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The selection of tree species suitable for restoration in diverse site conditions is still a challenge. Therefore, this study aimed to analyze the phenotypic and genetic characteristics of Dryobalanops aromatica seedlings growing in mineral soil media and peat media. Phenotypic characteristics were evaluated by analyzing the growth performance, leaf morphological characteristics, leaf color, and chlorophyll content, while genetic characteristics were evaluated by using microsatellite markers. The study revealed that seedlings planted in peat media exhibited greater height and shoot length growth, although the difference was not statistically significant compared to those in mineral soil media. However, seedlings in mineral soil media displayed a significantly higher survival rate than those in peat media. Peat-grown seedlings had higher chlorophyll content in their leaves, while mineral soil-grown seedlings displayed a lighter green leaf color based on digital analysis. Genetic analysis indicated a high genetic diversity of overall D. aromatica seedlings (He = 0.635) and unclear genetic structure between the two media. Overall, these findings demonstrate the successful adaptation of D. aromatica seedlings to peat media, positioning them as a promising choice for peatland restoration.

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.

The crab and seafood processing industry must fulfill standard requirements for sanitation, hygiene, and good manufacturing methods to ensure the safety of the products and free from foodborne bacteria. However, equipment and processing unit surfaces are challenging to clean optimally, which can cause persistent bacteria to emerge. Eliminating persistent bacteria is the latest challenge in the fish processing industry for optimal disinfection, preventing cross-contamination, and controlling foodborne outbreaks. Microbiological testing in industry has been limited to selective culture-media techniques; thus, a rapid, sensitive, accurate, and routine applicable analytical method is urgently needed. The significant reduction in the costs of high-throughput sequencing technologies supports the possibility of routine applications in the industry. This study aimed to determine the profile of the microbial community on the surface of the production room and blue-swimming crab processing unit equipment using short-read metagenomic techniques. The analysis included the stages of sampling, bacterial incubation, bacterial DNA isolation, sequencing, and bioinformatics analysis. The first important step to increase the possibility of routine adoption in the seafood industry is to reduce the cost, complexity, and time required to complete the analysis. Therefore, in this protocol, we generate a scalable, flexible, cost-effective, and auditable workflow. • Collection of bacterial samples by swabbing the surface of the equipment using a sterile cotton swab and sterile cloth, which is easy to apply and follow in the blue-swimming crab processing plant industry. • Effective and efficient sample-pooling is an important step in identifying bacterial communities by metagenomic analysis.

Balsa (Ochroma pyramidale) is fast-growing forest plant species introduced to Indonesia with limited genetic information. Genetic information can be obtained through molecular assessment which is now feasible due to sequencing technology development. This is supported by the third-generation sequencer technology, which has been developed using long-read sequencing technology. MinION Oxford Nanopore Technology is one of the long-read sequence-based sequencers with a real-time process and portable. This study aims to generate genomic data and analyze the phylogenetic relationship of balsa (O. pyramidale) based on long-read sequences with MinION Oxford Nanopore Technologies. Balsa long-read sequencing generated a partial chloroplast genome (cpDNA) sequence of 155,430 bp, which can be used for further DNA barcode-based phylogenetic analysis from the chloroplast genome. Phylogenetic analysis showed that the balsa species (O. pyramidale) was genetically grouped in one clade with other O. pyramidale species in phylogeny analysis based on rbcL, matK, and a combination of rbcL and matK genes indicated that those genes were a suitable marker for phylogenetic analysis in balsa species (O. pyramidale).

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.

AbstractDalbergia latifolia is commercial tropical tree species known for its beautiful heartwood, mainly used for furniture and musical instrument. High market demand has put concerns on its sustainability and conservation aspects in Indonesia. Ninety-five specimens of D. latifolia were collected from eight populations of Java, Lombok, and Sumbawa Island to study intraspecific variability and diversity using SRAP. One hundred and eighty SRAP loci with 54.03% ± 4.35% polymorphism obtained from PCR amplification of 10 primer combinations, with the average PIC for these primers of 0.28. Genetic diversity and variability measures were calculated using GenAlEx software indicating a relatively low-mid level of percentage of polymorphic loci (PPL) (54.03%), effective number of alleles (Ne) (1.255), Shannon information index (I) (0.242), and heterozygosity (He) (0.156) on average. The highest value (I = 0.309, He = 0.196) was observed in population P2CJ (Central Java), followed by West Java of P1WJ (I = 0.300, He = 0.191) and West Sumbawa of P7Wsumb (I = 0.257, He = 0.169), while the lowest (I = 0.202, He = 0.129) was found in West Lombok (P4WL). The genetic relationships were measured from genetic distance and identity from the two-pairwise calculation, PCoA, and STRUCTURE analysis. The relative homologous population is found between populations Central and West Java of P2CJ and P1WJ (Nei uD = 0.031), suggesting these populations have the same origin and formed one population, while the most distinct (Nei uD = 0.157) was recorded between Sumbawa regency (P6Sumb) and East Java (P3EJ). The results from PCoA showed that all individuals are placed in three groups almost in accordance with their respective islands, i.e. a group comprised inclusively trees from Sumbawa island, a group of Lombok and some Central Java trees, and a group of trees from Java with the exclusion of some trees of Central Java that were clustered with trees from Lombok island. This result was also supported by STRUCTURE analysis, which showed that Sumbawa, Lombok, and West-East Java populations formed their respective clusters, and Central Java population contains a mixture of West-East Java and Lombok populations. This may suggest evidence of complex origin, thus needing further study to clarify. It is recommended that the populations with the highest value of genetic diversity (Central and East Java) are to be maintained as the source of the gene pool for genetic enrichment programs.

