scholarly journals Molecular Characteristics of Batanghari, Tambago, Orange, and Mandiangin Giant Gourami Strains

2017 ◽  
Vol 9 (3) ◽  
pp. 592
Author(s):  
Agus Nuryanto ◽  
Anatasia Endang Pulungsari
Keyword(s):  
Cytochrome B ◽  
Nucleotide Diversity ◽  
Taxonomic Status ◽  
Single Species ◽  
Genetic Distances ◽  
Cytochrome B Gene ◽  
Molecular Characteristics ◽  
Neighbor Joining ◽  
Morphological Variations ◽  
Genetic Structures

<p class="IsiAbstrakIndo"><span lang="EN-GB">Morphological variations among geographic and can be identified as different species. However, a lot of studies proved that morphological variations are also common in conspecific individuals. Therefore, precise identification using additional characters is vital, such as using a molecular marker. Here, we characterized Batanghari, Tambago, Orange, and Mandiangin gourami strains using the cytochrome b gene to evaluate their taxonomic status. Partial sequences of cytochrome b gene were sequenced for 40 individuals. Taxonomic status was checked for giant gourami sequences available in GenBank. Kimura 2-Parameter genetic distances were calculated in MEGA6 software. Haplotype and nucleotide diversity within population and </span><span lang="EN-GB">Φ</span><sub><span lang="EN-GB">st</span></sub><span lang="EN-GB">-value among populations were estimated in Arlequin software. Phylogenetic relationship was reconstructed using the neighbor-joining method in MEGA6 software based on Kimura 2-parameter model with 1000 pseudobootstraps. Taxonomic identification results in 99% sequences homology to </span><em><span lang="EN-GB">Osphronemus goramy</span></em><span lang="EN-GB"> sequences (accession number KU984978.1 and AY763768.1), means that all strains belong to single species. Low genetic distances, medium haplotype and low-level nucleotide diversity were observed among strains. Pairwise </span><span lang="EN-GB">Φ</span><sub><span lang="EN-GB">st</span></sub><span lang="EN-GB">-comparison indicates no genetic differences among Sumatera strain, whereas strong genetic structures observed between Sumatera and Mandiangin strains. The phylogenetic tree showed that Mandiangin formed separate subclades from other strains with bootstraps value of 100%. This finding has important implication for breeding sciences and efforts.</span></p>

Study on the origin and taxonomic status of yak (Poephagus) using cytochrome b gene of mitochondrial DNA

2007 ◽  
Vol 1 (3) ◽  
pp. 329-333 ◽  
Author(s):  
Qifa Li ◽  
Yinxia Li ◽  
Xingbo Zhao ◽  
Zhenshan Liu ◽  
Yefen Xu ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Cytochrome B ◽  
Taxonomic Status ◽  
Cytochrome B Gene

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 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 Cryptic species and genetic structure in Didemnum granulatum Tokioka, 1954 (Tunicata: Ascidiacea) from the southern Brazilian coast

2014 ◽  
Vol 74 (4) ◽  
pp. 923-932 ◽  
Author(s):  
JL Bouzon ◽  
SM Vargas ◽  
JF Oliveira Neto ◽  
PH Stoco ◽  
FP Brandini
Keyword(s):  
Spatial Distribution ◽  
Genetic Structure ◽  
Cryptic Species ◽  
Nucleotide Diversity ◽  
Mitochondrial Gene ◽  
Haplotype Diversity ◽  
Single Species ◽  
Brazilian Coast ◽  
Neighbor Joining ◽  
Haplotype Networks

Didemnum granulatum is a colonial fouling ascidian that lives in subtidal substrates, worldwide. It exhibits two morphotypes, orange and beige. In this study, we verified if the color morphotypes and/or the spatial distribution of specimens in different islands might be associated to patterns of genetic structure of a single species, or if they represent distinct cryptic species. Specimens were collected in four islands, along the coast of the Santa Catarina state. A segment of 490 bp from the mitochondrial gene cytochrome c oxidase subunit 1 (COI) was amplified from 45 samples. Twenty-one haplotypes were identified. The total haplotype diversity (0.912) and the total nucleotide diversity (0.044) were high. The global Fst of the populations analyzed was 0.97, with most of the variation occurring between orange and beige groups (82.19%). The variation found between populations within groups was 15.37%, and 2.45% within populations. Haplotype networks and the neighbor-joining tree showed clear genetic divergence between individuals of distinct colors, and between the islands. These evidences strongly support the presence of a complex of two cryptic species for D. granulatum occupying the studied area. Both species were also highly genetically structured between islands, suggesting that the conservation process of these populations is complex.

Metacercarial polymorphism and genetic variation of Paragonimus heterotremus (Digenea: Paragonimidae), and a re-appraisal of the taxonomic status of Paragonimus pseudoheterotremus

2013 ◽  
Vol 89 (2) ◽  
pp. 182-188 ◽  
Author(s):  
P.N. Doanh ◽  
U. Thaenkham ◽  
P.T. An ◽  
H.V. Hien ◽  
Y. Horii ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Taxonomic Status ◽  
Haplotype Network ◽  
Genetic Distances ◽  
Maximum Diameter ◽  
Molecular Characteristics ◽  
Extensive Collection ◽  
Different Populations ◽  
A New Species ◽  
India And China

