Influence of pairwise genetic distance computation and reference sample size on the reliability of species identification using Cyt b and COI gene fragments in a group of native passerines

Ikan tiger fish (Datnioides sp.) merupakan ikan hias air tawar yang memiliki nilai ekonomis penting. Distribusi populasi ikan ini meliputi Papua, Kalimantan, dan Sumatera, dengan tingkat eksploitasi yang cukup tinggi di dua lokasi terakhir. Penelitian ini dilakukan untuk mendapatkan informasi keragaman genetik ikan tiger fish yang mendiami perairan Kalimantan dan Sumatera. Sebanyak 24 sampel ikan uji dikoleksi dari Sungai Kapuas, Kalimantan Barat dan Sungai Musi, Sumatera Selatan. Penelitian dilakukan dalam dua tahap, tahap pertama yaitu identifikasi molekuler dengan menggunakan DNA barcoding gen cytochrome oxidase 1 (COI), tahap kedua adalah analisis keragaman genetik dengan menggunakan marka DNA mitokondria gen cytochrome b (Cyt b), dan DNA inti gen recombination activating gene (RAG2). Hasil identifikasi secara molekuler menunjukkan bahwa ikan hasil koleksi memiliki kesamaan genetik sebesar 100% dengan spesies D. undecimradiatus. Keragaman genetik ikan tiger fish antar populasi berkisar pada nilai 0,023 (standar deviasi 0,001) sedangkan keragaman intra populasi adalah sebesar 0,002 dan 0,003 masing-masing untuk populasi Kalimantan dan Sumatera. Jarak genetik sampel baik yang berasal dari Sumatera maupun Kalimantan dengan spesies D. undeciumradiatus masing-masing 0,003 dan 0,006; sedangkan dengan spesies D. microlepis yaitu 0,142. Analisis menggunakan gen RAG2 menunjukkan sampel yang diuji memiliki struktur populasi yang terpisah ditandai dengan terjadinya mutasi pada enam nukleotida dan tiga asam amino.The Tiger fish (Datnioides sp.) is a freshwater ornamental fish that has important economic value. The distribution of this fish included Papua, Kalimantan, and Sumatra, but intensive exploitation occurs in the last two population. This research was conducted to obtain the genetic diversity of tiger fish that inhabited in Kalimantan and Sumatra. A total of 24 fish were collected from Kapuas River, West Kalimantan and Musi River, at Sumatra. The study was conducted in two stages, the first stage is molecular identification of sample by using DNA barcoding cytochrome oxidase 1 (COI) gene, the second stage is analyses of genetic diversity of tiger fish within and between population by using the mitochondrial DNA cytochrome b (Cyt b) gene, and nucleus DNA recombination (RAG2) gene. The molecular identification has shown that the collected fish has a genetic similarity of 100% with D. undecimradiatus. The genetic diversity of tiger fish between populations is 0.023 (standard deviation of 0.001) whereas intra-population is 0.002 and 0.003 for Kalimantan and Sumatra, respectively. The genetic distance of samples with species D. undeciumradiatus were 0.003 and 0.006 for Kalimantan and Sumatera, respectively, whereas the genetic distance with D. microlepis was 0.142. The analysis of mutation on RAG2 gene shows there are six nucleotides and three amino acids have mutation.

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DNA barcoding of bats (Chiroptera) from the Colombian northern region

Mammalia ◽

10.1515/mammalia-2020-0138 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Álvaro J. Benítez ◽

Dina Ricardo-Caldera ◽

María Atencia-Pineda ◽

Jesús Ballesteros-Correa ◽

Julio Chacón-Pacheco ◽

...

Keyword(s):

Dna Barcoding ◽

Species Identification ◽

Dna Sequences ◽

Genetic Distances ◽

Northern Region ◽

Coi Gene ◽

Individual Species ◽

Species Variation ◽

Molossus Molossus ◽

Artibeus Lituratus

Abstract Bats are mammals of great ecological and medical importance, which have associations with different pathogenic microorganisms. DNA barcoding is a tool that can expedite species identification using short DNA sequences. In this study, we assess the DNA barcoding methodology in bats from the Colombian Northern region, specifically in the Córdoba department. Cytochrome oxidase subunit I (COI) gene sequences of nine bat species were typified, and their comparison with other Neotropic samples revealed that this marker is suitable for individual species identification, with ranges of intra-species variation from 0.1 to 0.9%. Bat species clusters are well supported and differentiated, showing average genetic distances ranging from 3% between Artibeus lituratus and Artibeus planirostris, up to 27% between Carollia castanea and Molossus molossus. C. castanea and Glossophaga soricina show geographical structuring in the Neotropic. The findings reported in this study confirm DNA barcoding usefulness for fast species identification of bats in the region.

