Molecular Characterization of Indonesian Indigenous Chickens based on Mitochondrial DNA Displacement (D)-loop Sequences

The Mitochondrial DNA (mtDNA) displacement (D)-loop sequences were used to study the genetic diversity and relationship of Indonesian indigenous chickens. A total of 483 individuals belonging to 15 population breeds and 43 individuals belonging to 6 populations of jungle fowl (2 populations of Gallus gallus and 4 populations of Gallus varius) were sampled. The hypervariable I (HVI) segment of the D-loop was PCR amplified and subsequently sequenced. The sequences of the first 397 nucleotides were used for analysis. Sixty nine haplotypes were identified from 54 polymorphic sites with polymorphism between nucleotides 167 and 397 contributing to 94.5% of the sequence variation. Phylogenetic analysis indicates that Indonesian indigenous chickens can be grouped into five distinct clades (clade I, II, IIIc, IIId, and IV) of the previously identified seven clades (clade I, II, IIIa, IIIb, IIIc, IIId, and IV) in Asian indigenous chickens. Fifty haplotypes belong to clade II, seven haplotypes are in clade IV, six are in clade IIId, three are in clade I and one haploype is in clade IIIc. There was no breed-specific clade. Analysis of Molecular Variance (AMOVA) based on partial D-loop sequences of Indonesian chicken indicates that 67.85% of the total sequence variation between haplotypes was present within the population and 32.15% between populations. One of the haplotypes (represented by PLC4) was shared by all populations, suggesting that these populations may share the same maternal ancestor. These results show a high mitochondrial D-loop diversity and indicate multiple maternal origins for Indonesian indigenous chickens. Key words: Indonesian indigenous chicken, mitochondrial DNA, D-loop, haplotype, phylogenetic analysis and clad

Teknik molekuler untuk identifikasi spesies ordo Cetartiodactyla menggunakan DNA barcode

Di Indonesia banyak terjadi kasus produk makanan yang berasal dari ternak tidak jelas identitasnya. Sebagian besar kasus yang terjadi berasal dari ordo Cetartiodactyla yang banyak dikonsumsi sebagai sumber protein hewani. Oleh sebab itu diperlukan alat identifikasi spesies yang akurat dari organ tubuh/daging atau produk olahan yang berasal dari hewan tersebut untuk menyelesaikan berbagai kasus yang dapat merugikan konsumen. Keragaman urutan sekuen gen sub unit cytochrome c oxidase subunit I (COI) telah terbukti menjadi alat yang efektif untuk identifikasi spesies hewan. Studi ini menganalisis 112 spesimen terdiri dari 4 Famili, 10 Genus dan 15 spesies dari ordo Cetartiodactyla yang dikumpulkan dari berbagai lokasi di Indonesia. Hasil yang didapat dari studi ini menunjukkan bahwa gen ini sangat cocok untuk mengidentifikasi tingkat spesies pada hewan tercermin pada pohon filogeni yang terbentuk. Jarak genetik dalam spesies berkisar antara 0-0,7% (rata-rata 0,13±0,05%) dan antar spesies berkisar antara 2-28%, dalam genus berkisar antara 8,8-27,4% (rata-rata1,36±0,037%) dan antar genus berkisar antara 8,8-27,4%, sedangkan dalam famili berkisar antara 5,8-11,9% (rata-rata 7,8±2,85%) dan antar famili berkisar antara 18,6-26,3%. Hasil konstruksi pohon filogeni Cetartiodactyla menunjukkan semua spesies membentuk sebuah cluster kohesif yang jelas berbeda

DNA barcoding pada Familia Bovidae berdasarkan gen Co1 (Cytochrome C Oxydase Sub Unit 1)

DNA barcoding merupakan suatu teknik identifikasi spesies berbasis molekuler dengan menggunakan gen Cytochrome C Oxydase Subunit 1 (CO1). DNA barcoding terhadap famili Bovidae berguna dalam rangka identifikasi spesies, monitoring perdagangan daging ternak, penegakkan hukum, serta klarifikasi spesies dalam suatu produk pangan yang berasal dari hewan ternak. Penelitian ini bertujuan untuk mengetahui efektivitas gen CO1 sebagai DNA barcode dengan melihat  jarak genetik antar-spesies dan inter-spesies Bovidae dengan spesies outgrup serta kekerabatan spesies dalam konstruksi filogenetik. Analisis sekuen CO1 dilakukan terhadap tujuh spesies Bovidae dan dua spesies out grup. Data sekuen CO1 diperoleh dari NCBI (https://www.ncbi.nlm.nih.gov/) lalu dilakukan analisis jarak genetik dan filogenetik menggunakan metode neighbor-joining (NJ) pada software Moleculer Evolutionary Genetics Analysis (MEGA) versi 6. Hasil penelitian menunjukkan jarak genetik intra-spesies Bovidae berkisar antara 0,044-0,69% dengan jarak terendah terlihat pada spesies Bos taurus (0,044%) dan tertinggi pada spesies Bos javanicus (4,69%). Sedangkan jarak genetik inter-spesies berkisar antara 2,2-24,6% dengan jarak tertinggi ditunjukkan oleh Bos javanicus dan spesies outgrup yakni sebesar 24,6% (rata-rata ±2,2-0,05%). Sekuen gen CO1 pada spesies famili Bovidae menunjukkan adanya variasi yang tinggi antar-spesies namun rendah dalam spesies (intra-spesies). Oleh karena itu, gen CO1 efektif digunakan sebagai DNA barcode pada famili Bovidae