AbstractParagonimus heterotremus, which is an important pathogen for human paragonimiasis in Asia, is recognized as having the smallest metacercariae (maximum diameter < 300 μm) of any previously reported Paragonimus species. Recently, P. pseudoheterotremus has been described from Thailand as a new species having metacercariae (about 200 μm) slightly smaller than those of Thai P. heterotremus. In fact, the small size of P. pseudoheterotremus metacercariae is compatible with those of P. heterotremus from India and China. In this study in Vietnam, we found variably sized small metacercariae which are expected to consist of both P. heterotremus and P. pseudoheterotremus. Contrary to expectation, the adult flukes obtained by separate infection of experimental cats with different sized metacercariae were all identified as P. heterotremus, using both morphological and molecular characteristics. The molecular analyses of an extensive collection of P. heterotremus/P. pseudoheterotremus isolates from Asian countries also indicated that genetic distances between different populations of P. heterotremus are even larger than that between P. pseudoheterotremus and P. heterotremus. The haplotype network showed that all P. heterotremus and P. pseudoheterotremus isolates formed a P. heterotremus complex consisting of three groups with strong geographical origins. In addition, the Indian P. heterotremus group is the root of the other P. heterotremus and P. pseudoheterotremus populations. Based on the observed metacercarial polymorphisms and genetic variation in P. heterotremus,P. pseudoheterotremus should be considered a geographically isolated population of the P. heterotremus complex.

scholarly journals Genetic diversity and taxonomic status of Gymnocypris chilianensis based on the mitochondrial DNA cytochrome b gene

2015 ◽  
Vol 14 (3) ◽  
pp. 9253-9260 ◽  
Author(s):  
J.P. Zhang ◽  
Z. Liu ◽  
B. Zhang ◽  
X.Y. Yin ◽  
L. Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Cytochrome B ◽  
Taxonomic Status ◽  
Cytochrome B Gene

scholarly journals Xerophilic fungal genus Wallemia: Bioactive inhabitants of marine solar salterns and salty food

2011 ◽  
pp. 7-18 ◽  
Author(s):  
Janja Zajc ◽  
Polona Zalar ◽  
Kristina Sepcic ◽  
Nina Gunde-Cimerman
Keyword(s):  
Water Activity ◽  
Molecular Mechanisms ◽  
Taxonomic Status ◽  
Single Species ◽  
Ecological Niches ◽  
Molecular Characteristics ◽  
Food Spoilage ◽  
Salty Food ◽  
Wallemia Sebi ◽  
Bioactive Potential

Wallemia is a genus of cosmopolitan xerophilic fungi, frequently involved in food spoilage of particularly sweet, salty, and dried food. Until recently, only a single species, Wallemia sebi, was recognized in the genus. When a large group of strains globally collected in salterns and other different ecological niches was analyzed on the level of physiological, morphological and molecular characteristics, a new basidiomycetous class, Wallemiomycetes, covering an order of Wallemiales was proposed and three Wallemia species were recognized: W. ichthyophaga, W. sebi and W. muriae. Wallemia ichthyophaga was recognized as the most halophilic eukaryote known, thus representing an appropriate eukaryotic model for in depth studies of adaptation to hypersaline conditions. Our preliminary studies indicated that all three Wallemia species synthesized a yet undescribed haemolytic compound under, surprisingly, low water activity conditions. Due to the taxonomic status w hich was unrevealed only recently, there were so far no reports on the production of any bioactive compounds by the three newly described species. The article aims to present the taxonomy, ecology, physiology and so far described molecular mechanisms of adaptations to life at low water activity, as well as bioactive potential of the genus Wallemia, a phylogenetically ancient taxon and a taxonomic maverick within Basidiomycota.

scholarly journals Molecular Barcoding Reveal the Existence of Mole Crabs Emerita emeritus in North Coast of Central Java

2020 ◽  
Vol 12 (1) ◽  
pp. 104-110
Author(s):  
Dian Bhagawati ◽  
Elly Tuti Winarni ◽  
Agus Nuryanto
Keyword(s):  
Sustainable Use ◽  
Taxonomic Status ◽  
Single Species ◽  
First Record ◽  
Genetic Distances ◽  
North Coast ◽  
Local Alignment ◽  
Northern Coast ◽  
Molecular Barcoding ◽  
Central Java

The existence of mole crabs had been reported from the southern coast of Central Java. However, no mole crab data was available from the northern coast Central Java.  This study aimed to figure out the existence of mole crabs in the northern coast of Central Java as revealed from the cytochrome c oxidase 1 (COI) barcoding. Mole crabs samples collected in Sendang Sikucing Beach Kendal. Taxonomic status of the samples was inferred from sequences similarity test using basic local alignment search tool to conspecific sequence deposited in GenBank. Pairwise genetic distances were calculated based on the Kimura 2-parameter model. A phylogenetic tree had reconstructed in molecular evolution genetic analysis (MEGA) software based on neighbor-joining algorithm. Branching reliability was obtained from 1000 bootstraps replication while branching polarity was obtained from the out-group comparison. The mole crab samples from the northern coast of Central Java had unambiguously identified as Emerita emeritus based on high sequences similarities (98.27%-99.70%), low genetic distances (0.002-0.005), and their monophyly with Emerita emeritus (KR047035) in GenBank. Pairwise analysis among each possibility pair of samples had genetic distances ranged between 0.000 and 0.005, indicated that all sample belong to single species. The data provide the first record of the existence of Emerita emeritus in the northern coast of Central Java. Our data on the existence of E. emeritus in the northern coast of Central Java is among essentials information as a scientific basis in creating policy for the management of sustainable use of the mole crabs in the areas.

Sign in / Sign up

Export Citation Format

Share Document