Judul: Trancriptomic Analysis of Kamper (Dryobalanops aromatica) Grown in Peat Media and Mineral Soil
Abstrak: Dryobalanops aromatica is a highly economic value resin-producing tree. It has been known as an essential international trade commodity widely used in the perfume, cosmetics, medicine, and wood industries. In natural habitats, this adaptive species has been found to grow well on peatland and mineral soils. The information regarding adaptive genes in Indonesian native trees to abiotic stress is still very limited. The research was conducted to analyse the differential gene expression (DGEs) that can elucidate the role of several up-regulated and down-regulated genes under peat media and mineral soil treatments. DGE analysis was carried out using R software, Bioconductor package 'edgeR'. Using the Benjamini and Hochberg approach to control FDR (false discovery rate) with the value of FDR is 0.05), with a log2FC (log2 fold change) with minimal value 2 and p-value of 0.05, showed 320 contigs were up-regulated, and 439 contigs were down-regulated, while 58129 contigs were not significantly expressed. Furthermore, this study also presents an overview of the genes involved in different pathways, such as photosynthesis, carbon and energy metabolism, phytohormone-related genes, nitrogen metabolism, reactive oxygen species, and transcription factor. This information will be helpful in understanding D. aromatica molecular responses to stress conditions that may be useful for selecting genotypes in the breeding programs or peatlands restoration. We found that genes involved in plant stress phytohormone biosynthesis, such as JA (jasmonic acid), ET (ethylene), GB (gibberellic acid), were up-regulated. In contrast, genes involved in ABA and IAA showed down-regulated on peat media treatment. Further, genes encode biological functions of the cell wall, and molecular functions as metal ion binding were up-regulated. Genes that function as antibiotics and ROS scavengers such as Peroxidase and Superoxide dismutase [Fe]2, chloroplastic were also found up-regulated. The transcription factors MYB26, NAC43, and NAC73 are thought to be transcription factors involved in the defense responses to D. aromatica in peat stress treatment. Molecular phylogeny analysis was carried out on the sequences of genes related to the adaptability of D. aromatica to the peat media stress to determine the evolutionary history, kinship relationships, and related gene functions. Homologous genes show different expression up-/down-regulations patterns. However, the alignment and phylogenetic analysis results showed an identity matrix and a distance matrix showing differences between up-regulated and down-regulated homologous genes. The differences between these genes are thought to be due to differences in the specific motifs of their constituent bases.
Keyword: adaptation, Dryobalanops, phylogenetic, Transcriptome, RNA-seq

Judul: Analysis of Long-read Sequences with MinION Technology on Kapur (Dryobalanops aromatica C.F Gaertn).
Abstrak: Salah satu spesies penting dari famili Dipterokarpa adalah kayu kapur (D. aromatica C.F Gaertn) dengan status konservasi rentan (vulnerable). Status tersebut mencerminkan perlunya upaya konservasi genetik berbasis sains yang didukung dengan teknologi baru, salah satunya adalah Oxford Nanopore Technology (ONT) MinION yang mampu menyajikan analisis long-read DNA sequences yang terjangkau. Saat ini penggunaan ONT masih jarang dilakukan pada pohon hutan asli Indonesia. Penelitian ini bertujuan untuk mendapatkan data sekuens whole genome liputan rendah (low coverage) dan memanfaatkannya untuk menganalisis kekerabatan D. aromatica. Prosedur penelitian mencakup tahapan isolasi dan sekuensing DNA hingga analisis bioinformatika. Hasil menunjukkan bahwa sekuensing DNA D. aromatica dengan pembacaan urutan basa DNA long-read 1,55 Gb dengan genom parsial kloroplas D. aromatica 148.856 bp. Analisis kekerabatan menunjukan D. aromatica berkerabat dekat dengan D. rappa dengan marka kombinasi gen (matK dan rbcL) lebih direkomendasikan untuk digunakan dalam analisis lanjutan D. aromatica., One important species of the dipterocarps is kapur (D. aromatica C.F. Gaertn) with a vulnerable conservation status. This status indicates the need for science based conservation through new technology, among other Oxford Nanopore Technoloy (ONT) MinION, that is able to provide affordable analysis for long-read DNA sequences. Nowadayas, the use of ONT is still rare being applied to native Indonesian forest trees. The objective of this study was to generate long- read sequence data of the whole genome with low coverage and use it to analyze genetic relationship D. aromatica. The research procedure included DNA isolation and sequencing to bioinformatics analysis. The results showed that DNA sequencing of D. aromatica resulted in 1,55 Gb of DNA base long read sequences in which a partial chloroplast genome length was constructed with a total of 148.856 bp. The genetic relationship analysis showed that D. aromatica was closely related to D. rappa with a combined marker of matK and rbcL are recommended for future use of phylogenetic analysis of D. aromatica.
Keyword: Dryobalanops aromatica, genome, markers, MinION, sequencing

Judul: Cycle Hamilton pada Graf Lengkap, Graf Regular, dan Graf 2-Connected 4-Regular Berorder Kurang dari Sepuluh
Abstrak: Suatu graf disebut graf Hamilton apabila graf tersebut memuat cycle Hamilton, yaitu cycle yang melewati setiap vertex tepat satu kali. Menentukan keberadaan cycle Hamilton pada suatu graf dapat menggunakan syarat cukup yang berupa teorema-teorema yang telah diperkenalkan sejak tahun 1950-an. Beberapa syarat cukup yang dibahas dalam karya ilmiah ini adalah syarat cukup yang berhubungan dengan graf lengkap dan graf regular. Suatu graf lengkap berorder 𝑛������ ≥ 3 dan graf r-regular berorder 𝑛������ ≤ 2𝑟������ + 1 merupakan graf Hamilton, Karena kedua graf tersebut memuat cycle Hamilton. Selanjutnya, syarat cukup tersebut digunakan untuk menentukan keberadaan cycle Hamilton pada graf 2-connected 4- regular berorder kurang dari 10.
Keyword: graf Hamilton, graf regular, graf lengkap, graf 2-connected 4-regular