Comparison of horned, polled Bali cattle and Banteng based on microsatellite markers

Bali cattle (Bos javanicus) are domesticated cattle from Banteng. Bali cattle have unique characteristics that is the white sock. In the Maiwa breeding center, Enrekang district, South Sulawesi Province, polled Bali cattle are being kept in large quantities, both male and female. The microsatellites are widely used in the study of population genetics and quantitative trait locus. Therefore, the study aims to observe genetic diversity and determine whether microsatellites can distinguish horned Bali cattle, polled Bali cattle, and Banteng as their wild relatives. DNA was isolated from blood samples of 57 Bali cattle from two different populations: horned Bali (n=20) from Nusa Penida Island Bali province, polled Bali cattle (n=37) from Maiwa Breeding Center, South Sulawesi province, and 20 samples of Banteng from Ragunan Zoo (n=10), Jakarta Province and Surabaya Zoo (n=10), East Java Province. Genotyping was done using 11 microsatellite markers. The size of each microsatellite marker was determined using GeneMapper version 5.0. The observed heterozygosity value (Ho), expected heterozygosity value (He), the heterozygote deficit within the breed (Fis), gene flow (Nm), Hardy-Weinberg equilibrium (HW), and allele frequency were performed using CERVUS version 3.0.7 program. The FSTAT 2.9.4 was performed to obtain Fis value from two different populations.Similarly, bayesian clustering assignments were analyzed using STRUCTURE version 2.2. The polymorphism information content of eleven microsatellite markers ranged from 0.390-0.879. Moreover, we found Fis values of all markers which depicted that there is no inbreeding in horned and polled Bali cattle populations. We also found that polled Bali cattle have more private alleles than horned Bali cattle. Using Bayesian analysis, we found different genetic structures between polled Bali and horned Bali cattle with the K optimal at K=3. Findings indicated that ILST6 allele 288, TGLA53 allele 132, and TGLA227 allele 70 can be considered as the private allele to differentiate between the horned, polled Bali cattle and Banteng

Exploring the vertebrate fauna of the Bird’s Head Peninsula (Indonesia, West Papua) through DNA barcodes

Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebratecommunities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.Fieldwork and laboratory activities were supported by the Lengguru 2014 Project (www.lengguru.org), conducted by the French National Research Institute for Sustainable Development (IRD), the Indonesian Institute of Sciences (LIPI) with the Research Centre for Biology (RCB), and the Politeknik KP Sorong, with the help of the Institut Français in Indonesia (IFI) and the French embassy in Jakarta, with corporate sponsorship from COLAS SA Company (Environment Department), Total Foundation, ABS, Wasco, Veolia Eau, SDV-Bolloré,Peer reviewe

BARKODING DNA BURUNG ELANG (FAMILI ACCIPITRIDAE) DI INDONESIA

The cytochrome c oxidase subunit I (COI) gene is a reprensentative of all the protein-coding genes of the mitochondrial DNA genome that has been widely used as an animal species identification tool. In this study, 86 sequences of DNA barcodes of members of the family Accipitridae in Indonesia including Nisaetus bartelsi, Nisaetus cirrhatus, Haliaeetus leucogaster, Spilornis cheela, Haliastur indus, and 11 sequences from Genbank were examined. Each species was confirmed through the Basic Local Alignment Search Tool (BLAST). The construction of phylogeny trees based on COI gene sequences was performed by the Neighbors-joining method where the calculation of the genetic distance matrix with the Kimura 2-parameter model was implemented in pairwise distance calculation in the Mega version 6.05 programe. The results of the analysis showed that the divergence within species ranged from 0 to 0.3% (0.13 ± 0.12%), between species ranged from 1.6 to 18.5% (12.8 ± 3.73%), between genera ranged from 13 to 18.6%, and the average in the Accipitridae Family was 11.8%. Therefore, it could form clusters in each species cohesively and clearly separated between the taxa analyzed

