The whale shark (Rhincodon typus) inhabits Cenderawasih Bay at the Birdhead Seascape of Papua in high frequent sightings, but little is known about its genetic characteristics and connectivity. The study was conducted to characterize of the R. typus COI gene fragment from Cenderawasih Bay, in order to accurately compare with the 27 COI gene fragment sequences from the global whale shark deposited in the GenBank. A total of 28 meat samples of whale shark were collected by biopsy punch on a pole spear. The meat samples were extracted to obtain whole genome then amplified and sequenced to obtained COI nucleotides. The determined COI is a 669 bp, comprising of A = 26.5%, T/U = 30.5%, C = 28.3%, dan G = 14.7%. In total, 41 cutting sites of all the sequences ranged in size from 5-7 bp long. One COI single nucleotide polymorphisms and 2 haplotypes were identified. Single site substitution change from T to C for both haplotypes was observed. Overall, the haplotype diversity (Hd= 0.137) and nucleotide diversity (π=0.0002) were relatively low. A different nucleotide composition, number and arrangement of the sequences with the whale shark COI sequences from Cenderawasih Bay compared to COI gene fragment sequences from GenBank were observed. This study shows the availability of sequence of whale shark will contribute to aid further studies of molecular systematics, phylogeography, genetic differentiation, and conservation genetics.

Abstract. Abbas B, Tjolli I, Dailami M, Munarti. 2019. Phylogenetic of sago palm (Metroxylon sagu) and others monocotyledon based on mitochondrial nad2 gene markers. Biodiversitas 20: 2249-2256. Sago palm forest and sago palm semi cultivated are found in the Papua islands as well as Ambon and Seram islands. The diversity center of sago palm is found in the Papua Islands. The objectives of this study are revealed sequence DNA mitochondrial associated with nad2 genes in sago palm accessions and molecular phylogenetic of sago palm and other monocotyledon plants. Plant materials used in the studies were derived from Sago Research Center (SRC) and sequencing and other monocotyledon were retrieved from the GenBank, NCBI accessions. Young fresh leaflets were derived from the experimental field of SRC and DNA extraction by following the procedure of Plant Genomic DNA Mini Kit and then PCR performed by using nad2 primer sets. Thereafter, DNA PCR product was sequenced by Macrogen Inc., Seoul, Korea. Sequences of nad2 genes in sago palm accessions from Papua, Indonesia were registered by GenBank NCBI for further used in the future as biological authenticity from the certain location. Mitochondrial DNA sequences associated with nad2 genes in the genome of sago palm were shown no differences among sago palm accessions. Molecular phylogenetic of sago palm and others monocotyledon based on nad2 gene markers showed the sago palm and others monocotyledon incorporated into two major clades and five subclades. Sago palm, coconut, and date palm were described as close related and being in the same subclades.

Cirrhilabrus cf. ryukyuensis from Cenderawasih Bay and Raja Ampat have different colormorphs with Cirrhilabrus ryukyuensis. This study was conducted to determine the phylogenetic relationship, evolution and genetic diversity of Cirrhilabrus cf. ryukyuensis based on Cytochrome oxidase sub unit 1 (COI) gene. Mitochondrial DNA extracted by using chelex 10%. FISH-BCH and BCL primers were used to amplify COI gene fragment and sequencing. Data analysis conducted by using software Sequencher 4.1 and MEGA 5. COI genes from six samples of C. cf rykyuensis from Cenderawasih Bay and Raja Ampat have total 613 base pairs. The average compositions of nucleotides are T 32.8%, C 26.3%, A 23.2% and G 17.7%. There is six positions of polymorphism that caused by transition. Conversion of nucleotides to amino acid sequence resulted in 204 amino acid with the same sequence. The phylogenetic tree from six sample showed that all in one clade, but different clade from Cirrhilabrus cyanopleura from GenBankAbstrakCirrhilabrus cf. ryukyuensis asal Teluk Cenderawasih dan Raja Ampat secara morfologi memiliki perbedaan warna dengan Cirrhilabrus ryukyuensis. Penelitian ini bertujuan menentukan hubungan filogenetik, evolusi, dan keragaman genetik  Cirrhilabrus cf. ryukyuensis berdasarkan gen Sitokrom Oksidase sub Unit I (COI). Genom DNA mitokondria diekstrak menggunakan larutan chelex 10%. Primer FISH-BCH dan BCL digunakan untuk mengamplifikasi fragmen Gen COI dan sekuensing. Analisis data dilakukan dengan menggunakan perangkat lunak Sequencher 4.1 dan MEGA 5. Gen COI dari enam sampel C. cf. rykyuensis asal Teluk Cenderawasih dan Raja Ampat, memiliki panjang basa men-capai 613 bp. Komposisi rata-rata nukleotida T 32,8%, C 26,3%, A 23,2% dan G 17,7%. Terdapat enam posisi poli-morfisme yang kesemuanya disebabkan oleh mutasi transition. Hasil penerjemahan nukleotida, diperoleh asam amino dengan panjang 204 asam amino dengan urutan yang sama. Pohon filogenetik menunjukkan keenam sampel berada dalam satu clade yang sama dan berbeda dari clade Cirrhilabrus cyanopleura data Gene Bank.

