic analysis.

Comparing genetic diversity of Sitophilus zeamais (Motchulsky) popula-tions sampled in several agro-ecological areas between Central African Republic and Senegal

2014 ◽  
Vol 4 (4) ◽  
pp. 172-182
Author(s):  
Asta Eliane Bambou ◽  
Serge Florent Bolevane Ouantinam ◽  
Cheikh Thiaw ◽  
Jean Alain Mokossesse ◽  
Assane Ndong ◽  
...  
Keyword(s):  
Cytochrome B ◽  
Phylogenetic Trees ◽  
Central African Republic ◽  
Geographical Origin ◽  
Sitophilus Zeamais ◽  
Cyt B ◽  
Popula Tions ◽  
Agroecological Zones ◽  
Two Populations ◽  
Very High

Maize is attacked by many post-harvest pests including Sitophilus spp and Prostephanus spp, which causes remarkable loss during storage. Approxi-mately 30 to 40 % loss in the absence of treatment has been reported world-wide. This study compare genetically Central African and Senegalese popula-tions of Sitophilus zeamais from various agroecological zones using 3 mark-ers namely cytochrome b, cytochrome oxidase and nuclear 28S gene. S. zeamais samples were analyzed on both of two other sites 34 for the 28S gene; 68 for cytochrome b and 36 for the cytochrome oxydase. Results ana-lyzed by AMOVA have shown high genetic variation outside population of each country (6.17 % with Cyt b; 21.45 % with 49.83 % and COI in the case of 28S) and low within subpopulations (-10.06 % for Cyt b, 9.36 % for the COI and -15.23 % for 28S). Majority haplotype is shared between the two popula-tions for 28S and cytochrome b genes and there is a very high haplotype di-versity in populations of Senegal considering the Cytochrome b gene (0.781 + / - 0.00364) while with COI and 28S, high values of diversity are observed in Central African sequences, respectively 1.000 + / - 0.00274 and 0.867 + / - 0.011. Genetic differentiation obtained according to the geographical origin is significant between the two populations; however, it is not at the level of subpopulations. Developed by the three approaches (parsimony, likelihood and Bayesian) phylogenetic trees are resolved and show a speciation of the two populations according to the geographical origin.

scholarly journals Genetic diversity and phylogenetic relationship of higher termite Globitermes sulphureus (Haviland)(Blattodea:Termitidae)

Sociobiology ◽  
2021 ◽  
Vol 68 (2) ◽  
pp. 5911
Author(s):  
Nurul Akmar Hussin ◽  
Abdul Hafiz Ab Majid
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Relationship ◽  
Phylogenetic Trees ◽  
Haplotype Diversity ◽  
Evolutionary Genetics ◽  
Neighbor Joining ◽  
Geographic Isolation ◽  
Neutral Genetic Diversity ◽  
Coii Gene ◽  
Relationship Of

The subterranean higher termite Globitermes sulphureus (Blattodea: Termitidae), is a peridomestic forager and regarded as a significant pest in Southeast Asia. In this study, the populations of G. sulphureus from the USM main campus area were investigated based on partial sequences of the mitochondrial COII gene. The genetic diversity was determined using DnaSP v5 software while the phylogenetic relationship was defined using Neighbor-joining (NJ) and maximum likelihood (ML) methods using Molecular Evolutionary Genetics Analysis (MEGA 7) software. A total of 2 haplotypes were detected among the 5 sample sequences that differed by two variable sites. In addition, both phylogenetic trees gave similar topology and supporting the results from haplotype diversity. Based on the haplotype diversity and molecular phylogeny, it is proposed that geographic isolation and lack of human activities have contributed to the neutral genetic diversity of G. sulphureus.   

scholarly journals Current understanding of an Emerging Coronavirus using in silico approach: Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2)

2023 ◽  
Vol 83 ◽  
Author(s):  
S. Khalid ◽  
R. Siddique ◽  
S. Shaheen ◽  
M. N. Shahid ◽  
Z. Shamim ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Genetic Lineage ◽  
Envelope Membrane ◽  
Neighbor Joining ◽  
Genomic Features ◽  
Novel Coronavirus ◽  
High Level ◽  
Relationship Of ◽  
Full Length Genome