Barcoding DNA pada komunitas kelelawar pemakan buah di Indonesia

Family Pteropodidae known as fruit bats which has ecological services as seed dispersers, pollinator, and plays important role in the forest regeneration. Identification of bat species frequently encountered problems, i.e., criptic morphology and behaviour. Therefore it is necessary to confirm its identity using DNA barcodes. Cytochrome c oxidase subunit I (COI) mitochondrial DNA is representative of the protein coding mitochondrial DNA and has been used extensively as a means of animal species identification. This study evaluated 141 specimens consist of 42 species and 17 genera which were collected from Java, Nusa Tenggara, Sumatra, Kalimantan, Sulawesi, Maluku, and Papua. Phylogenetic analysis using the neighbor-joining method, in which the genetic distance matrix calculation by Kimura-2 parameter models are implemented on the pairwise distance calculation in the program MEGA version 6:05. The results of the analysis showed variation intraspecific ranging from 0 to 7.9% (0.9 ±0.014%) and there were 4 species with very high intraspecific average sequence divergence, i.e., Penthetor lucasi (3.2%), Thoopterus nigrescens (3.7%), and Chironax melanocephalus (8.7 %). Average interspecific of genetic distance of fruit bats in Indonesia was 20% (1.3-26.1%). These results produce a phylogeny tree construction to form a clearly different cohesive cluster, except in the genus Dobsonia ( D. moluccensis, D. viridis, and D. crenulata), Cynopterus (C. brachyotis C. minutus, and C. luzoniensis), and Macroglossus (M. minimus and M. sobrinus ), because this did not correspond with currently recognized species boundaries based on morphology

Aplikasi Kajian DNA Molekuler dan Fenotipik Pada Program Pelepasliaran Burung Kakatua (Application of Molecular DNA and Phenotypic Study for Reintroduction Programme of Cockatoos )

Ada enam spesies burung kakatua di Indonesia yang diketahui sebagai satwa eksotis, cerdas, dan dapat dilatih untuk berbagai atraksi. Oleh sebab itu banyak komunitas pecinta burung ingin memiliki dan memeliharanya. Semua satwa yang telah dipelihara masyarakat perlu dilakukan evaluasi dari berbagai aspek sebelum dilepas kembali ke habitat alam. Identifikasi spesies dan jenis kelamin kakatua peliharaan ilegal memiliki peran kunci untuk program reintroduksi. Tujuan dari penelitian ini adalah untuk mengevaluasi realibilitas dan efektivitas teknik morfometri dan molekuler untuk program reintroduksi kakatua ke habitat alam. Sebanyak 68 sekuen gen COI kakatua yang dikoleksi dari komunitas pecinta burung di sekitar Jakarta dan empat sekuen dari GenBank digunakan dalam kajian ini. Analisa filogenetik menggunakan metoda neighbor-joining, dimana kalkulasi matrik jarak genetik dengan model Kimura-2 parameter diimplementasikan pada pairwise distance calculation dalam program MEGA Versi 6.05. Hasil analisa menunjukkan variasi intraspesifik adalah Cacatua alba (n=4)= 0%, C. galerita (n=53)= 0,3%, C. goffiniana (n=3)= 0%, C. moluccensis (n=7)= 0,1%, dan C. sulphurea (n=2) = 0,3%, dengan kisaran antara 0-0,6%. Rata-rata divergensi intraspesifik sekuen COI adalah 0,25±0,055% dan interspesifik berkisar antara 3,1-11,6%. Pohon filogenetik menunjukkan clade monofiletik spesies kakatua di Indonesia. Selain itu, analisis DNA barcode dan penentuan jenis kelamin dengan teknik molekuler telah melakukan koreksi terhadap lima individu hasil identifikasi spesies dan dua individu hasil identifikasi jenis kelamin C. galerita triton. Hasil kajian C. galerita triton jantan dan betina berdasarkan berat tubuh, panjang tubuh, dan panjang kepala-paruh tidak berbeda nyata (P≥0,5). Akhirnya, sebanyak 19 ekor C. galerita triton dan dua ekor P. aterrimus telah dilepasliarkan di habitat alam

Investigasi Asal Usul Ayam Indonesia Menggunakan Sekuens Hypervariable-1 D-loop DNA Mitokondria

Chicken taxonomy and pedigree investigation are important parts to understand the domesticationprocess occurred on chicken in Indonesia. The Indonesian native chickens have very different clade with thechickens from other Asian countries and others. This study was conducted to construct phylogeny junglefowls (red and green jungle fowls) and Indonesian native chickens, in order to know their relationship.Among the available DNA marker, the region D-loop on DNA mitochondria is the most effective markerused in the investigation. Mitochondrial DNA D-loop (hypervariable-1 segment) was PCR amplified andsubsequently sequenced for a total 33 individuals of green jungle fowls (Gallus varius), 9 individuals of redjungle fowls (Gallus g. gallus) from Indonesia, and 30 individuals of Indonesian native chickens (Lombok,Cemani, Kedu, Kedu Putih, Nunukan, Kate, Pelung, Gaok, Merawang, dan Sentul). Seventy two (72)sequences were used for analysis. Seven (7) published reference D-loop sequences of genus Gallus fromGenBank were also included in the analysis: Gallus varius (GenBank accession number D64163 danD82912), Gallus gallus (GenBank accession number AB098668), G. gallus spadiceus (GenBank accessionnumber AB007721), Gallus gallus bankiva (GenBank accession number AB007718), Gallus lafayetti(GenBank accession number D66893), and Gallus sonneratii (GenBank accession number D66892). Phylogenyanalysis indicates that Indonesia jungle fowls can be grouped into two clades (clades of red jungle fowls/Indonesia native chicken and green jungle fowls). Monophyletic phylogeny trees of jungle fowls from Indonesiawere shown in this study for pedigree investigation of domesticated chickens