Mitochondrial DNA study of Mongolian horses

2018 ◽  
Vol 22 (03) ◽  
pp. 12-16
Author(s):  
Bolor-Oyut B ◽  
Ochirkhuyag B ◽  
Khulan J
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Nucleotide Diversity ◽  
Sequence Variation ◽  
Maternal Inheritance ◽  
Haplotype Diversity ◽  
Research Field ◽  
Important Research ◽  
Evolutionary Studies ◽  
High Level

Studies of population genetic diversity is important research field in conservation and restoration of animal breeds and genetic resources. The control region of mitochondrial DNA is widely used for population and evolutionary studies because of its‘ maternal inheritance and high level of sequence variation as well as its‘ much less recombination rate. To determine genetic diversity and maternal inheritance, we collected 10 blood samples of Tes horses from Zavkhan, Mongolia. In this study, 8 haplotypes and 44 polymorphic sites were detected. Haplotype diversity was 0.9333 and nucleotide diversity was 0.0224. 4 haplogroups (A, C, F, I) were identified among 8 haplotypes.

scholarly journals MITOCHONDRIAL DNA STUDY OF MONGOLIAN EQUUS CABALLUS

2018 ◽  
pp. 77-86
Author(s):  
Bolor-Oyut B ◽  
Ochirkhuyag B ◽  
Khulan J
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Control Region ◽  
Nucleotide Diversity ◽  
Sequence Variation ◽  
Haplotype Diversity ◽  
Sequence Analyses ◽  
Mitochondrial Dna Control Region ◽  
Evolutionary Studies ◽  
High Level

In order to assess the genetic diversity and maternal lineages of Mongolian native horse populations, we examined using mitochondrial DNA control region sequence analyses. The control region of mitochondrial DNA is widely used for population and evolutionary studies because of its high level of sequence variation, in addition to a lack of recombination and maternal heritance. To determine genetic diversity and maternal heritance, we collected 19 blood samples of Darhad horses from Khuvsgul, Tes horses from Zavkhan and Taij horses from Dundgobi, Mongolia.In this study, 16 haplotypes and 51 polymorphic sites were detected. Haplotype diversity was 0.9766 and nucleotide diversity was 0.0212 in Mongolian native horses. Finally, 5 horse haplogroups (A, C, D, F, I) were identified in 16 haplotypes in this study.

scholarly journals Mitochondrial DNA control region diversity in Common Terns Sterna hirundo from Slovenia and Croatia

Acrocephalus ◽  
2019 ◽  
Vol 40 (180-181) ◽  
pp. 69-78
Author(s):  
Ida Svetličić ◽  
Jelena Kralj ◽  
Miloš Martinović ◽  
Davorin Tome ◽  
Tilen Basle ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Control Region ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Mitochondrial Control Region ◽  
Diversity Indices ◽  
Common Tern ◽  
Sterna Hirundo ◽  
Mitochondrial Dna Control Region ◽  
High Level

Abstract63 Common Tern Sterna hirundo samples from Croatia and Slovenia were analysed with respect to their genetic diversity and differentiation. Samples originated from two freshwater populations (areas of the rivers Sava and Drava) and one coastal population (Sečovlje Salina). The molecular marker of choice was 709 bp long fragment of the mitochondrial control region, the fastest-evolving part of the mitochondrial genome. 21 haplotypes with 12 polymorphic sites were identified. Overall haplotype diversity was substantial and estimated at 0.8599, while the overall nucleotide diversity was low and estimated at 0.0025. Diversity indices were highest for the Drava population, followed by the Sava and the lowest for the Sečovlje population. Overall genetic structure was significantly low (Fst=0.0377) and attributed to the differences in haplotype frequencies between the populations. The high level of genetic diversity found in continental populations illustrates the importance of their habitats as reservoirs of genetic diversity and calls for their further protection and management.

scholarly journals Polymorphisms of Mitochondrial COII and16S rRNA Gene in Meloidogyne enterolobii on Mulberry

