scholarly journals Genetic structure and phylogenetic relationships of Phyllidiellapustulosa species from Seribu Islands, North Sulawesi, Halmahera, and West Papua

2021 ◽  
Vol 944 (1) ◽  
pp. 012028
Author(s):  
N O Yonatika ◽  
N Widiasih ◽  
M Hamidah ◽  
M D Nurhakim ◽  
H Budiarto ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Genetic Distance ◽  
Dna Sequence ◽  
Maximum Likelihood Method ◽  
Likelihood Method ◽  
Neighbor Joining ◽  
Tree Reconstruction ◽  
Genetic Characteristics ◽  
North Sulawesi ◽  
West Papua

Abstract Phyllidiella pustulosa are brightly coloured gastropod molluscs frequently found in coral reefs of the tropical Indo-Pacific. Phyllidiella pustulosa is widely distributed in Indonesia, such as Seribu Island, North Sulawesi, West Papua, and Halmahera. Based on the genetic characteristics of an individual’s DNA sequence, differences between species can be identified. In this paper, we would like to provide the molecular analysis and phylogenetic relationship among nudibranchs from Indonesian waters. Identification was made by measuring the genetic distance between species. The phylogenetic tree reconstruction was made using the Kimura 2-parameter model with 1000 times bootstrap with neighbor-joining and maximum likelihood method. There is 46 DNA Sequence obtained from 4 different regions (Seribu Island, Halmahera, North Sulawesi, and West Papua). The genetic distance of West Papua and Halmahera has the smallest value among other populations, which is between 0.0051-1.4629, compared to the population in Halmahera. The phylogenetic tree also shows populations from West Papua and Halmahera are on the same lineage, indicating that the population in West Papua and Halmahera had the closest relation. The study suggested that North Sulawesi, Halmahera and West Papua have genetic mixing of the same region, which is distinctive from Seribu Island.

scholarly journals S-D614G Mutation Reveals the Euro-America and East-Asia Origin SARS-CoV-2 Virus Spread in Indonesia

2021 ◽  
Vol 3 (2) ◽  
pp. 45-53
Author(s):  
Nina Bunga Anggraini ◽  
Dwi Listyorini
Keyword(s):  
Phylogenetic Tree ◽  
East Asia ◽  
Neighbor Joining ◽  
Control Sequence ◽  
Tree Reconstruction ◽  
Spike Gene ◽  
Phylogenetic Tree Reconstruction ◽  
First Case ◽  
Multiple Alignments ◽  
The City

COVID-19 is a pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The first case was found in the city of Wuhan, Hubei province, China. The first case in Indonesia was reported in March 2020 and currently there are 0.5 million cases with a death rate of 3.1%. This rapid increase in cases is thought to due to presence of the mutant strain S-D614G, which causes a faster rate of infection and spread. The purpose of this study was to determine the presence of S-D614G mutations in Indonesian samples in order to find the origin of COVID-19 which was spread in Indonesia based on the Spike gene sequences and the RdRp genes from 25 countries, and one control sequence China/Wuhan-Hu-1 obtained from the NCBI and GISAID databases. Mutation analysis was carried out through multiple alignments using BioEdit software. Phylogenetic tree reconstruction using MEGA6 software with the Neighbor Joining method. This study found mutation of S-D614G in one Indonesian sample, namely the Indonesian/SBY9 sample along with 23 samples from Europe, America, and Africa. The phylogenetic tree reconstruction confirmed these findings; the mutated samples were closely related to samples from these continents, while the non-mutated Indonesian samples were closely related to sample from East Asia. These findings indicate that the origin of the SARS-CoV-2 virus in Indonesia possibly came from the East Asia cluster and the European-American cluster.

scholarly journals Molecular characterization based on chloroplast (trnl-f) DNA sequence of the apple genotypes in Ardahan/Turkey

2019 ◽  
Vol 48 (4) ◽  
pp. 1099-1106
Author(s):  
Emre Sevindik ◽  
Zehra Tuğba Murathan ◽  
Sümeyye Filiz ◽  
Kübra Yalçin
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Tree ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Nucleotide Composition ◽  
Neighbor Joining ◽  
Sequencing Data ◽  
F Region ◽  
Phylogenetic Studies