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DNA barcodes provide evidence for the independent origin of the cultivated silkworms Samia ricini and Samia cynthia

Journal of Insects as Food and Feed ◽

10.3920/jiff2021.0077 ◽

2021 ◽

pp. 1-8

Author(s):

J.-C. Huang ◽

X.-Y. Li ◽

Y.-P. Li ◽

R.-S. Zhang ◽

D.-B. Chen ◽

...

Keyword(s):

Genetic Distance ◽

Phylogenetic Relationship ◽

Dna Barcode ◽

Distinct Species ◽

Coi Gene ◽

Molecular Evidence ◽

Dna Barcodes ◽

Close Relationship ◽

Molecular Phylogenetic ◽

Phylogenetic Framework

Samia ricini (Wm. Jones) and Samia cynthia (Drury) (Lepidoptera: Saturniidae) have been used as traditional sources of food as well as silk-producing insects. However, the phylogenetic relationship between the two silkworms remains to be addressed. In this study, the mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences corresponding to DNA barcodes from 13 Samia species were analysed, and a DNA barcode-based phylogenetic framework for these Samia species was provided. Phylogenetic analysis showed that multiple individuals of a species could be clustered together. Our analysis revealed a close relationship among Samia yayukae Paukstadt, Peigler and Paukstadt, Samia abrerai Naumann and Peigler, Samia kohlli Naumann and Peigler, Samia naessigi Naumann and Peigler, Samia naumanni Paukstadt, Peigler and Paukstadt, and Samia kalimantanensis Paukstadt and Paukstadt. The mixed clustering relationship and low Kimura-2-parameter (K2P) genetic distance (0.006) between individuals of S. ricini and Samia canningi (Hutton) indicated that the cultivated silkworm S. ricini was derived from the non-cultivated silkworm S. canningi. The remote phylogenetic relationship and high K2P genetic distance (0.039) indicated that S. ricini and S. cynthia are distinct species, thus providing solid molecular evidence that they had entirely independent origins. The relationships between S. kalimantanensis and S. naumanni and between S. cynthia and Samia wangi Naumann and Peigler, as well as the potential cryptic species within S. abrerai were also discussed. This is the first study to assess the DNA barcodes of the genus Samia, which supplements the knowledge of species identification and provides the first molecular phylogenetic framework for Samia species.

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Fatal Pneumonia Associated With a Novel Genotype of Human Coronavirus OC43

Frontiers in Microbiology ◽

10.3389/fmicb.2021.795449 ◽

2022 ◽

Vol 12 ◽

Author(s):

Susanna Kar Pui Lau ◽

Kenneth Sze Ming Li ◽

Xin Li ◽

Ka-Yan Tsang ◽

Siddharth Sridhar ◽

...

Keyword(s):