Pengelolaan dan pelestarian keanekaragaman hayati berawal dari pengetahuan tentang ketersediaan sumberdaya, identifikasi, dan sistematika spesies. Banyaknya spesies Turbinidae dengan berbagai bentuk morfologi dan transformasi bentuk menjadikan identifikasi dengan gen COI sangat penting dalam mempercepat pengungkapan identitas spesies. Penelitian ini dilakukan dengan tujuan menganalisis pola pertumbuhan dan mengidentifikasi gastopoda Turbinidae dengan pendekatan DNA barcode. Hasil identifikasi berdasarkan karakter morfologi menunjukkan bahwa genus Turbo yang diamati adalah dari spesies Turbo stenogyrus. Analisis pola pertumbuhan menunjukkan bahwa pola pertumbuhan T. stenogyrus adalah allometrik negatif. Amplifikasi DNA dengan gen COI menghasilkan panjang sekuen DNA 650 bp dengan hasil identifikasi sesuai dengan pengamatan morfologi yaitu Turbo stenogyrus. Berdasarkan analisis filogenetik dan jarak genetik, sekuen DNA yang dianalisis membentuk clade yang sama dengan spesies Turbo stenogyrus dengan jarak genetik terdekat 4,2%. Analisis genetik melalui gen COI sangat baik dan memberi kemudahan dalam identifikasi spesies gastropoda.

Morphological dan genetic identification is an essential part of biology and ecological study. Environmental degradation, physical and chemical facto in water, and utilization of gastropod by society will give impact in distribution pattern, population size, morphology and genetic characteristic of the snail. This research aims to analyze the growth pattern and molecular aspect of Turbo setosus. The variable that examined is total weight and length, and cytochrome oxidase subunit one gene sequence. The growth factor of T. setosus is negative allometric, which means weight growth is slower than the length growth. The total length of cytochrome oxidase subunit 1 of these samples were 650 base pairs. Based on the DNA barcoding analysis, the sequence is 96.92% identic with the sequence of T. setosus in GenBank. The phylogenetic tree was reconstructed with neighbour-joining methods and 1000 replication bootstrap, show the clade grouping based on the similarity and genetic distance of the species. The sequence data is vital for species identification fast and accurately.    Identifikasi morfologi dan genetik menjadi bagian penting dari setiap studi biologi maupun ekologi, degradasi lingkungan, faktor fisik-kimia lingkungan dan pemanfaatan gastropoda secara terus menerus akan mempengaruhi penyebaran, penurunan populasi, karakteristik morfologi dan juga karakter molekuler spesies. Penelitian ini bertujuan untuk menganalisis pola pertumbuhan dan karakter molekuler Turbo setosus. Variabel yang diukur adalah berat total dan panjang total serta identifikasi molekuler dengan menggunakan gen sitokrom oksidase I. Pola pertumbuhan T. setosus adalah allometrik negatif yang berarti pertambahan berat lebih lambat dari pertambahan panjang. Hasil identifikasi dengan DNA barcoding diperoleh spesies T. setosus dengan panjang sekuen DNA 650 bp. Rekonstruksi filogenetik dengan metode Neighbor-Joining boostrap 1000x memperlihatkan pengelompokan sekuen berdasarkan kimiripan dan jarak genetik antar spesies. penting dalam identifikasi spesies secara cepat, tepat dan akurat.

Orchidaceae has known as an attractive flower and immense species. We have found a large species of Orchidaceae grow naturally in Papua's jungle, Indonesia territorial. This study aims to reveal genetic variation and genetic relationships among endemic orchids in Papua based on RAPD markers. The study included 26 accessions of Papua's endemic orchids used for genomic DNA extraction. Genomic DNAs were extracted by using DNA extraction kit from Qiagen and genomic DNA amplification by using 10 decamer RAPD primers. DNA fragments that were amplified by Polymerase Change Reaction (PCR) were visualized and documented by using UV illumination apparatus. Genetically, endemic Orchids in Papua were described high variation. Fragments amplification by using ten RAPD primers and performed in the PCR tools resulted in 54 numbers of polymorphic fragments and no monomorphic band. The number of polymorphic bands per primer ranged from 4 to 7 with averaged 5.4 bands per assay unit. The genetic dissimilarities (GDs) among examined orchids ranged from 0.10 to 0.94 based on Nei's unbiased coefficients. Dendrogram construction showed that Papua's endemic orchid (PEO) samples different from another and separated to form group by their own at the 0.40 coefficient value and at the 0.6 coefficient value indicate that PEO sample is divided into nine groups i.e. samples at the genera level were separated into their own groups.

Sago palm is flowering and fruiting just once in their life cycle. Sago palms that grow naturally and semi cultivated were generally occurred natural pollination to form fruits and seeds, if not cut down to take the starch contained in their trunk. Sago palm pollination may occur as self-pollinated and cross-pollinated. If cross-pollinated was occurred in the pollination process, it will be varied of their progenies. This study aims to reveal the genetic variation of sago palms progenies with naturally pollinated process. The research method is to collect seeds from one parent trees that have produced ripe fruit. Fruit seeds germinated to be made and tested genetic variation using RAPD markers. Isolation of DNA is done by using the fresh young leaves. DNA amplification is done by using RAPD primers. The results showed that the progenies derived from naturally pollinated of sago palms were genetically varied based on RAPD markers and also varied based on morphological phenotypic. Variations occurred in the progenies of sago palm indicated that the sago palms were estimated cross-pollinated naturally, as a result fruits and seeds with genetically differences.

Mantis shrimp is one of the marine organisms that has a very abundant diversity of species. The similarity of morphology of this group make it difficult to identify morphologically. Therefore, identification was carried out using a DNA barcoding approach. The purpose of this study was to identify the mantis shrimp species from Manokwari waters using molecular techniques. The CO1 gene fragments were amplified by using LCO and HCO primers. The DNA sequences obtained were analyzed for homology, phylogeny, and genetic distance using MEGA X software. A total of 537 base pairs of CO1 gene fragments of mantis shrimp from Manokwari were obtained. The results of the homology analysis on GenBank, show the highest similarity of 91.18% with sequences from the genus Gonodactylus. Analysis of phylogenetic tree and genetic distance showed the same results and supported each other with homology analysis on GenBank data.