Abstract Novel coronavirus (nCoV) namely “SARS-CoV-2” is being found responsible for current PANDEMIC commenced from Wuhan (China) since December 2019 and has been described with epidemiological linkage to China in about 221 countries and territories until now. In this study we have characterized the genetic lineage of SARS-CoV-2 and report the recombination within the genus and subgenus of coronaviruses. Phylogenetic relationship of thirty nine coronaviruses belonging to its four genera and five subgenera was analyzed by using the Neighbor-joining method using MEGA 6.0. Phylogenetic trees of full length genome, various proteins (spike, envelope, membrane and nucleocapsid) nucleotide sequences were constructed separately. Putative recombination was probed via RDP4. Our analysis describes that the “SARS-CoV-2” although shows great similarity to Bat-SARS-CoVs sequences through whole genome (giving sequence similarity 89%), exhibits conflicting grouping with the Bat-SARS-like coronavirus sequences (MG772933 and MG772934). Furthermore, seven recombination events were observed in SARS-CoV-2 (NC_045512) by RDP4. But not a single recombination event fulfills the high level of certainty. Recombination mostly housed in spike protein genes than rest of the genome indicating breakpoint cluster arises beyond the 95% and 99% breakpoint density intervals. Genetic similarity levels observed among “SARS-CoV-2” and Bat-SARS-CoVs advocated that the latter did not exhibit the specific variant that cause outbreak in humans, proposing a suggestion that “SARS-CoV-2” has originated possibly from bats. These genomic features and their probable association with virus characteristics along with virulence in humans require further consideration.

scholarly journals Mutation and Phylogenetic Analysis of Spike Glycoprotein of Indonesian Isolates of Severe-Acute-Respiratory-Syndrome-Coronavirus-2 (SARS-CoV-2)

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Shabarni Gaffar ◽  
◽  
Syifa Al Fauziah Rahmani ◽  
Ari Hardianto
Keyword(s):  
Amino Acid ◽  
Phylogenetic Trees ◽  
Point Mutations ◽  
Surface Protein ◽  
Amino Acid Sequences ◽  
Effective Vaccine ◽  
Neighbor Joining ◽  
Multiple Sequence ◽  
Spike Gene ◽  
Relationship Of

Coronavirus disease-2019 (COVID-19) is an infectious acute respiratory disease caused by SARS-CoV-2. The protein that plays a role in the entry of SARS-CoV-2 into human cells is the surface protein, or the Spike, which is thought to be the effective vaccine target to prevent SARS-CoV-2 infection. Until December 2020, Indonesia has reported 106 SARS-CoV-2 genome sequences identified from COVID-19 positive patients. The purpose of this study was to analyze the phylogenetic relationship of the Spike protein of the Indonesian isolates of SARS-CoV-2 Indonesian, as well as the virus mutations and their effects on changes in the amino acid. The 106 Indonesian SARS-CoV-2 genomes were downloaded from GISAID and the Spike nucleotide and amino acid sequences were analyzed by multiple sequence alignment (MSA) and mutation analysis using the ClustalW method. Phylogenetic trees were created using the Neighbor-Joining method in MEGA-X software. The results showed that 30 of the 106 Indonesian isolate SARS-CoV-2 Spike were 100% identical to the Wuhan-Hu-1, while the remaining 76 had experienced mutations at 1-4 sites. There were 43-point mutations in the Spike gene, 27 of which led to amino acid changes and four had not been reported in other countries. The global mutation D614G was found in 60 Indonesian isolates , of which West Java was the province with the most reports. The phylogenetic of Spike showed that the Indonesian samples have been divided into several branches that are far from Wuhan-Hu-1. This study indicates the possibility of differences in the protein structure of Indonesian isolate SARS-CoV-2 Spike that need to be further studied to manufacture a vaccine against the Indonesian strain of SARS-CoV-2.

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