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All Journal HAYATI Journal of Biosciences MANAJEMEN HUTAN TROPIKA Journal of Tropical Forest Management REINWARDTIA BERITA BIOLOGI JURNAL BIOLOGI INDONESIA Reinwardtia Indonesian Journal of Forestry Research
KUSUMADEWI SRI YULITA
Pusat Penelitian Biologi-LIPI Cibinong Science Center, Jln. Raya Bogor, Km 46. Cibinong, Kab. Bogor.
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences Education Immunology & microbiology

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Optimizing DNA Extraction and Selecting Suitable Regions for Biodiversity Assessment: A Study on Shorea leprosula Rachmat, Henti Hendalastuti; Yulita, Kusumadewi Sri; Dwiyanti, Fifi Gus; Susilowati, Arida; Arrofaha, Nawwall; Susila, Susila; Kamal, Irsyad; Siregar, Iskandar Zulkarnaen
Jurnal Manajemen Hutan Tropika Vol. 30 No. 1 (2024)
Publisher : Institut Pertanian Bogor (IPB University)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.7226/144

Abstract

The extraction method plays a crucial role in obtaining high-quality DNA samples, which is indispensable for various molecular biology techniques and analyses, enabling a deeper comprehension of genetic information and biological processes. The objectives of the study were: a) to optimize the chloroplast DNA extraction protocol by comparing modified CTAB methods and GeneAid for both leaf and wood samples of Shorea leprosula, a major commercial timber species, and b) to identify a suitable cpDNA region that exhibits variability and universality across taxa. Total DNA was analyzed by gel electrophoresis followed by Sanger sequencing to determine the amplification success. The results revealed that trnL intron, trnL-trnF, and trnG yielded readable sequences of the expected length (maximum 586 bp, 480 bp, and 908 bp, respectively), while the rps 16 intron failed to assemble a contig. The petL-psbE region provided long readability for reverse sequences (769 bp) but not for the forward sequence (195 bp). Higher successful DNA extraction was achieved from the leaves compared to the woods. The lower sequencing quality may be attributed to suboptimal primer design, the structural features of the regions resulting from extensive repetitive sequences, and the suboptimal condition of the extraction method in eliminating wood chemical compounds.
Secondary Structures of Chloroplast trnL Intron in Dipterocarpaceae and its Implication for the Phylogenetic Reconstruction YULITA, KUSUMADEWI SRI
HAYATI Journal of Biosciences Vol. 20 No. 1 (2013): March 2013
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (116.483 KB) | DOI: 10.4308/hjb.20.1.31

Abstract

Unambiguous insertion-deletion events were previously identified in trnL intron of 110 species of subfamily Dipterocarpoideae (Dipterocarpaceae).  These indels are associated with the formation of four stem loop structures and featuring characteristic for generic/infra-generic level depended upon which taxonomic classifications are followed. Phylogenetic analyses were performed by including and excluding these structures to examine the robustness of resulted topologies. Results indicated that inclusion of such structures yielded more resoved topologies, and that none of the stemloop structures were homoplasious. Results of this present study was also in agreement with the previous molecular phylogenetic studies that using several genes of cp genomes in that tribe Dipterocarpae was polyphyletic by the placement of all members of the genus Dipterocarpus within tribe Shoreae, and that tribe Shoreae was a potential monophyletic group. The phylogenetic relationships between  variable genera of Hopea and Shorea was also in accordance to earlier studies that suggested a potential monophyly of the two with inclusion of Parashorea and Neobalanocapus heimii. Genera that were recived strong branch support (Dipterocarpus, Dryobalanops, Vatica, and Stemonoporus) possessed certains indels exclusive to each and this may contributed to the monophyletic nature of these genera.  
ENUMERATION OF THE GENUS ATHYRIUM IN JAVA AND BALI WARDANI, WITA -; ADJIE, BAYU -; YULITA, KUSUMADEWI SRI; LESTARI, WENNI SETYO; SALAMAH, ANDI -
REINWARDTIA Vol 23, No 2 (2024): Reinwardtia
Publisher : Research Center for Biology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55981/reinwardtia.2024.4769

