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Tropical Genetics
Published by Genetikawan Muda Indonesia
ISSN : -     EISSN : 27984710     DOI : 10.24036/tg.v3i2.38
Core Subject : Agriculture,
Agriculture, Biological Sciences & Forestry
The scope of this journal is; Genetics Basics, Classical Genetics, Theoretical and Applied Genetics, Molecular Genetics, Cytogenetics, Bioinformatics, Genetic Diversity, Population Genetics, Genetic Engineering, Forensic Genetics, Behavioural Genetics, Advanced Genetics and Evolution, Clinical Genetics and Genetic Counselling Genomics, Biotechnology and Genetics Education.
Arjuna Subject : Ilmu Pertanian dan Biologi (Semua) - Ilmu Pertanian dan Biologi (Lain-Lain)
Articles 51 Documents
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Phylogenetic analysis in silico of orchid species Dendrobium based on rbcl marker Febriansyah, Muhammad; Mahfut
Tropical Genetics Vol. 4 No. 2 (2024): Genetics
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/tg.v4i2.68

Abstract

Dendrobium is one of the genera of the third largest Orchidaceae family which reaches about 1184 species in the world. In Indonesia, this genus of orchids is a wealth of genetic resources that are abundant in the Eastern region, such as Papua and Maluku. These genetic resources have not been optimally utilized as elders in crossbreeding to produce offspring that have characteristics according to what consumers want. Due to the limitations of these morphological characteristics, another character is needed that can support the systematics of orchids, namely molecular characters. Plant kinship analysis can use molecular characters in the form of DNA strands that can overcome the weaknesses of morphological data that are known to have limitations and tend to be influenced by the environment. This study aims to analyze the kinship of several types of Dendrobium based on the rbcL gene and add to the basic data source of germplasm from the genus Dendrobium. The samples used were nucleotide sequences of 11 nucleotide sequences consisting of 10 types of Dendrobium (D. anosmum, D. jinghuanum, D. catenatum, D. nobile, D. jenkinsii, D. pahangense, D. nobile, D. pulchellum, D. fimbriatum, and D. pulchellum) which is used as an in group and 1 species of the genus Phalaenopsis namely Phalaenopsis equestris which is used as an outgroup. The results of Dendrobium kinship analysis with an in silico based rbcL gene molecular approach show that species in the same genus are not necessarily closely related. The species that is a member of the out group is Phalaenopsis equestris,. Phalaenopsis equestris forms its own tree branches, while the other 10 species are on the same phylogeny tree branches.
Morphometric characterization and genetic distance of rabbits (Oryctolagus cuniculus) in several region in Indonesia Muhamad Sholichin; Arafah, Auliani; Razak, Abdul
Tropical Genetics Vol. 5 No. 1 (2025): Genetics
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/tg.v5i1.51

Abstract

Rabbits are a group of animals that are very popular and enjoyed by the community. Rabbits, in general, have the high biological and economic potential to produce quality meat, skin, and hair, as well as pets (ornamental) and modern business farming. Rabbits are well known in Indonesia and developed mostly for farming. This literature study discusses morphometric characteristics and genetic distances among rabbits. The parameters used were head length (PK), head width (LK), ear length (PTL), ear width (LTL), chest circumference (LKD), chest width (LD), humerus bone length (PH), radius-ulna bone length (PRU), tibial bone length (PT), and body length (PB). The results of body variables measurement in FG rabbits had a higher mean for body size, including PK (12.64 cm), PTL (13.59 cm), LTL (6.47 cm), PH (9.52 cm), PRU (8, 95 cm), and PB (41.97 cm) compared to other families. Genetic distance shows that it has a close genetic distance (0.63106), while the farthest genetic distance is found between Rexb rabbits and ES rabbits, which is 6.96749. The genetic distances and tree phenogram construction are useful for estimating kinship between Rabbits clumps.
Variasi fenotip cadel (disartria) pada populasi mahasiswa Biologi Fakultas Matematika dan Ilmu Pengetahuan Alam, Universitas Negeri Padang Hambali, Ahmad; Elviana, Alifah Hazelia; Achyar, Afifatul
Tropical Genetics Vol. 5 No. 1 (2025): Genetics
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/tg.v5i1.78

