Phylogenetic of Marble Goby (Oxyeleotris marmorata Blkr.) in South Sumatra Based on Cytochrome C Oxidase Subunit I (COI) Gene

Marble goby (Oxyeleotris marmorata) in Indonesia, spread across Sumatra, Kalimantan and Papua. The purpose of this study was to utilize a sequence of mitochondrial DNA Cytochrome Oxidase Subunit I gene, to analyze the phylogenetic tree and genetic distance between cultured and captured populations. This research was conducted on March-August 2020. The methods used in barcoding species were DNA isolation, amplification using PCR (Polymerase Chain Reaction) and sequencing of the COI mtDNA gene. The domesticated samples (n=3) were collected from Gandus Fish Seed Center (GFSC), while the wild samples (n=3) were captured from the Musi River in Beruge Village, Babat Toman District, both in Musi Banyuasin Regency. The sequenced COI mtDNA gene fragments were obtained from the PCR method. Three samples performed good PCR results, while the other three didn’t amplify properly. After the editing process, the COI gene sequencing produced a nucleotide length of 610 bp. Based on the BLAST (Basic Local Alignment Search Tool), domesticated marble goby (OMD2, OMD3) was in the same cluster with marble goby from the Musi River (OMS3). The genetic distance indicated that two specimens of domesticated marble goby were 100% identical, while the wild (OMS3) indicated a genetic distance of 0.0066 to domesticated species.

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Morphology and Molecular Biology of Benthic Java Sea Shark Ray Rhina ancylostoma Bloch and Scheider 1801 (Elasmobranchia: Rhinidae)

Annual Research & Review in Biology ◽

10.9734/arrb/2020/v35i430208 ◽

2020 ◽

pp. 19-31

Author(s):

Agus Hartoko ◽

Delianis Pringgenies ◽

Amelia Cahya Anggelina ◽

Takashi Matsuishi

Keyword(s):

Molecular Biology ◽

Genetic Distance ◽

Dna Analysis ◽

Pcr Amplification ◽

Local Alignment ◽

Total Length ◽

Search Tool ◽

Java Sea ◽

Bootstrap Replication ◽

Pcr Method

Aims: Morphology and molecular biology of a rare shark-rays Rhina ancylostoma caught from Java sea.Indonesia. Study Design: Morphology, morphometry and DNA analysis of the fish specimen. Place and Duration of Study: Sample wascollected from fish auction hall at north Java, specimen now stored in Lab of Ichtiology. Department of Fisheries. Faculty of Fisheries and Marine Science. Diponegoro University, between March to December 2019. Methodology: DNA extraction, amplification and molecular identification of fish sample.Yield of DNA supernatant transferred in an eppendeorf tube and stored in 4°C for further process. PCR amplification. Part of Mithocondrial DNA COI (Cytochrome Oxidase subunit-I) gen was amplified using Polymerase Chain Reaction (PCR) method. Then matched up with GenBank database at NCBI using Basic Local Alignment Search Tool (BLAST) analysis. Philogenetic tree was set using Neighbor-Joining method, Kimura-2 parameter model and 1,000 bootstrap replication. Some sequence from NCBI GenBank were inputted into philogenetic tree as comparison. Results: Rhina ancylostoma as one of demersal shark rays catch from tropical shallow Java sea. Range of Total Length 73 – 200 cm and dominant Total Length catch 125 cm. Morphologyis characterised with three lines of spine thorn on the head, morphometry characteriswide of head to TL ratio 0.77. DNA analysis had confirmed the specimen of AH2 as Rhina ancylostoma based on homological match up of sequence of Gen Bank database with reference accesion number KU721837.1 with length sequence of 665 bpand identical similarity of 99.84% for specimen Accession number LC 505461. Conclusion: Rhina ancylostoma as one of demersal shark rays catch from Java sea. Range Total Length (TL) of catch 73 – 200 cm and dominant TL catch range 101 – 125 cm. Morphologically character of wide head ratio with three lines of spine thorn on the head. Nearest genetic distance of 0.02 to Rhincobatushorkelii and 0.017 to R. australiae. Longest genetic distance of 0.243 to Potamotrygon motoro.