Abstract

We present a list of Athyrium species from Java and Bali based primarily on morphological examination. Some of disputed species were confirmed through molecular assess-ment. There are eight species of Athyrium in Java and two in Bali, none of them are endemic, but distribution of one species outside Java is uncertain. We provide the list with description, key to the species, and notes on taxonomy or distribution.
ENUMERATION OF THE GENUS ATHYRIUM IN JAVA AND BALI WARDANI, WITA -; ADJIE, BAYU -; YULITA, KUSUMADEWI SRI; LESTARI, WENNI SETYO; SALAMAH, ANDI -
REINWARDTIA Vol 23, No 2 (2024): Reinwardtia
Publisher : Research Center for Biology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55981/reinwardtia.2024.4769

Abstract

We present a list of Athyrium species from Java and Bali based primarily on morphological examination. Some of disputed species were confirmed through molecular assess-ment. There are eight species of Athyrium in Java and two in Bali, none of them are endemic, but distribution of one species outside Java is uncertain. We provide the list with description, key to the species, and notes on taxonomy or distribution.
GROWTH AND WOOD TRAITS EVALUATION OF 15-YEAR-OLD TENGKAWANG (Shorea spp.) TREE STANDS IN GUNUNG WALAT UNIVERSITY FOREST, WEST JAVA, INDONESIA Fifi Gus Dwiyanti; Rosdayanti, Henti; Yulita, Kusumadewi Sri; Rachmat, Henti Hendalastuti; Ayyasy, Yahya; Muharam, Karima Fauziah; Rahman, Mohamad Miftah; Adzkia, Ulfa; Siregar, Iskandar Zulkarnaen
Indonesian Journal of Forestry Research Vol. 11 No. 2 (2024): Indonesian Journal of Forestry Research
Publisher : Association of Indonesian Forestry and Environment Researchers and Technicians

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.59465/ijfr.2024.11.2.243-258

Abstract

Gunung Walat University Forest (GWUF) in Sukabumi Regency, Indonesia, plays a crucial role in providing various ecosystem services. Five important Shorea trees, i.e., S. stenoptera, S. mecisopteryx, S. pinanga, S. palembanica, and Shorea leprosula have been planted in GWUF as an effort for its conservation and object of research. An evaluation of the adaptability and suitability of these species to the GWUF ecosystem, as well as their wood characteristics, needs to be carried out regularly. Therefore, the study aimed to examine the growth performances and physical wood properties of five Shorea species, i.e., Shorea stenoptera, S. mecisopteryx, S. pinanga, S. palembanica, and S. leprosula at the age of 15-year-old planted in GWUF. The results indicated that S. leprosula exhibited the best growth performance in terms of average diameter (19.64 cm), volume (0.27 m3), slenderness (126.58), and wood density (0.94 g/cm3), and S. stenoptera showed the best performance in average height (23.35 m). While the poor performance was shown by S. palembanica in terms of average diameter (6.73 cm), height (11.15 m), volume (0.02 m3), wood density (0.87 g/cm3), and specific gravity (0.45), and S. stenoptera in terms of average slenderness (202.73). In addition, significant differences in tree height, diameter, volume, wood density, specific gravity, and moisture content were found in S. palembanica compared with other species. The relationship between the growth and physical wood properties parameters varied between species. The study revealed that planting the five Shorea species in GWUF is suitable for increasing vegetation cover and conserving the species.
Co-Authors ADJIE, BAYU - Adzkia, Ulfa Arida Susilowati Iswanto Arrofaha, Nawwall Ayyasy, Yahya Bora, Charles Y. Bora, Charles Y. Diyah Martanti, Diyah FAJARUDIN AHMAD Fifi Gus Dwiyanti Henti Rosdayanti, Henti Herlina Herlina I.G.B. Adwita Arsa Irsyad Kamal ISKANDAR ZULKARNAEN SIREGAR Muharam, Karima Fauziah Murnianjari, Muna Naiola, BP Naiola, BP Rachmat, Henti Hendalastuti Rahman, Mohamad Miftah SALAMAH, ANDI - Susila, Susila Tri Murningsih, Tri Tri Murniningsih Tukirin Partomihardjo WARDANI, WITA - Wenni Setyo Lestari, Wenni Setyo Yuyu S. Poerba, Yuyu S.