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All Journal HAYATI Journal of Biosciences MANAJEMEN HUTAN TROPIKA Journal of Tropical Forest Management BIOTROPIA - The Southeast Asian Journal of Tropical Biology JURNAL PEMULIAAN TANAMAN HUTAN AGRIVITA, Journal of Agricultural Science Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan (Journal of Natural Resources and Environmental Management) REINWARDTIA Jurnal Penelitian Pendidikan IPA (JPPIPA) Indonesian Journal of Chemistry Action Research Literate (ARL) Journal Of Sustainability Perspectives Journal of Sustainability Perspectives Global Forest Journal Policy Brief Pertanian, Kelautan, dan Biosains Tropika Reinwardtia Indonesian Journal of Forestry Research
Fifi Gus Dwiyanti
Department Of Silviculture, Faculty Of Forestry And Environment, IPB University, IPB Darmaga Campus, Dramaga, Bogor, 16680, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Earth & Planetary Sciences Economics, Econometrics & Finance Education Engineering Environmental Science Immunology & microbiology Languange, Linguistic, Communication & Media Law, Crime, Criminology & Criminal Justice Materials Science & Nanotechnology Mathematics Physics Public Health Social Sciences Veterinary

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Microsatellite Identification Based on Genome Assembly Reveals Potentials Marker of Macassar Ebony (Diospyros celebica Bakh.) Majiidu, Muhammad; Matra, Deden Derajat; Dwiyanti, Fifi Gus; Siregar, Iskandar Z
Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan (Journal of Natural Resources and Environmental Management) Vol 14 No 2 (2024): Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan (JPSL)
Publisher : Pusat Penelitian Lingkungan Hidup, IPB (PPLH-IPB) dan Program Studi Pengelolaan Sumberdaya Alam dan Lingkungan, IPB (PS. PSL, SPs. IPB)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/jpsl.14.2.399

Abstract

Macassar ebony (Diospyros celebica Bakh.) is an endemic tree species native to Sulawesi. To date, there are limited comprehensive publications regarding its genome assembly. In this study, we employed paired-end libraries of HiSeq 4000 Illumina, generating 141.2 million paired-end reads (42.4 Gigabases). Our analysis revealed the presence of 950,081 Scaffolds, with an N50 value of 6,023. Notably, BUSCO analysis identified 183 (12.7%) complete and single-copy BUSCOs (S), as well as 9 (0.6%) complete and duplicated BUSCOs (D). Furthermore, we identified 12,890 microsatellites within the Macassar Ebony genome. These microsatellites encompass 14 dinucleotide SSR motifs, 12,090 trinucleotide SSRs, 780 tetranucleotide SSR motifs, and 6 pentanucleotide SSRs. This dataset represents a valuable resource for assessing Macassar Ebony genetic makeup in its natural habitats and for subsequent analyses of the Macassar Ebony genome.
Optimizing DNA Extraction Methods from Leaf and Wood Tissues to Support Dipterocarp Conservation and Sustainable Forest Management Arrofaha, Nawwall; Rachmat, Henti Hendalastuti; Dwiyanti, Fifi Gus; Adinugroho, Wahyu Catur; Siregar, Iskandar Zulkarnaen; Kamal, Irsyad; Syaputra, Dhika; Salamah, Andi
Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan (Journal of Natural Resources and Environmental Management) Vol 16 No 1 (2026): Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan (JPSL)
Publisher : Pusat Penelitian Lingkungan Hidup, IPB (PPLH-IPB) dan Program Studi Pengelolaan Sumberdaya Alam dan Lingkungan, IPB (PS. PSL, SPs. IPB)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/jpsl.16.1.13

Abstract

Dipterocarpaceae are economically important, contributing over 85% of Indonesia's timber exports. However, this crucial resource is increasingly threatened by illegal logging, habitat destruction, and the illegal timber trade, which jeopardize dipterocarp population. Furthermore, conservation efforts utilizing genetic and forensic techniques often encounter substantial challenges due to the complexities in DNA extraction protocol. To address this, the study aimed to enhance the efficiency of DNA extraction methodologies by comparing two methods: the modified cetyltrimethylammonium bromide (CTAB) and the Genomic DNA Mini Kit (Plant) from Geneaid Biotech Ltd. The research focused on leaf and wood samples from two species, spesifically Rubroshorea leprosula (Miq.) P.S.Ashton & J.Heck and Shorea laevis Ridl. For each of these species, five leaf and five wood samples were extracted using both methods. The quality of the DNA extraction was evaluated using electrophoresis and quantified with a Qubit fluorometer. Higher DNA concentrations were obtained with the modified CTAB method compared to the GeneAid kit for both R. leprosula and S. laevis, particularly in leaf tissue. The GeneAid kit consistently exhibited low DNA yield efficiency compared to the modified CTAB method for both species. Additionally, PCR amplification of both leaf and wood samples confirmed that the extracted DNA was suitable formolecular analyses. These findings not only contributed to laboratory applications but also served as practical tools for species identification and genetic conservation for sustainable forest management and law enforcement.
Co-Authors Adinugroho, Wahyu Catur Adzkia, Ulfa Alfi Hudatul Karomah Alfian Helmi Amigunani, Zahra Wajdini Amperanoto, Agus Andi Salamah Arida Susilowati Iswanto Arief Sabdo Yuwono Arrofaha, Nawwall Aulia Andi Mustika Ayyasy, Yahya Boedi Tjahjono Budi Purwanto Cut Rizlani Kholibrina Deden Derajat Matra Dien Atin Boritnaban Dodik Ridho Nurrochmat Dwi Utami , Anisa Febrita, Joana Handian Purwawangsa Henti Hendalastuti Rachmat Henti Rosdayanti, Henti Hudaya, Aang Husin Alatas IBNUL QAYIM Ida Mallia Ginting IPB, BPKB Irsyad Kamal Iskandar Z. Siregar ISKANDAR ZULKARNAEN SIREGAR Khairunnisa, Zayyaan Nabiila Khoirunisa, Hana Ko Harada Ko Harada Koichi Kamiya Koichi Kamiya Kustiyarini, Nur Fadila KUSUMADEWI SRI YULITA Laswi Irmayanti, Laswi Majiidu, Muhammad Matra, Deden Derajat Meti Ekayani Mohamad Rafi Muhammad Majiidu Muhammad Majiidu Muharam, Karima Fauziah Mutya Kana Purba Nyoto Santoso Putra, Heriansyah Rachmat, Henti Hendalastuti Rahadian Pratama Rahman, Mohamad Miftah Rai Sita Rakhmad Fadillah Rifnadhi, Bayu RIKA RAFFIUDIN Rina Mardiana Rukmana, Adi Sari, Windi Mayang Septaningsih, Dewi Anggraini Siska Nurfajri Slamet, Alim S Susila, Susila Syaputra, Dhika Ulfah Juniarti Siregar Utami, Anisa Dwi Utami, Annisa Dwi Wati, Ridha WINDRA PRIAWANDIPUTRA, WINDRA Zaenal Abidin