2021 ◽  
Author(s):  
Hudie Shao ◽  
Pan Zhang ◽  
Chunping You ◽  
Chuanren LI ◽  
Yan Feng
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Nucleotide Diversity ◽  
Phylogenetic Analyses ◽  
Haplotype Diversity ◽  
Rrna Gene ◽  
Meloidogyne Enterolobii ◽  
High Level ◽  
Network Mapping ◽  
Cytochrome Oxidase Subunit Ii

Abstract This study explores the genetic diversity and polymorphisms of Meloidogdyne enterolobii (M enterolobii) on mulberry in China. The sequence of cytochrome oxidase subunit II (COII) and 16S rRNA gene in M enterolobii populations in Guangdong, Guangxi, and Hunan Provinces were PCR-amplified, sequenced, and analyzed for genetic diversity. The haplotypes (Hap) numbers, the total number of mutations, the average number of nucleotide differences (K), haplotype diversity (Hd), and nucleotide diversity (π) of mtCOII gene were 14, 25, 3.563, 0.942 and 0.00429, respectively. The significant differences in Fst value (0.125) and a high level of gene flow (2.83) were detected among the 19 M enterolobii populations. High genetic variation within each population and a small genetic distance among populations was observed. Both phylogenetic analyses and network mapping of the 14 haplotypes revealed a dispersed distribution pattern of the 19 M enterolobii populations. There was an absence of branches strictly corresponding to the 19 range sampling sites. The analysis of molecular variance (AMOVA) revealed that the genetic differentiation of M enterolobii populations was mainly contributed by the variation within each of the defined geographical groups. No significant correlation was found between the genetic distance and geographical distance of 19 M enterolobii populations. This study provides theoretical basis for the future control of M enterolobii and also provides a guarantee for the production of other hosts of M enterolobii.

scholarly journals Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene

2021 ◽  
Vol 22 (10) ◽  
Author(s):  
ABDUL BASITH ◽  
Abinawanto Abinawanto ◽  
ENI KUSRINI ◽  
YASMAN YASMAN
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Tree ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Phylogenetic Reconstruction ◽  
Partial Sequence ◽  
Diversity Analysis ◽  
Epinephelus Coioides ◽  
Substitution Model ◽  
Genetic Diversity Analysis

Abstract. Basith A, Abinawanto, Kusrini E, Yasman. 2021. Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene. Biodiversitas 22: 4282-4290. Groupers populations in Indonesia, particularly from Madura Island, East Java are indicated to be over-fished, thereby requiring data collection of more accurate genetic resources as an important step for grouper conservation. A total of 14 samples of the Epinepheplus groupers were obtained from the fish landing port on Madura Island. The 617 bp CO1 gene sequence was utilized for genetic diversity analysis and phylogenetic tree reconstruction. Genetic diversity is based on the value of haplotype diversity (Hd) and nucleotide diversity (?). Reconstruction of the phylogenetic tree includes neighbor-joining (NJ) implementing K2P substitution model, while maximum likelihood (ML) is conducted by implementing HKY+G+I substitution model, both of which were evaluated by employing a bootstrap of 1000 replications. Analysis of genetic distance between species indicated that the farthest distance between E. heniochus and E. fasciatus was 0.189, while the closest distance between E. erythrurus and E. ongus was 0.099. Intrapopulation genetic diversity indicated a high value with details of Hd=0.978 and ?=0.12107. Furthermore, NJ and ML phylogenetic tree demonstrated similar topology in the observed Epinephelus spp. obtained from Madura Island grouped into 7 clades, that is Epinephelus coioides, E. bleekeri, E. areolatus, E. erythrurus, E. heniochus, E. fasciatus, and E. ongus.

scholarly journals Genetic divergence in mitochondrial DNA of Anopheles nuneztovari (Diptera: Culicidae) from Brazil and Colombia