Genetic Distance ◽

Respiratory Infections ◽

Endotracheal Aspirate ◽

Human Coronavirus ◽

Genotype I ◽

Viral Loads ◽

Pairwise Genetic Distance ◽

Distinct Cluster ◽

Upper Respiratory ◽

Novel Genotype

Since its first discovery in 1967, human coronavirus OC43 (HCoV-OC43) has been associated with mild self-limiting upper respiratory infections worldwide. Fatal primary pneumonia due to HCoV-OC43 is not frequently described. This study describes a case of fatal primary pneumonia associated with HCoV-OC43 in a 75-year-old patient with good past health. The viral loads of the respiratory tract specimens (bronchoalveolar lavage and endotracheal aspirate) from diagnosis to death were persistently high (3.49 × 106–1.10 × 1010 copies/ml). HCoV-OC43 at a 6.46 × 103 copies/ml level was also detected from his pleural fluid 2 days before his death. Complete genome sequencing and phylogenetic analysis showed that the present HCoV-OC43 forms a distinct cluster with three other HCoV-OC43 from United States, with a bootstrap value of 100% and sharing 99.9% nucleotide identities. Pairwise genetic distance between this cluster and other HCoV-OC43 genotypes ranged from 0.27 ± 0.02% to 1.25 ± 0.01%. In contrast, the lowest pairwise genetic distance between existing HCoV-OC43 genotypes was 0.26 ± 0.02%, suggesting that this cluster constitutes a novel HCoV-OC43 genotype, which we named genotype I. Unlike genotypes D, E, F, G, and H, no recombination event was observed for this novel genotype. Structural modeling revealed that the loop with the S1/S2 cleavage site was four amino acids longer than other HCoV-OC43, making it more exposed and accessible to protease, which may have resulted in its possible hypervirulence.

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DNA BARCODING USING COI GENE SEQUENCES OF WILD BETTA FIGHTING FISH FROM INDONESIA: PHYLOGENY, STATUS AND DIVERSITY

Indonesian Fisheries Research Journal ◽

10.15578/ifrj.26.2.2020.97-105 ◽

2020 ◽

Vol 26 (2) ◽

pp. 97

Author(s):

Melta R. Fahmi ◽

Eni Kusrini ◽

Erma P. Hayuningtiyas ◽

Shofihar Sinansari ◽

Rudhy Gustiano

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Gene Sequence ◽

Ornamental Fish ◽

Coi Gene ◽

Tree Construction ◽

In The Wild ◽

Blast Program

The wild betta fish is a potential ornamental fish export commodity normally caught by traders or hobbyists in the wild. However, the population of wild betta in nature has declined and become a threat for their sustainability. This research was conducted to analyze the genetic diversity, phylogenetic relationships, and molecular identification through DNA COI gene sequence of Indonesian wild betta fish. A total of 92 wild betta fish specimens were collected in this study. Amplification of COI genes was carried out using Fish F1, Fish R1, Fish F2, and Fish R2 primers. The genetic diversity and phylogenetic relationships were analyzed using MEGA version 5 software program. Species identification of the specimen was conducted using BLAST program with 98-100% similarity value of the DNA sequences to indicate the same species. Phylogenetic tree construction showed seven monophyletic clades and showed that Betta smaragdina was the ancestral species of genus Betta in Indonesian waters. Genetic distance among species ranged from 0.02 to 0.30, whereas intra-species genetic distance ranged from 0 to 6.54.

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Current issues in species identification for forensic science and the validity of using the cytochrome oxidase I (COI) gene

Forensic Science Medicine and Pathology ◽

10.1007/s12024-010-9172-y ◽

2010 ◽

Vol 6 (3) ◽

pp. 233-241 ◽

Cited By ~ 34

Author(s):

Linzi Wilson-Wilde ◽

Janette Norman ◽

James Robertson ◽

Stephen Sarre ◽

Arthur Georges

Keyword(s):

Forensic Science ◽

Cytochrome Oxidase ◽

Species Identification ◽

Cytochrome Oxidase I ◽

Coi Gene

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New records and their associated DNA barcodes of the butterfly family Hesperiidae in Tibet, China

Zootaxa ◽

10.11646/zootaxa.4674.4.2 ◽

2019 ◽

Vol 4674 (4) ◽

pp. 426-438

Author(s):

CHENGLONG CAO ◽

SIYAO HUANG ◽

YONGQIANG XU ◽

HAOMIN WU ◽

TIANPENG CHEN ◽

...

Keyword(s):

Genetic Distance ◽

Morphological Study ◽

New Records ◽

Coi Gene ◽

Dna Barcodes ◽

Species Cluster ◽

The Family ◽

Interspecific Genetic Distance ◽

Coi Sequences ◽

First Time

The specimens of the family Hesperiidae collected from Tibet during 2016–2018 are identified using morphology. COI sequences of 76 individuals are newly obtained. The result of our morphological study is congruent with COI gene analyses. Maximum likehood (ML) and Bayesina inferences (BI) analyses reveal that individuals identified morphologically as the same species cluster cohesively. The minimum interspecific genetic distance is 1.7% between Halpe aucma and H. filda, and the genetic distance between conspecific individuals ranged from 0 to 0.2% for the genus Halpe. A total of 51 species are recognized, and six of them, Celaenorrhinus consanguineus Leech, 1891, Barca bicolor (Oberthür, 1896), Aeromachus propinquus Alphéraky, 1897, Pedesta bivitta (Oberthür, 1886), Baoris penicillata chapmani Evans, 1937, and Ochlodes brahma Moore, 1878, are reported from Tibet for the first time, and the last species is new to China.