Abstract

Lisp (Dysarthria) is an abnormality in the nervous system that can affect the performance of the articulatory muscles or speech organs. The Hardy-Weinberg Law states that the frequency of genes in a population remains constant from one generation to the next if there are no evolutionary processes such as migration, mutation, natural selection and gene flow. This research aims to analyze the variation in the Lisp (Dysarthria) phenotype in the Biology Faculty student population. Mathematics and Natural Sciences, Padang State University. Data was obtained through an online questionnaire that identified the predominance of Lisp (Dysarthria) (Dysarthria or not Dysarthria). The results of the study showed that Lisp (Dysarthria) was found in a number of students in a proportion 10 people out of a total of 105 respondents. Analysis using the Hardy-Weinberg law shows that the frequency of dominant (p) and recessive (q) alleles. The frequency of the recessive allele (q) which causes the absence of lisp (dysarthria) is around 0.30, while the frequency of the dominant allele (P) is around 0 .7. Based on calculations, the estimated genotype proportions are 49% homozygous dominant (CC), 42% heterozygous (Cc), and 9.6% homozygous recessive (cc). These results indicate that the population of FMIPA UNP biology students is in Hardy-Weinberg equilibrium regarding the characteristic of lisp (dysarthria). Phenotypic variations of Lisp (Dysarthria) provide an overview of genetic diversity in the population environment of Biology students, Faculty of Mathematics and Natural Sciences, Padang State University and can be the basis for further research regarding the relationship between genetic factors and phenotypic expression in human populations. Keywords: Disartria, Phenotype, Variation, Student, Genetics. ABSTRAK Cadel (Disartria) merupakan kondisi kelainan pada sistem saraf yang dapat memengaruhi kinerja otot artikulator atau organ bicara. Hukum Hardy-Weinberg menyatakan frekuensi gen dalam suatu populasi tetap konstan dari satu generasi ke generasi berikutnya jika tidak ada proses evolusi seperti migrasi, mutasi, seleksi alam dan aliran gen.Penelitian ini bertujuan untuk menganalisis variasi fenotip Cadel (Disartria) pada populasi mahasiswa Biologi Fakultas Matematika dan Ilmu Pengetahuan Alam, Universitas Negeri Padang.Data diperoleh melalui kuisioner daring yang mengidentifikasi dominasi Cadel(Disartria) (Disartria atau tidak Disartria).Hasil penelitian menunjukkan bahwa Cadel (Disartria) ditemukan pada sejumlah mahasiswa dengan proporsi 10 orang dari jumlah total responden 105 orang. Analisis menggunakan hukum Hardy-Weinberg menunjukkan bahwa Frekuensi alel dominan (p) dan resesif (q).frekuensi alel resesif (q) yang menyebabkan tidak adanya Cadel (Disartria) adalah sekitar 0,30, sedangkan frekuensi alel dominan (P) adalah sekitar 0,7. Berdasarkan perhitungan, proporsi genotip yang diestimasi adalah 49% homozigot dominan (CC), 42% heterozigot (Cc), dan 9,6% homozigot resesif (cc). Hasil ini mengindikasikan bahwa populasi mahasiswa biologi FMIPA UNP berada dalam keseimbangan Hardy-Weinberg terkait sifat Cadel (Disartria) . Variasi fenotip Cadel (Disartria) memberikan gambaran keberagaman genetik di lingkungan populasi mahasiswa Biologi Fakultas Matematika dan Ilmu Pengetahuan Alam, Universitas Negeri Padang dan dapat menjadi dasar untuk penelitian lebih lanjut mengenai hubungan antara faktor genetik dan ekspresi fenotipik pada populasi manusia. Kata kunci: Disartria, Fenotip, Variasi, Mahasiswa, Genetika.
The ABO system blood group determination in genetics class: ABO system blood group determination in genetics class Ulandari, Eva Yasin; Maulina, Alfika Cahaya; Khimalaya, Anifia
Tropical Genetics Vol. 5 No. 1 (2025): Genetics
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/tg.v5i1.79

Abstract

This study aims to determine the blood type of genetics class students based on the ABO system. Blood type is a grouping of human blood based on the presence of agglutinogen on the surface of red blood cells and agglutinin in blood plasma. The activity was carried out in the laboratory of the Faculty of Tarbiyah and Teacher Training, Sulthan Thaha Saifuddin State Islamic University of Jambi, using the slide test method using Anti-A, Anti-B, and Anti-AB reagents. The results of the observation showed that the majority of students had blood type O (63%), while blood types A (18%), B (9%), and AB (9%). This examination utilizes the principle of agglutination, where a clotting reaction occurs if agglutinogen on red blood cells reacts with the relevant agglutinin in the reagent. Determination of blood type is very important for blood transfusions, organ transplants, and medical identification. This study provides students with a practical understanding of the blood type examination procedure and its significance in the health sector.
Variasi Fenotip Lesung Pipit pada Populasi Mahasiswa Biologi Fakultas Matematika dan Ilmu Pengetahuan Alam, Universitas Negeri Padang Ara, Farrah Azzahra; Suryani, Elisa; Achyar, Afifatul
Tropical Genetics Vol. 5 No. 1 (2025): Genetics
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/tg.v5i1.80