2000 ◽  
Vol 23 (1) ◽  
pp. 71-78 ◽  
Author(s):  
Vera Margarete Scarpassa ◽  
Silvia Geurgas ◽  
Ana Maria L. Azeredo-Espin ◽  
Wanderli Pedro Tadei
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Divergence ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Sequence Divergence ◽  
Brazilian Amazon ◽  
Restriction Endonucleases ◽  
Separate Species ◽  
Geographic Populations

In the present study, we have examined the variability in Anopheles nuneztovari mitochondrial DNA of three populations from the Brazilian Amazon and one from western Colombia (Sitronela), using four restriction endonucleases (BclI, ClaI, HindIII, SstI). The haplotype diversity (h) was slightly elevated in all populations (0.5000 to 0.6765), whereas the nucleotide diversity (pi) was lower in the Sitronela population (0.0029) and higher in populations from the Brazilian Amazon (0.0056 to 0.0098). The degree of sequence divergence (delta) estimated within the Brazilian Amazon and that in Sitronela (0.0329 to 0.0371) suggests that these geographic populations of A. nuneztovari may eventually constitute separate species. The low sequence divergence values among the three Brazilian Amazon populations (0.0012 to 0.0031) indicate that these populations are genetically similar. These results are consistent with those recently reported for allozymes of these same populations.

scholarly journals Genetic Diversity in the mtDNA control region and population structure of Chrysichthys nigrodigitatus from selected Nigerian rivers: Implications for conservation and aquaculture

2016 ◽  
Vol 24 (2) ◽  
pp. 85-97 ◽  
Author(s):  
Sylvanus A. Nwafili ◽  
Tian-Xiang Gao
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Control Region ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Recent Population Expansion ◽  
Base Pair Fragment ◽  
Population Structures ◽  
High Level

Abstract The genetic diversity and population structure of Chrysichthys nigrodigitatus were evaluated using a 443 base pair fragment of the mitochondrial control region. Among the eight populations collected comprising 129 individuals, a total of 89 polymorphic sites defined 57 distinct haplotypes. The mean haplotype diversity and nucleotide diversity of the eight populations were 0.966±0.006 and 0.0359±0.004, respectively. Analysis of molecular variance showed significant genetic differentiation among the eight populations (FST =0.34; P < 0.01). The present results revealed that C. nigrodigitatus populations had a high level of genetic diversity and distinct population structures. We report the existence of two monophyletic matrilineal lineages with mean genetic distance of 10.5% between them. Non-significant negative Tajima’s D and Fu’s Fs for more than half the populations suggests that the wild populations of C. nigrodigitatus underwent a recent population expansion, although a weak one since the late Pleistocene.

scholarly journals Keragaman genetik ikan lemuru (Sardinella lemuru) di wilayah perairan Indonesia

2020 ◽  
Vol 7 (1) ◽  
pp. 28
Author(s):  
I Gusti Ayu Diah Hendiari ◽  
Aida Sartimbul ◽  
I Wayan Arthana ◽  
Gde Raka Angga Kartika
Keyword(s):  
Genetic Diversity ◽  
Human Body ◽  
Value Of Information ◽  
Haplotype Diversity ◽  
High Rate ◽  
Fish Diversity ◽  
Omega 3 ◽  
Economic Values ◽  
High Level ◽  
High Diversity