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Fish Identification based on Partial Fragments of The Mitochondrial COI Subunit I Gene

E3S Web of Conferences ◽

10.1051/e3sconf/202132201038 ◽

2021 ◽

Vol 322 ◽

pp. 01038

Author(s):

Tuah N. M. Wulandari

Keyword(s):

Phylogenetic Tree ◽

Coi Gene ◽

Local Alignment ◽

Mtdna Sequences ◽

Mitochondrial Coi ◽

Search Tool ◽

Very High ◽

I Gene

The mtDNA sequences revealed that several of the fish studied were Hampala macrolepidota and Barbonymus gonionotus. The objective of this research was to learn the pattern of COI gene in mtDNA and establish a phylogenetic tree. Basic Local Alignment Search Tool-nucleotide (BLASTn) confirmed that Barbonymus gonionotus froma the Ranau Lake, South Sumatera has 100% matching ranges to the species from Memberamo River (Indonesia), India, Bangladesh, Thailand (Mae Khlong), Indo-Myanmar, and Malaysia_1. The lowest closeness (98.76%) is related to species from Thailand (Lower Ing). The Blast investigation appears us that the level of familiarity was very high, it is coming to 98-100% in Barbonymus gonionotus. Hampala macrolepidota had 100% matching ranges to the species from Indonesia (SouthaSumatera_1) and Vietnam. They had 99.05%-99.84% closeness from Malaysia_1,2&3, Indonesia (South Sumatera_2&3, Java and Bali_1,2&3).

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Evaluasi Deteksi Berbasis PCR untuk Bakteri Bifidobacterium longum dalam Sampel Feses Bayi dari Kota Manado

JURNAL ILMIAH SAINS ◽

10.35799/jis.20.1.2020.27702 ◽

2020 ◽

Vol 20 (1) ◽

pp. 18

Author(s):

Beivy Jonathan Kolondam

Keyword(s):

Polymerase Chain Reaction ◽

16S Rrna ◽

16S Rrna Gene ◽

Detection Method ◽

Bifidobacterium Longum ◽

Local Alignment ◽

Rrna Gene ◽

Chain Reaction ◽

Search Tool ◽

Polymerase Chain

Bifidobakteria merupakan mikroflora yang umum hidup dalam usus manusia sejak bayi. Peran Bifidobacterium longum yang positif sebagai salah satu bakteri yang menunjang kesehatan inangnya membuat bakteri ini menjadi objek studi yang menarik. Salah satu instrumen dalam penelitian adalah adalah metode deteksi bakteri B. longum yang berbasis PCR (Polymerase Chain Reaction) gen 16S rRNA. Dengan mempertimbangkan bahwa perancangan primer untuk deteksi ini sudah lebih dari 20 tahun, penelitian ini bertujuan mengevaluasi hasil deteksi melalui PCR terhadap B. longum dalam feses bayi. Akurasi hasil dilihat melalui sekuensing terhadap hasil PCR sampel yang terdeteksi positif. Dua sampel feses bayi di Manado yang diperiksa menunjukkan hasil positif dan produk PCR tersebut dilakukan sekuensing. Panjang DNA yang nyata dari hasil deteksi ini yaitu 829 bp dan bukan 831 bp. Sekuens DNA kedua sampel ini identik satu sama lain. Hasil BLAST (Basic Local Alignment Search Tool) mengonfirmasi kesamaan 100% (identik) dari kedua specimen dari Kota Manado dengan sekuens gen 16S rRNA specimen bakteri B. longum yang telah ada dalam GenBank.Kata-kata kunci: Bifidobacterium longum, Polymerase Chain Reaction, deteksi, feses, bayi. Evaluation of PCR-Based Detection for Bifidobacterium longum in Infant Fecal Samples from Manado City ABSTRACTBifidobacteria are common members of the gut microflora of humans since infant. The Bifidobacterium longum has positive roles and one of supportive bacteria to the host, which made interesting as a study object. One instrument in studying this bacterial species is the detection method based on PCR of 16S rRNA gene. In consideration of the design of primers for this detection method is already more than 20 years, this research aimed to evaluate the PCR-based detection of B. longum in infant feces. The accuracy of the method was evaluated from sequencing of DNA fragment from positive results. Two fecal samples in Manado City shown positive result were sent for sequencing. The actual length of DNA amplified by PCR was 829 bp, not 831 bp. The DNA sequence of both samples were identical to each other. The BLAST (Basic Local Alignment Search Tool) result confirmed the similarity of both samples from Manado with 16S rRNA gene sequence of B. longum specimens in GenBank.Keywords: Bifidobacterium longum, Polymerase Chain Reaction, detection, feces, infant.