Abstract

Lesung pipi merupakan salah satu variasi fenotip yang mudah diamati pada manusia dan dipengaruhi oleh faktor genetik serta non-genetik. Penelitian ini bertujuan untuk menganalisis variasi fenotip lesung pipit pada populasi mahasiswa Biologi Fakultas Matematika dan Ilmu Pengetahuan Alam, Universitas Negeri Padang. Metode penelitian ini bersifat deskriptif dengan pendekatan survei. Data dikumpulkan melalui pengamatan langsung dan pencatatan karakteristik lesung pipit, meliputi keberadaannya. Hasil penelitian menunjukkan bahwa lesung pipit ditemukan pada sejumlah mahasiswa dengan proporsi 25 orang dari jumlah total responden 105 orang. Analisis menggunakan hukum Hardy-Weinberg menunjukkan bahwa frekuensi alel resesif (d) yang menyebabkan tidak adanya lesung pipi adalah sekitar 0,48, sedangkan frekuensi alel dominan (D) adalah sekitar 0,52. Berdasarkan perhitungan, proporsi genotip yang diestimasi adalah 27,04% homozigot dominan (DD), 49,92% heterozigot (Dd), dan 23,04% homozigot resesif (dd). Hasil ini mengindikasikan bahwa populasi mahasiswa biologi FMIPA UNP berada dalam kesetimbangan Hardy-Weinberg terkait sifat lesung pipi. Variasi fenotip lesung pipit memberikan gambaran keberagaman genetik di lingkungan populasi mahasiswa Biologi Fakultas Matematika dan Ilmu Pengetahuan Alam, Universitas Negeri Padang dan dapat menjadi dasar untuk penelitian lebih lanjut mengenai hubungan antara faktor genetik dan ekspresi fenotipik pada populasi manusia.
Literature review on the genetic variability of Escherichia coli in clinical isolates: relationship with antibiotic resistance and virulence factors Rum, Magfirah Rahimah; Muthiadin, Cut
Tropical Genetics Vol. 5 No. 1 (2025): Genetics
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/tg.v5i1.82

Abstract

Escherichia coli is a natural flora found in the intestine, but Escherichia coli is also a major repository of resistance genes that may be responsible for treatment failure in humans and animals. This study aims to understand and evaluate the genetic variability of Escherichia coli in clinical isolates and to determine the correlation between genetic variability and antibiotic resistance. This study uses a literature review method. This study presents the results of a search for studies related to the topic, namely the genetic variability of Escherichia coli in clinical isolates and the relationship with antibiotic resistance and virulence factors. The criteria for articles used as data are articles published in the last 10 years, namely from 2015 to 2025. Based on the research that has been done, it can be concluded that genetic variability in Escherichia coli in clinical isolates plays an important role in adaptation, pathogenicity, and antibiotic resistance. Mechanisms such as horizontal gene transfer (HGT), mutations, and genome rearrangements allow E. coli to acquire virulence genes and antibiotic resistance genes, such as genes encoding extended-spectrum β-lactamases (ESBLs) including TEM, SHV, and CTX-M. These genes are often located on mobile plasmids, which support the spread of resistance between bacterial strains and species, complicating infection control and clinical treatment.
In Silico Analysis of Non-synonymous Mutations in the durA Gene and Their Effects on the Stability and Physicochemical Properties of Duramycin Ade Prasetya, Yulianto; Kok, Tjie; Wahjudi, Mariana
Tropical Genetics Vol. 5 No. 2 (2025): Genetics
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/tg.v5i2.84

Abstract

Duramycin is a lantibiotic peptide encoded by the durA gene, known for its antimicrobial activity against Gram-positive bacteria. This study aimed to evaluate the effects of single-point mutations on the stability and structural integrity of duramycin using a comprehensive in silico approach. Five variants—C1S, F7A, T11Y, D15E, and K19V—were designed and assessed using I-Mutant2.0 to predict their impact on protein stability. ProtParam analysis was conducted to determine molecular weight, isoelectric point (pI), net charge at pH 7, instability index, aliphatic index, and hydropathicity (GRAVY). In addition, PEP-FOLD3 was employed to model the 3D conformations of each mutant peptide. Results showed that K19V improved peptide stability and increased aliphatic index and GRAVY score, indicating enhanced hydrophobicity and potential thermal stability. In contrast, F7A led to a major structural shift marked by an α-helical conformation and reduced stability. C1S and T11Y induced minor destabilizing effects, while D15E offered a moderately stabilizing substitution with minimal structural deviation. Overall, this study highlights the functional relevance of C-terminal and hydrophobic residues in maintaining duramycin’s structural compactness and provides a framework for future design of optimized antimicrobial peptides through rational mutation
Genetic Diversity and Relationships of Dendrobium Based on TrnL-F Markers: An Approach In-silico Ismail, Ikhwan; Mahfut, Mahfut
Tropical Genetics Vol. 5 No. 2 (2025): Genetics
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/tg.v5i2.87