Ikan Lemuru (Sardinella lemuru) merupakan komoditas perikanan pelagis yang sangat bernilai ekonomis dikalangan masyarakat Indonesia. Ikan Lemuru memiliki kelebihan yaitu keberadaannya yang berlimpah di perairan lau Indonesia, harganya yang sangat murah serta kandungan omega-3 yang sangat baik untuk tubuh. Kebutuhan akan ikan lemuru (Sardinella lemuru) yang tinggi menyebabkan tingginya angka penangkapan komoditas ini di perairain, sehingga dapat menyebabkan resiko penurunan jumlah populasi dialam. Pengelolaan yang tepat pada komoditas ini tentunya diperlukan akan dapat meminimalisir resiko yang dapat terjadi. Pengelolaan akan dapat terlaksana dengan tepat apabila berdasarkan atas data informasi yang memadai, salah satunya adalah informasi mengenai keragaman genetiknya. Kajian ini mengumpulkan pustaka dari penelitian terdahulu mengenai keragaman genetik ikan lemuru (Sardinella lemuru) di Wilayah Perairan Indonesia untuk dapat memberikan gambaran mengenai keragaman Ikan Lemuru dari segi genetiknya. Nilai keragaman genetik dilihat dari nilai keragaman haplotipe (Hd) karena keduanya memiliki kolerasi yang positif untuk menggambarkan keragaman genetik dari suatu komoditas. Hasil kajian memperlihatkan nilai keragaman genetik ikan lemuru (Sardinella lemuru) di Wilayah Perairan Indonesia memiliki nilai yang termasuk kategori tinggi. Hasil ini menggambarkan bahwa ditengah tingginya kegiatan penangkapan, ikan lemuru (Sardinella lemuru) secara genetik masih memiliki keragaman yang tinggi sehingga dimungkinkan komoditas Ikan Lemuru memiliki adaptasi yang tinggi terhadap kondisi lingkungan.Kata kunci: Sardinella lemuru, keragaman genetik, keragaman haplotipe Sardinella lemuru is pelagic commodities that have economic values for the Indonesian. S. lemuru has some of the major advantages, such as much population on Indonesian marine, low price, and has Omega-3 for the human body. The high demands of Lemuru Fish cause a high rate of cached, that can cause the risk of population degradation. Proper management of these commodities are needed to decrease the risk impact, that can be done rightly based on the equal value of information, and one of them is genetic diversity. This research compiles the recent researches about the genetic diversity of the Sardinella lemuru in Indonesian to get the explanation about Lemuru Fish diversity. The value of genetic diversity observed is based on the diversity value of Haplotype (Hd), because these two values have a positive correlation to make a whole representation from a commodity. The results of this review show that the genetic diversity of Lemuru Fish on Indonesian marine territorial has the high-value category. These results explain that in the high activities of fishing, Lemuru Fish genetically still have a high diversity that leads to the conclusion Lemuru Fish commodities has a high-level ability to adapt from environmental conditions.Keywords: Sardinella lemuru; genetic diversity; haplotype diversity 

scholarly journals Short Communication: Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences

2018 ◽  
Vol 20 (1) ◽  
pp. 17-22
Author(s):  
TETY HARTATIK ◽  
DWI NUR HAPPY HARIYONO ◽  
YUDI ADINATA
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Cytochrome B ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Cytochrome B Gene ◽  
Cyt B ◽  
Gene Sequences ◽  
Cattle Breeds ◽  
Cyt B Gene

Hartatik T, Hariyono DNH, Adinata Y. 2019. Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences. Biodiversitas 20: 17-22. Genetic diversity and phylogenetic relationships of two Indonesian local cattle breeds (Pasundan and Pacitan cattle) were investigated using mitochondrial DNA (mtDNA) cytochrome b (cyt b) gene analysis. Partial sequences of cyt b gene, 404 bp in length, were determined for 21 individuals from the two breeds. Genetic diversity of the breeds was assessed based on the number of polymorphic sites, number of haplotypes, haplotype diversity, nucleotide diversity and average number of differences. In addition, a neighbour-joining (NJ) haplotype tree was constructed based on Kimura’s two-parameter model. Among the two breeds, haplotype and nucleotide diversity of Pacitan cattle were the highest with values of 0.3778 and 0.00099, respectively. In contrast, Pasundan cattle had the lowest value for haplotype (0.1818) and nucleotide (0.00045) diversity. Four haplotypes (Hap_16, Hap_17, Hap_18 and Hap_19) were found across the two breeds and around 85.71% of investigated individuals were classified as Hap_16. Phylogenetic analysis with the inclusion of the cyt b sequences from 39 cattle breeds from Genbank database, showed that Indonesian cattle made a separated lineage together with Bos javanicus, B. bison, and B. bonasus. Pasundan and Pacitan cattle were considered from the same lineage based on haplotype distribution as well as phylogenetic analysis. This study may help the future researchers and livestock breeders for designing a breeding program based on a better understanding of the genetic diversity and history of local breeds.