Ebony (Diospyros celebica Bakh) is an endemic forest tree species found in Sulawesi whose basic information on its metabolite profile is still lacking. The objective of this research was to separate and identify putatively metabolite present in the leaves and wood of ebony across Sulawesi. Separation and identification of ebony metabolites were carried out using UHPLC-Q-Orbitrap HRMS analysis. Using ultrasonication with ethanol as the extracting solvent, we used powdered ebony leaves and wood. The results showed that the metabolites contained in the leaves and wood of ebony were 59 metabolites. About 14 compounds were found in the leaves and wood, 21 compounds in the wood, and 24 compounds in the leaves. The identified metabolites are flavonoids, terpenoids, amino aldehydes, alkaloids, quinones, steroids, amino acids, fatty acids, and saccharides. Clustering of ebony using principal component analysis obtained leaves and wood groups using peak area of known compounds as the variable.

Camphor (Dryobalanops aromatica C. F. Gaertn.) is a vulnerable tropical tree species that has been exploited for its timber as well as its resin, which is used for medicinal uses. The use of camphor in Indonesia is limited owing to the decreasing size of the species' population in its native habitat. Therefore, replanting programs have been encouraged for this species owing to its adaptability to mineral soils and shallow peatlands. However, experimental evidence of the effect of different growing media on morphology, physiology, and biochemistry is very limited, which is needed to evaluate the replanting program's success. Therefore, this study aimed to determine the responses of camphor (D. aromatica) seedlings grown in two different types of potting media i.e. mineral and peat, for 8 weeks of planting. In particular, the types of bioactive compounds produced in camphor leaves and their levels were assessed by analyzing their metabolite profiles. Leaf growth was evaluated morphologically using the plastochron index, while photosynthetic rates were measured with LI-6800 Portable Photosynthesis System. Metabolites were identified by using liquid chromatography-tandem mass spectrometry. The percentage of LPI of 5 or more was lower in the peat medium at 8% than in the mineral medium at 12%. The photosynthetic rate of camphor seedlings was 1–9 μmol CO2 m⁻2 s⁻1, with a higher rate in the peat medium than in the mineral medium, suggesting that the peat medium was better for growth. Lastly, the metabolomic analysis in the leaf extract revealed the presence of 21 metabolites, which were dominated by flavonoid compounds.

Sample collection activities for a study of population genetics across the natural distribution of targeted tree species require a lot of resources, mainly if repeated field visits are necessary. Conventionally, population genetic studies use good sample material like leaves. In addition, cambium or small pieces of fresh wood can be used to replace leaf samples. Currently, restrictions from the permit regulation have caused only a limited number of samples that can be collected. Therefore, efficient use of samples must be designed to maximize their uses for research. Due to the small amount of successfully sampled materials, hence there are limitations to extend their uses for other analyses and are often sufficient only for genetic analysis. Therefore, innovation in sampling methods using pickering punch (https://www.agroisolab.com/pickering-punch) to collect ebony wood cores in this study is required to cover multi-analyses not only limited to genetics but also for other analyses such as isotopes, near-infrared spectroscopy (NIRs), anatomy, and chemical compounds. • Pickering punch is recommended for efficient wood core sample collection from ebony standing trees. • 323 wood core samples were successfully collected from 16 natural populations across Celebes (Sulawesi). • Multi-analyses studies on sampled wood cores are possible for ebony wood identification (e.g., species and origin/provenance).

Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) belongs to the Magnoliids group and is mainly distributed in Indonesia and Southeast Asia. The complete chloroplast (cp) genome of C. burmanni sampled from Indonesia was assembled and annotated for the first time in this study. The length of the cp genome is 152,765 bp with a GC content of 39%, and it consists of four subregions: a large single-copy (LSC) region of 93,636 bp, a small single-copy (SSC) region of 18,893 bp and two inverted repeats (IR) regions (IRA 20,121 bp; IRB 20,115 bp) . The cp genome of C. burmanni encodes a total of 173 unique genes, which are 96 protein-coding genes, 19 rRNA genes, and 68 tRNA genes that can be utilized for advanced genetic and genomic studies of the species.

Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) belongs to the Magnoliids group and is mainly distributed in Indonesia and Southeast Asia. The complete chloroplast (cp) genome of C. burmanni sampled from Indonesia was assembled and annotated for the first time in this study. The length of the cp genome is 152,765 bp with a GC content of 39%, and it consists of four subregions: a large single-copy (LSC) region of 93,636 bp, a small single-copy (SSC) region of 18,893 bp and two inverted repeats (IR) regions (IRA 20,121 bp; IRB 20,115 bp) . The cp genome of C. burmanni encodes a total of 173 unique genes, which are 96 protein-coding genes, 19 rRNA genes, and 68 tRNA genes that can be utilized for advanced genetic and genomic studies of the species.