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KARAKTERISTIK SEKUEN cDNA PENGKODE GEN ANTI VIRUS DARI UDANG WINDU, Penaeus monodon

Jurnal Riset Akuakultur ◽

10.15578/jra.4.1.2009.1-13 ◽

2016 ◽

Vol 4 (1) ◽

pp. 1

Author(s):

Andi Parenrengi ◽

Alimuddin Alimuddin ◽

Sukenda Sukenda ◽

Komar Sumantadinata ◽

Andi Tenriulo

Keyword(s):

Polymerase Chain Reaction ◽

Penaeus Monodon ◽

Viral Gene ◽

Local Alignment ◽

Chain Reaction ◽

Crustacean Species ◽

Viral Genes ◽

Tiger Prawn ◽

Search Tool ◽

Polymerase Chain

Transgenesis pada ikan merupakan sebuah teknik modern yang berpotensi besar dalam menghasilkan organisme yang memiliki karakter lebih baik melalui rekombinan DNA gen target termasuk gen anti virus dalam peningkatan resistensi pada udang. Gen anti virus PmAV (Penaeus monodon Anti Viral gene) merupakan salah satu gen pengkode anti virus yang berasal dari spesies krustase. Penelitian ini dilakukan untuk mengetahui karakteristik gen anti virus yang diisolasi dari udang windu, Penaeus monodon. Isolasi gen anti virus menggunakan metode Polymerase Chain Reaction (PCR) dan selanjutnya dipurifikasi untuk sekuensing. Data yang dihasilkan dianalisis dengan program Genetyx Versi 7 dan basic local alignment search tool (BLAST). Hasil penelitian menunjukkan bahwa gen anti virus PmAV yang berhasil diisolasi dari cDNA udang windu dengan panjang sekuen 520 bp yang mengkodekan 170 asam amino. BLAST-N menunjukkan tingkat similaritas yang sangat tinggi (100%) dengan gen anti virus yang ada di GeneBank. Komposisi asam amino penyusun gen anti virus yang paling besar adalah serin (10,00%), sedangkan yang terkecil adalah asam amino prolin dan lisin masing-masing 1,76%. Analisis sekuen gen dan deduksi asam amino (BLAST-P) memperlihatkan adanya C-type lectin-like domain (CTLD) yang memiliki kemiripan dengan gen C-type lectin yang diisolasi dari beberapa spesies krustase.Transgenic fish technology is a potential modern technique in producing better character organism through DNA recombinant of target genes including anti viral gene for improvement of shrimp immunity. PmAV (Penaeus monodon Anti Viral) gene is one of anti viral genes isolated from crustacean species. The research was conducted to analyze the characteristics anti viral gene isolated from tiger prawn, Penaeus monodon. Anti viral gene was isolated using Polymerase Chain Reaction (PCR) technique and then purified for sequencing. Data obtained were analyzed using Genetyx Version 7 software and basic local alignment search tool (BLAST). The results showed that the PmAV antiviral gene has been isolated from cDNA of tiger prawn at the position of approximately 520 bp consisting of 170 amino acids. BLAST-N showed high similarity (100%) compared to the other anti viral genes deposited at the GeneBank. The highest percentage of amino acid encoding anti viral gene is serine (10.00%), while the lowest is proline and lysine (1.76%). Sequence analysis and amino acid deduction (BLAST-P) revealed a C-type lectin-like domain (CTLD) that is similar with the C-type lectin gene isolated from several crustacean species.

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A review and notes on the phylogenetic relationship of the centipede genus Otostigmus Porat, 1876 (Chilopoda: Scolopendromorpha: Scolopendridae) from Vietnam

Zootaxa ◽

10.11646/zootaxa.4808.3.1 ◽

2020 ◽

Vol 4808 (3) ◽

pp. 401-438

Author(s):

HA T. VU ◽

HUNG D. NGUYEN ◽

SON X. LE ◽

KATSUYUKI EGUCHI ◽

ANH D. NGUYEN ◽

...

Keyword(s):

Cytochrome C ◽

Genetic Distance ◽

Cytochrome C Oxidase ◽

Phylogenetic Relationship ◽

Genetic Data ◽

Identification Key ◽

Coi Gene ◽

Oxidase Subunit ◽

Relationship Of

The genus Otostigmus Porat, 1876 is reviewed based on recent material collected from parts of Vietnam. A total of nine species are documented and imaged. The phylogeny of the genus Otostigmus is analyzed based on a 603-bp dataset of the cytochrome c oxidase subunit I (COI) gene. The average K2P genetic distance between Otostigmus species is 19%, and eight of nine species are considered to be monophyletic, except O. amballae. The phylogenetic relationship between Otostigmus species necessitates a deeper study with more samples and genetic data. In addition, an identification key to all Otostigmus species is provided for the fauna of Vietnam.