Abstract

The development of DNA sequencing technologies has deepened our understanding of genetic variation within Dendrobium species and revealed evolutionary relationships among them. in-silico methods facilitate efficient phylogenetic determination, leveraging computational advantages to process sequence data with high accuracy. This study aims to significantly contribute to the understanding of genetic diversity within the genus Dendrobium based on the TrnL-F marker, with potential implications for the conservation and management of these plant genetic resourcesThis paper presents nucleotide diversity analysis and phylogenetic analysis to determine the kinship relationships among Dendrobium species. The analysis revealed a high degree of relatedness among the Dendrobium species, with kinship relationships dividing them into three distinct groups.
Phylogenetic and Genetic Distance Analysis of the Mangrove Worm (Namalycastis) Based on the 18S rRNA Gene Using in Silico Methods Aditya, Arielda Putri; Aditya, Junardi; Candramila, Wolly; Prabasari, Kartika
Tropical Genetics Vol. 5 No. 2 (2025): Genetics
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/tg.v5i2.100

Abstract

Namalycastis is a polychaete worm that inhabits dynamic aquatic environments and exhibits high genetic and morphological variability. This study investigates the phylogeny of the genus Namalycastis through an in silico analysis using the 18S ribosomal RNA (rRNA) gene. This genetic marker is considered ideal as it combines conserved and variable regions, both essential for taxonomic and evolutionary analyses. The objective of this research was to examine the phylogenetic relationships and genetic distances among 12 species of the genus Namalycastis based on their 18S rRNA gene sequences. DNA sequences were obtained from the NCBI database and aligned using Clustal-W in MEGA XI software. Phylogenetic reconstruction was performed using the Neighbor-Joining method with 1000 bootstrap replications, applying the Kimura 2-Parameter (K2P) model. The results revealed that Namalycastis jaya shares a very close evolutionary relationship with Namalycastis abiuma, forming a monophyletic clade that is distinct from Namalycastis hawaiiensis. The genetic distances among N. jaya, N. abiuma, and N. abiuma group sp. indicate a close evolutionary affinity, whereas N. hawaiiensis displays greater genetic divergence from the other two species. Overall, this study demonstrates that the 18S rRNA gene is an effective molecular marker for identifying phylogenetic relationships among Namalycastis species. The findings also highlight the potential of in silico methods in elucidating evolutionary patterns within the genus Namalycastis.
Analisis Filogenetik Bakteri Escherichia coli Berdasarkan DNA Genomik Gen BlaTEM Dari Data Sekuens NCBI: Pendekatan Bioinformatika terhadap Variasi Gen BlaTEM pada Escherichia coli Tahun 2016–2025 Palupi, Indria; Achyar, Afifatul
Tropical Genetics Vol. 5 No. 2 (2025): Genetics
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/tg.v5i2.102

Abstract

Resistensi antibiotik yang disebabkan oleh bakteri penghasil β-laktamase, seperti Escherichia coli, menjadi permasalahan global yang serius. Gen blaTEM merupakan salah satu gen utama yang berkontribusi terhadap resistensi tersebut. Penelitian ini bertujuan untuk menganalisis hubungan filogenetik antar isolat Escherichia coli berdasarkan sekuens DNA gen blaTEM yang diambil dari database NCBI dalam rentang waktu 2016 hingga 2025. Data sekuens diselaraskan menggunakan metode ClustalW dalam perangkat lunak MEGA X, kemudian dianalisis menggunakan metode Neighbor-Joining dan 1000 bootstrap. Hasil analisis menunjukkan pembentukan beberapa klade utama dengan tingkat kedekatan genetik yang bervariasi. Kelompok isolat tahun 2021–2024 memiliki kedekatan genetik tinggi, sedangkan isolat tahun 2020 dan 2025 menunjukkan divergensi yang signifikan. Temuan ini mengindikasikan adanya variasi evolusioner dalam gen blaTEM yang penting untuk dipantau sebagai bagian dari strategi pengendalian resistensi antibiotik.

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