scholarly journals Diversitas Genetika dan Identifikasi Jenis Kelamin Burung Pelikan (Pelecanus conspicillatus Temminck, 1824) di Penangkaran Taman Margasatwa Ragunan Jakarta

2021 ◽  
Vol 17 (2) ◽  
pp. 105-114
Author(s):  
Anik Budhi Dharmayanthi ◽  
Achmad Muchsinin ◽  
Afriana Pulungan ◽  
Moch Syamsul Arifin Zein
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Bird Populations ◽  
Low Genetic Diversity ◽  
In Captivity ◽  
D Loop ◽  
Haplotype 1

Pelicans (Pelecanus conspicillatus) is one of the wild species that have a widely distribution. This bird has been successfully bred in Ragunan Zoo, Jakarta. The indicator of inbreeding in the captive population is shown by the decrease of nucleotide diversity and number of haplotypes. The result of genetic diversity analysis using D-loop fragment sequences showed low genetic diversity with nucleotide diversity (p) = 0.00064 ± 0.00010 and haplotype diversity (Hd) = 0.532 ± 0.061 in Pelecanus conspicillatus populations in the Ragunan Zoo. However, negative Fu's Fs value (-3,246) indicates population expansion. We found that there were seven haplotypes in bird populations in the captivity: haplotype 1, 2 and 3 consist of 43 individuals (65.15%), five individuals (7.57%), and 14 individuals (21.21%), respectively. For each haplotype 4, 5, 6 and 7 is only represented by one individual of Pelecanus conspicillatus (1.51%). The sex ratio of males to females is 1: 8.86 with four males identified as haplotype 1, and one male on haplotypes 3, 5 and 7, respectively. Genetic diversity data of the population is an important way for designing long-term plans and goals in efforts to maintain genetic diversity of the Pelecanus conspicillatus population in captivity.

scholarly journals Phylogeography and Genetic Diversity of Humpback Grouper Cromileptes altivelis based on Cytochrome C Oxidase I

2012 ◽  
Vol 14 (1) ◽  
pp. 47
Author(s):  
Agus Hery Susanto ◽  
Agus Nuryanto ◽  
Petrus Hary Tjahja Soedibja
Keyword(s):  
Genetic Diversity ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Nucleotide Diversity ◽  
Asia Pacific ◽  
Cytochrome C Oxidase I ◽  
Base Pairs ◽  
High Gene ◽  
Fish Group ◽  
High Level

Humpback grouper is one of the most popular fish group in the international live trade in Asia-Pacific regions. The price for one kilogramlive of humpback grouper, especially in Spermonde Archipelago South of Sulawesi, is range from 350.000-400.000 IDR, whereas in theretail level in Hong Kong the price was about 92 US$. This condition leads to the reduction of nature population due to overexploitation.Population decreasing due to overexploitation may cause loss of genetic diversity within population and lead to reduce of potentialadaptive, population resistance, and productivity. Therefore, it is important to do some efforts to avoid adverse effect of overexploitationon humpback grouper population in Indonesia. One of the valuable efforts is providing genetic information such as phylogeography andgenetic diversity of humpback grouper Cromileptes altivelis. Analysis was based on 618 base pairs fragment of cytochrome c oxidase I genefrom 36 individuals (sequences) of Cromileptes altivelis collected at four different sites (e.g. Pulau Seribu, Jepara, Situbondo and SpermondeArchipelago). The results showed that humpback grouper population has a high haplotype and nucleotide diversity. However, high geneticdiversity and polymorphisms could not reveal population fragmentation (Φ stt = 0.000). It is suggested that high gene flow rather thanpopulation sub structuring was occurred. High level genetic diversity and polymorphisms are vital related to adaptive potential toenvironmental alteration.

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