Genetic diversity among Turkish apple genotypes in Ardahan province was conducted based on cpDNA trnL-F sequences. Apple genotypes were plotted on a phylogenetic tree where Pyrus x bretschneideri was used as the outgroup. The plant samples were collected from different locations and genomic DNA was isolated from healthy and green leaves. For sequence in trnL-F region trnLe and trnFf primers were used. Later obtained DNA sequences were edited using the BioEdit and FinchTV. Sequencing data were analyzed using MEGA 6.0 software. Neighbor joining and bootstrap trees were constructed in order to verify the relationships among the apple genotypes. Phylogenetic tree consisted of two clades. The divergence values of trnL-F sequences differed between 0.000 and 0.005. Average nucleotide composition was 38.3 T, 14.9 C, 31.9 A and 14.9% G. The phylogenetic tree constructed based on trnL-F region sequences was nearly parallel to prior phylogenetic studies on apple genotypes.

scholarly journals Cryptosporidium in asymptomatic children in Southern Xinjiang, China and the potential of zoonotic transmission

2021 ◽  
Author(s):  
Tian Wang ◽  
Zilin Wei ◽  
Ying Zhang ◽  
Qiyuan Zhang ◽  
Longxian Zhang ◽  
...  
Keyword(s):  
Infection Rate ◽  
Maximum Likelihood Method ◽  
Genetic Characterization ◽  
Pcr Amplification ◽  
Likelihood Method ◽  
Limited Information ◽  
Genetic Characteristics ◽  
Asymptomatic Children ◽  
Southern Xinjiang

Abstract Background: Cryptosporidium is a primary cause of diarrhea in children globally. However, there is limited information on the prevalence and genetic characterization of Cryptosporidium in children in Xinjiang, China. This study aimed to assess the genetic characteristics and epidemiological status of Cryptosporidium in asymptomatic children in Southern Xinjiang, China.Methods: A total of 609 fecal samples were collected from kindergartners aged 2-6 y from 11 counties of Southern Xinjiang, China. We used nested PCR amplification of partial SSU rDNA gene to screen the samples for Cryptosporidium spp. The isolates containing C. parvum and C. hominis were further subtyped by a 60-kDa glycoprotein (gp60). We used MEGA7 to construct a phylogenetic tree to study the genetic relationship between the gp60 subtypes of these two species via the Maximum Likelihood method based on the Tamura-Nei model.Results: Only 1.3% (8/609) of asymptomatic children were confirmed as infected with Cryptosporidium with 2.0% (6/299) infection rate in boys and 0.6% (2/310) infection rate in girls. Three Cryptosporidium species were identified including C. felis (37.5%; 3/8), C. hominis (37.5%; 3/8) and C. parvum (25.0%; 2/8). Three C. hominis subtypes (IbA9G3, IdA14 and IfA12G1) and two C. parvum subtypes (IIdA14G1 and IIdA15G1) were also found.Conclusions: This study was the first to identify the presence of cryptosporidium in asymptomatic children in Southern Xinjiang, China. The presence of zoonotic C. parvum subtypes IIdA14G1 and IIdA15G1 indicates possible crossspecies transmission of Cryptosporidium between children and animals.

scholarly journals Genetic similarities and phylogenetic analysis of Muntjac (Muntiacus spp.) by comparing the nucleotide sequence of 16S rRNA and cytochrome B genome

2023 ◽  
Vol 83 ◽  
Author(s):  
B. M. Khan ◽  
M. Sabir ◽  
M. N. Alyemeni ◽  
P. Kaushik ◽  
M. Saeed ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
16S Rrna ◽  
Phylogenetic Tree ◽  
Cytochrome B ◽  
Maximum Likelihood Method ◽  
Nucleotide Sequences ◽  
Likelihood Method ◽  
Rrna Gene ◽  
B Genome ◽  
The One

Abstract This study aimed to identify the phylogenetic similarities among the muntjac (Muntiacus spp.). The phylogenetic similarities among seven major muntjac species were studied by comparing the nucleotide sequence of 16s rRNA and cytochrome b genome. Nucleotide sequences, retrieved from NCBI databases were aligned by using DNASTAR software. A phylogenetic tree was created for the selected species of muntjac by using the maximum likelihood method on MEGA7 software. The results of nucleotide sequences (16s rRNA) showed phylogenetic similarities between, the M. truongsonensis and M. rooseveltorum had the highest (99.2%) while the lowest similarities (96.8%) found between M. crinifrons and M. putaoensi. While the results of nucleotide sequences (Cty b) showed the highest similarity (100%) between M. muntjak and M. truongsonensis and the lowest s (91.5%) among M. putaoensis and M. crinifrons. The phylogenetic tree of muntjac species (16s rRNA gene) shows the main two clusters, the one including M. putaoensis, M. truongsonensis, M. rooseveltorum, and M. muntjak, and the second one including M. crinifrons and M. vuquangensis. The M. reevesi exists separately in the phylogenetic tree. The phylogenetic tree of muntjac species using cytochrome b genes shows that the M. muntjak and M. truongsonensis are clustered in the same group.