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The Utility of DNA Barcoding for the Species Identification of Larval Fish in the Lower Ing River, Thailand

Turkish Journal of Fisheries and Aquatic Sciences ◽

10.4194/1303-2712-v20_9_02 ◽

2020 ◽

Vol 20 (9) ◽

pp. 671-679

Author(s):

Dutrudi Panprommin ◽

Kanyanat Soontornprasit ◽

Siriluck Tuncharoen ◽

Niti Iamchuen

Keyword(s):

Dna Barcoding ◽

Species Identification ◽

Larval Fish ◽

Average Length ◽

Conservation Status ◽

Morphological Characters ◽

Nucleotide Sequences ◽

Coi Gene ◽

Fishery Resource ◽

Sustainable Fishery

The species identification of larval fish is very important for sustainable fishery resource management. However, identification based on morphological characters is very difficult, complex and error-prone. DNA barcoding with the sequence of cytochrome c oxidase I (COI) gene was used to identify larval fish species from 10 stations in the tributaries of the lower Ing River. One hundred and six samples were collected between May 2016 and April 2017. The average length of the COI nucleotide sequences was approximately 640 bp. A total of 99 nucleotide sequences were identified in 35 species, 31 genera, 19 families and 9 orders, with 97-100% identity with entries in both the GenBank and BOLD databases. The genetic distance within species ranged from 0.000 to 0.004. However, seven samples were identified at only the genus level because their sequences had not been reported in any databases. Based on IUCN conservation status, most species were classified as least concern (77.14%). Approximately 69.23% of all species were related to human uses in fisheries, aquaculture or aquariums, whereas 30.77% of species were not assessed. Trichopsis vittata (family Osphronemidae) (90%) had the most frequency of occurrence, followed by Oryzias minutillus (family Adrianichthyidae) (70%) and Trichopodus trichopterus (family Osphronemidae) (70%).

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Sample size for determination of the physiological potential of coriander (Coriandrum sativum L.) seeds

Australian Journal of Crop Science ◽

10.21475/ajcs.19.13.04.p1482 ◽

2019 ◽

Vol 13 ((04) 2019) ◽

pp. 552-557

Author(s):

Érica Fernandes Leão Araújo ◽

Anderson Rodrigo da Silva ◽

Amanda Rithieli Pereira dos Santos ◽

Kaique Ferreira Alves, Lara Bernardes da S. Ferreira ◽

Hygor Amaral Santana ◽

...

Keyword(s):

Sample Size ◽

Reference Sample ◽

Seed Vigor ◽

Species Determination ◽

Germination Time ◽

Germination Speed ◽

Minimum Number ◽

Mean Germination Time ◽

Number Of Seeds

The objective of this work was to determine the minimum number of replications and seeds per replication to perform the germination and seed vigor tests with coriander seeds. Two seed lots were compared in terms of water content, vigor and viability. Eight hundred seeds per lot were used. Values of germination first count, germination, germination speed index and mean germination time were analyzed. Sample size scenarios were developed using different combinations of number of replications (from 2 to 10) and the number of seeds per replication (from 20 to 80) by means of a resampling with replacement technique. The reference sample consisted of four replications of 50 seeds, as it is commonly used in researches with this species. Determination of the minimum number of replications and seeds was based on comparing the 95% bootstrapped confidence intervals for the index of variation (CV/n0.5) of each scenario with the confidence interval of the reference sample. It is reasonable to reduce the number of seeds per replication from 50 to 30 in order determine germination first count, germination and germination speed index. Forty seeds per replication are recommended to quantify the mean germination time. However, reductions in the number of replications can affect negatively the accuracy of germination and vigor tests.

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