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BARKODING DNA BURUNG ELANG (FAMILI ACCIPITRIDAE) DI INDONESIA

BERITA BIOLOGI ◽

10.14203/beritabiologi.v17i2.3108 ◽

2018 ◽

Vol 17 (2) ◽

Cited By ~ 2

Author(s):

Moch Syamsul Arifin Zein

Keyword(s):

Animal Species ◽

Distance Matrix ◽

Pairwise Distance ◽

Coi Gene ◽

Local Alignment ◽

Protein Coding ◽

Genetic Distance Matrix ◽

The Family ◽

Search Tool ◽

Identification Tool

The cytochrome c oxidase subunit I (COI) gene is a reprensentative of all the protein-coding genes of the mitochondrial DNA genome that has been widely used as an animal species identification tool. In this study, 86 sequences of DNA barcodes of members of the family Accipitridae in Indonesia including Nisaetus bartelsi, Nisaetus cirrhatus, Haliaeetus leucogaster, Spilornis cheela, Haliastur indus, and 11 sequences from Genbank were examined. Each species was confirmed through the Basic Local Alignment Search Tool (BLAST). The construction of phylogeny trees based on COI gene sequences was performed by the Neighbors-joining method where the calculation of the genetic distance matrix with the Kimura 2-parameter model was implemented in pairwise distance calculation in the Mega version 6.05 programe. The results of the analysis showed that the divergence within species ranged from 0 to 0.3% (0.13 ± 0.12%), between species ranged from 1.6 to 18.5% (12.8 ± 3.73%), between genera ranged from 13 to 18.6%, and the average in the Accipitridae Family was 11.8%. Therefore, it could form clusters in each species cohesively and clearly separated between the taxa analyzed.

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Molecular classification and comparative phylogeographic study of insectivorous bat species (Pipisitrellus coromandra) from Punjab, Pakistan

Brazilian Journal of Biology ◽

10.1590/1519-6984.240725 ◽

2022 ◽

Vol 82 ◽

Author(s):

Z. Ahmad ◽

M. H. Abbasi ◽

S. R. Ahmad ◽

N. Sheikh

Keyword(s):

Molecular Classification ◽

Genetic Distances ◽

Coi Gene ◽

Local Alignment ◽

Identity Match ◽

Gene Coi ◽

Search Tool ◽

Identity Score ◽

First Time

Abstract Molecular based identification of bat fauna in Pakistan has been relatively less explored. The current study was therefore planned to report for the first time the molecular classification of insectivorous bats (Pipistrellus coromandra) based on mitochondrion gene (COI) from Punjab, Pakistan. Specimens were collected from five different locations followed by DNA extraction with subsequent gene amplification and sequencing. All samples in the study had shown close identity matches with species (Pipistrellus coromandra) from India and (Pipistrellus tenuis) from Vietnam with percentage identity score of 96.11 and 95.58 respectively except one sequence which only revealed 86.78% identity match on Basic Local Alignment Search Tool (BLAST) and could only be assigned to genus level Pipistrellus sp. The results indicated negligible intra-population genetic distance among collected samples whereas the comparison with species from other countries had shown high intraspecific (P. coromandra) and interspecific (P. tenuis) mean genetic distances. The current study hence successfully proved the efficiency of COI gene as a molecular marker for species identification and in analyzing the patterns of genetic variation with species from other countries.

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DNA barcoding of Crustacean larvae in the eastern areas of Segara Anakan Cilacap, Central Java Indonesia

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d211054 ◽

2020 ◽

Vol 21 (10) ◽

Author(s):

KUSBIYANTO KUSBIYANTO ◽

DIAN BHAGAWATI ◽

Agus Nuryanto

Keyword(s):