scholarly journals Characteristic of the 2010-2020 Earthquakes in North Arm of Sulawesi based on Focal Mechanism and b-value

2021 ◽  
Vol 873 (1) ◽  
pp. 012031
Author(s):  
A P Astuti ◽  
E M Elsera ◽  
M F I Massinai ◽  
M A Akbar
Keyword(s):  
Focal Mechanism ◽  
Subduction Zones ◽  
Maximum Likelihood Method ◽  
B Value ◽  
Strike Slip ◽  
Likelihood Method ◽  
B Values ◽  
The North ◽  
North Sulawesi ◽  
High Level

Abstract The north arm of Sulawesi has a fairly high level of seismicity. The North Sulawesi arm is bounded in the south by the Palu-Koro Fault, the northern part is bounded by the North Sulawesi Trench and the Molluca Sea Thrust in the east. Therefore, this study aims to analyze the characteristic of the 2010-2020 earthquakes in the north arm of Sulawesi by analyzing the earthquake’s focal mechanism and mapping the b-value using the maximum likelihood method. From this study, we obtained the focal mechanism consist of thrust and strike-slip, this is due to the activity of faults and subduction zones in the North arm of Sulawesi such as the Palu-koro fault, the Gorontalo Fault, North Sulawesi Trench, Molucca Sea Collision, and several other faults that affect the seismicity of this region. The variation of the b-value ranging from 0.5-1.1 These studies indicate that thrust fault regions have lower b-values, while strike-slip fault regions have intermediate b-values. Meanwhile, areas with active volcanoes tend to have high b-values. The results of this research can be used as a basis for decision making related to earthquake mitigation in this area in the future.

scholarly journals Genetic characteristic of giant featherback, Chitala lopis (Bleeker, 1851) from Lampung and Kalimantan using COI Gene

2021 ◽  
Vol 21 (1) ◽  
pp. 49-60
Author(s):  
Alam Putra Persada Putra Persada ◽  
Dedy Duryadi Solihin ◽  
Ridwan Affandi
Keyword(s):  
Phylogenetic Tree ◽  
Genetic Distance ◽  
Coi Gene ◽  
Nucleotide Polymorphism ◽  
Genetic Characteristic ◽  
The South ◽  
Tree Reconstruction ◽  
Single Nucleotide ◽  
West Kalimantan ◽  
Two Parameter

DNA barcoding based on partial Cytochrome Oxidase subunit I (COI) gene in the mitochondrial has widely used in species identification and biodiversity studies. COI gene application is expected to obtain genetic characteristic, genetic variations and phylogeny of giant featherback. The aim of this research was to analyze genetic diversity of giant featherback Chitala lopis in Lampung and Kalimantan. To analyse genetic distance, Kimura two parameter (K2P) model was performed where to determine nucleotide variation & polymorphism and also reconstructed of phylogenetic tree was used MEGA 7.0 software. Total nine individuals were obtained from three populations, i.e. Lampung, West Kalimantan and South Kalimantan. The results showed that giant featherback has 689 bp conserve, 18 bp variation, 13 bp parsimony-informative, and 2 bp singleton sites from 707 bp COI partial gene. The average within-species, in-group, and out-group based on K2P distances were 1.24%, 1.43% & 1.58% (AP008922.1; KM213054.1), and 13.00% respectively. The Single Nucleotide Polymorphism (SNP) was obtaining from 13 SNP sites. West Kalimantan samples have two SNP (471 and 528 site). The South Kalimantan samples showed more specific nucleotides with nine SNP (120, 129, 144, 201, 306, 324, 474, 615 and 644). Based on genetic distance, the biggest difference was in the South Kalimantan sample (1.58%) compared with Lampung and West Kalimantan. The results of the K2P neighbour-joining phylogenetic tree reconstruction show that the South Kalimantan samples are in a different group. The West Kalimantan sample shows that it is closely related to the Lampung.

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