Mahat Magandhi Reni Lestari ^* Muhammad Rifqi Hariri Ikhsan Noviady Aditya Nugroho Fitri Indriani

• National Research and Innovation Agency (BRIN), Bogor, Indonesia

Artocarpus tamaran Becc. is a member of the Artocarpus genus of the Moraceae family, comprising 74 plant species (POWO, 2024). The species tree may attain a height of 45 m and a stem diameter of 1 m, with buttresses up to 3 m in height (Kochummen, 2000). The species is endemic to Borneo, occurring in Sarawak, Sabah, Kalimantan, and Brunei Darussalam, specifically in low land to the hilly mixed Dipterocarpaceae forest, beside the river, on sandstone, clay, and alluvial substrate (POWO, 2024;Jarret, 1959). It has also been recorded in the primary or old secondary forests and logged forests at 20 m to 1800 m above sea level (Jarret, 1959). According to the Red List category of the International United Conservation Nations (IUCN), Artocarpus tamaran is classified as Vulnerable A2c according to the Red List category of the International Union for Conservation of Nature (IUCN, 2024). The species is endangered due to habitat loss, which has been converted into plantations, logged, burnt down, and climate affected such as in Sabah, Sarawak, and Kalimantan (IUCN, 2024;POWO, 2024). The species is utilized for fiber material sourced from the bark, which is used to produce cloth and hats (Kulip 2003, Fern 2014), fresh fruit, and edible seed after being boiled or roasted (Lim, 2012). The stem, referred to as "terap" in local terminology, has potential applications in construction (Kochummen, 2000). The log and timber prices of the species were 22.90 USD m -3 and 50.88 USD m -3 , respectively (Karmini et al., 2020).The chloroplast genome displays a quadripartite structure and is circular. The structure comprises a large single-copy region (LSC) and a small single-copy region (SSC), separated by a pair of inverted repeats (IRs), with some exceptions noted where the loss of an IR or the SSC has occurred. The size of the chloroplast genome in terrestrial plants ranges from 19 to 217 kb, with the IRs generally measuring 20-26 kb in length (http://www.ncbi.nlm.nih.gov/genome/organelle). The chloroplasts proteome consists of around 3000 proteins that play roles in photosynthesis, and the biosynthesis of fatty acids, amino acids, hormones, vitamins, nucleotides, and secondary metabolites (Dobrogojski et al., 2020). The advancement and utilization of chloroplast genome engineering technology may inform the investigation of chloroplast gene functions, gene editing, gene expression regulation, and genome analysis (An et al., 2022). Regulation of chloroplast gene expression in chloroplast genome engineering is employed to achieve high-value industrial targets, improve photosynthetic capacity, and biofortify food crops (Boynton et al., 1988). This study presents the results of the chloroplast genome sequencing of the A. tamaran species. A sample of A. tamaran was obtained from the living collection of Bogor Botanical Gardens in West Java, designated with collector number IN577. The plant sample originated from Central Kalimantan. Genomic DNA was extracted from fresh leaves utilizing the CTAB (cetyltrimethylammonium bromide) method as described by Doyle and Doyle (1987). The initial quantification and purity of DNA were evaluated using a Nanodrop 2000 (Thermo Scientific) and visualized through agarose gel electrophoresis with 1% TBE agarose. The Qubit dsDNA HS Assay Kit (Thermo Scientific) was utilized for enhanced DNA quantification accuracy. The integrity of DNA was assessed utilizing the 4150 TapeStation (Agilent).Genomic DNA was utilized as the input for library preparation. The genomic DNA was enzymatically fragmented to obtain the required insert size. The fragmented DNA was ligated with MGI-compatible adapters, each containing a unique barcode for each sample. PCR was performed to amplify the library. The quality and quantity of library samples were assessed using Tape Station and Qubit Fluorometer, respectively. The amplified library samples underwent circularization, and the resulting circular DNA served as input for the DNB formation process. The DNBs were loaded onto the flow cell, and sequencing was conducted for 612 cycles (PE300) utilizing the MGI DNBSEQ-G400. Quality control was conducted to evaluate the quality of reads utilizing FASTQC software version 0.11.8 (Andrews, 2010). Low-quality bases (less than 30), adapters, nucleotide position biases at the 3' and 5' ends, and sequence contamination were eliminated through trimming and filtering with Trimmomatic version 0.39. The parameters used were TruSeq3-PE.fa:2:30:10, SLIDINGWINDOW:4:28, LEADING:28, TRAILING:28, and MINLEN:20 (Bolger et al., 2014). The clean reads were then assembled using GetOrganelle version 1.7.7.1 (Jin et al., 2020). Annotation was conducted with CPGAVAS2 (http://47.96.249.172:16019/analyzer/annotate) (Shi et al., 2019), utilizing the cp genome of Artocarpus gomezianus Wall. ex Trécul (accession number: NC_080592) as a reference. This was followed by manual verification in Unipro Ugene v. 45.1 (Okonechnikov et al., 2012) andNCBI Genomic Workbench v. 3.8.2 (Kuznetsov andBollin, 2021). The circular genome was visualized with OrganellarGenomeDRAW (OGDRAW) via the MPI-MP Chlorobox (Greiner et al., 2019). The complete chloroplast genome of A. tamaran has been successfully assembled, measuring 160,294 bp and exhibiting a quadripartite structure comprising four regions: the large single-copy (LSC) region, the small single-copy (SSC) region, and two inverted repeats (IR) regions (Figure 1). The LSC region has a length of 88,789 bp, the SSC region measures 20,015 bp, and each IR region is 25,745 bp. The genome exhibits a total GC content of 36%, with the highest concentration observed in the IR regions at 46.2%, followed by the LSC region at 34.2% and the SSC region at 28.9%. A total of 129 genes, comprising 110 unique genes, were annotated in the A. tamaran chloroplast genome. The identified genes comprised 84 protein-coding genes (77 unique), 37 tRNAs (29 unique), and 8 rRNAs (4 unique). Of the 129 genes analyzed, 14 exhibited a single intron, while three genes (rps12, ycf3 and clpP) contained two introns (see Table 1). psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbM, psbN, psbT, psbZ, ycf3