Cytochrome C ◽

Genetic Distance ◽

Dna Barcoding ◽

Cytochrome C Oxidase ◽

Species Level ◽

Coi Gene ◽

Reference Species ◽

Oxidase Gene ◽

Oxidase Subunit ◽

Central Java

Abstract. Kusbiyanto, Bhagawati D, Nuryanto A. 2020. DNA barcoding of crustacean larvae in Segara Anakan, Cilacap, Central Java, Indonesia using cytochrome c oxidase gene. Biodiversitas 21: 4878-4887. Species-level identification of crustacean larvae is challenging due to morphological constraints. DNA barcoding offers a precise method to solve the problems. That method has never been applied to crustacean larvae from the eastern of Segara Anakan, Cilacap, Central Java, Indonesia. This study aims to identify crustacean larvae in the eastern of Segara Anakan using the cytochrome c oxidase subunit I (COI) gene as a barcode marker. Larvae morphotypes were identified under a binocular microscope. The COI gene was sequenced from one individual of each morphotype. Microscopic observation placed the samples into 15 morphotypes. DNA barcoding placed twelve morphotypes as Crustacea with sequence homologies from 72.21% to 99.21%. Intra-species genetic divergences between samples and reference species ranged between 0.9% and 31.9%, while genetic distance ranged from 0.0% to 17.80%. Intra-species genetic divergences ranged between 0.00% and 3.9%, while genetic distance ranged from 0.00% to 3.8%. The phylogenetic tree proved the monophyly between samples and reference species and showed clear separation among species. All parameters proved that nine morphotypes were identified into species level and were counted for five species. Three morphotypes were identified into the genus level and were counted for three genera. Eight species of crustacean larvae were successfully identified using the cytochrome c oxidase subunit 1 gene.

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Two Cases of Cokeromyces recurvatus in Liquid-Based Papanicolaou Tests and a Review of the Literature

Archives of Pathology & Laboratory Medicine ◽

10.5858/arpa.2011-0493-cr ◽

2012 ◽

Vol 136 (12) ◽

pp. 1593-1596 ◽

Cited By ~ 6

Author(s):

Shelley I. Odronic ◽

Thomas Scheidemantel ◽

Marion J. Tuohy ◽

Deborah Chute ◽

Gary W. Procop ◽

...

Keyword(s):

Medical History ◽

Deoxyribonucleic Acid ◽

Paracoccidioides Brasiliensis ◽

Female Genital Tract ◽

Molecular Techniques ◽

Local Alignment ◽

Past Medical History ◽

Search Tool ◽

Polymerase Chain ◽

Female Genital

We present 2 cases of Cokeromyces recurvatus in routine, liquid-based Papanicolaou tests (ThinPrep). Patient 1 is a healthy, asymptomatic, 26-year-old woman with no pertinent past medical history. Patient 2 is a healthy, asymptomatic, 47-year-old woman with no pertinent past medical history. The Papanicolaou tests from both patients showed many fungal-like elements as globose, yeastlike forms measuring 10 to 30 µm in diameter with multiple, narrowly attached apparent “daughter” buds. This morphology was consistent with Paracoccidioides brasiliensis. However, broad-range fungal polymerase chain reaction and deoxyribonucleic acid sequence analysis performed with GenBank Basic Local Alignment Search Tool showed an exact match for C recurvatus. Our cases highlight the importance of molecular techniques to prevent misdiagnosis of C recurvatus as P brasiliensis, based on morphology alone. There have been 8 previously published cases of C recurvatus infection in humans, 3 of which were reported in the female genital tract.

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A new Rhopalomeris species (Diplopoda: Glomerida: Glomeridae), and notes on the phylogenetic relationships between glomeridans in Vietnam

Zootaxa ◽

10.11646/zootaxa.4927.2.5 ◽

2021 ◽

Vol 4927 (2) ◽

pp. 257-264

Author(s):

ANH D. NGUYEN ◽

SON G. NGUYEN ◽

KATSUYUKI EGUCHI

Keyword(s):

New Species ◽

Cytochrome C ◽

Genetic Distance ◽

Cytochrome C Oxidase ◽

Phylogenetic Relationships ◽

Coi Gene ◽

Oxidase Subunit

A new pill millipede, Rhopalomeris nagao sp. nov., is described from Vietnam. It is recognized by the following combination of characters: antennal tip with numerous sensory cones; telopods with short prefemoral and femoral trichosteles, with long, straight and acute tuberculiform femoral process, and with shorter lobuliform tibial process; syncoxial lobe being slightly concave medially, syncoxial horns being longer than lobe. A fragment of the cytochrome c oxidase subunit I (COI) gene is also provided for the new species. The K2P genetic distance of the COI between the new species and other Vietnamese glomeridans is from 10.7% to 16.9%. Two genera, Hyperglomeris and Hyleoglomeris, are considered to be non-monophyletic, but more data and samples will be needed for confirmation.

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