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Gyrinops versteegii and Aquilaria malaccensis are two important species of the Aquilarieae tribe. The main problem of this tribe is the challenge of species identification that is strongly dependent on the presence of flowers and fruit, which are not always available. The availability of whole genome information is expected to address the problems of species identification. This research aims to construct and compare the chloroplast and mitochondrial genomes of G. versteegii and A. malaccensis from short-read data using the NOVOplasty and GetOrganelle assembler. The chloroplast genome assembly revealed a full-length quadripartite circular structure with sizes of 174.814 bp (G. versteegii) and 174.821–174.822 bp (A. malaccensis), with highly conserved gene and organization. Meanwhile, the mitochondrial genome is multipartite with a size of 400.012 bp (G. versteegii) and 400.000 bp (A. malaccensis), with highly variable genes and organization due to the presence of gene cluster repeats. The LSC/IR/SCC region borders and phylogenetic analysis in chloroplasts indicate variations between the genomes of these two species. The investigation of nucleotide diversity in the chloroplast genome revealed that the trnL-rpl32 region had the highest nucleotide diversity (Pi = 0.03). This information will be useful in the future for a variety of downstream analyses.

Sengon (Falcataria falcata) is an economically important legume tree widely cultivated in community forests, especially in Java Island. However, attacks of gall rust disease by Uromycladium falcatariae is difficult to manage. Understanding sengon genes expressions when artificially infected with gall rust fungi can help unravel its resistance mechanisms. Total RNA was extracted from sengon seedlings samples inoculated with U. falcatariae fungi at 7, 21, and 35 days after inoculation (DAI) and from the control group. Total RNA sequencing was performed using the PCR-cDNA Sequencing protocol (SQK-PCB109) from Oxford Nanopore Technologies. The RNA-Seq obtained varies from 1.3 million to 1.9 million total reads. The assembled full-length transcript was constructed using the RATTLE program, resulting in 21,819 transcripts. The TransDecoder program used to define open reading frames (ORFs) generated 2,342 transcripts, of which 34.15% were 5′prime_partial, 8.15% were 3′prime_partial, 8.5% were internal, and 49.14% were complete. Analysis of differentially expressed genes (DEGs) between resistant and susceptible seedlings, found that 1,013 genes that were up-regulated and 1,130 genes that were down-regulated in the resistant lines. The transcriptome data discussed in this article have been deposited in the DDBJ with accession number DRA015681.

Abstract Objectives Falcataria moluccana, known locally as Sengon, is a fast-growing legume tree that is commonly planted in community forests of Java Island, Indonesia. However, the plantations face attacks of Boktor stem borer (Xystrocera festiva) and gall-rust disease (Uromycladium falcatariae) as major threats to its productivity. To control those pest and disease, it is necessary to grow resistant sengon clones, which are developed through tree improvement program, of which needs genetic and genomic information. This dataset was created to construct draft of sengon chloroplast genome and to study the evolution of sengon based on matK and rbcL barcode genes. Data description Genomic DNA was extracted from leaf samples of one individual healthy tree in a private plantation. The DNA was sequenced using Illumina Novaseq 6000 (Novogen AIT, Singapore) for short-reads data, and MinION of Nanopore following manufacture’s protocols SQK-LSK110 for long-reads data. The 66,3 Gb short-reads and 12 Gb long-reads data were hybrid assembled and used to construct a 128.867 bp of F. moluccana chloroplast genome with a quadripartite structure, containing a pair of inverted repeats, a large single-copy and a small single-copy region. Phylogenetic tree constructed using matK and rbcL showed monophyletic origin of F. moluccana and other legume trees.

Sengon (Falcataria falcata (L.) Greuter & R. Rankin) plantations in Indonesia are threatened by attacks from Boktor stem borers and gall rust disease. Controlling pests and diseases is difficult; therefore, planting resistant trees obtained from tree selection programs is necessary. Currently, genomic breeding often incorporates GWAS, which uses thousands of SNP markers to identify markers with significant associations with the traits studied. This study aimed to bypass such expensive studies by identifying and developing SNP markers from sequences of putative resistance genes to Boktor stem borer and gall rust disease, identified from sengon transcriptomic data analysis. A total of 496,194 putative SNP sites were identified from transcriptomic sequences using the SAMtools and BFCtools programs, of which 119 SNP sites were associated with resistance genes. Of the 101 non-synonymous SNPs selected, only 12 were located in the conserved domain of each gene and were used for primer design. Of the 13 primers designed, only 10 were successfully amplified. Validation of 10 developed SNP markers on 100 sengon accessions using the HRM method confirmed a significant association between SNP markers and resistance traits, with a -log 10 (P-value) between 10.49 and 16.63. A few SNPs markers developed from putative resistance gene sequences are associated with resistance traits in sengon. Therefore, the SNP markers could be applied in selection programs for sengon trees resistant to Boktor stem borers and gall rust disease.

Highlight Research • One of the content of microalgae that is beneficial for health is polysaccharides • Polysaccharides of Indonesian microalgae can be promoted as anti-malarial • Polysaccharides from Glagah, Spirulina and East Java microalgae inhibited the growth of plasmodium in vitro and had IC50 values of 3.18 µg/mL, 5.43µg/mL and 9.87 µg/mL, respectively Abstract Malaria is an infectious disease caused by protozoan parasites of the genus Plasmodium that categorized as deadliest diseases in the world. Artemisinin and its derivatives are still recommended drugs for malaria therapy, however, there have been indications that Plasmodium parasites are resistant to this drug. Therefore, a study on polysaccharides from microalgae may be a potential as bioactive compound for anti-malaria. The aim of this study was to determine the effectiveness of the mixed microalgae polysaccharides as anti-malarial in vitro. Polysaccharides were extracted from three microalgae Spirulina sp., mixed microalgae Glagah and mixed microalgae East Java using the alkaline extraction method. The anti-malarial activity test refers to the concentration of polysaccharides used in calculating the IC50 value by probit analysis. The concentration of polysaccharides of the three microalgae used were 0; 0.01; 0.01, 1, 10 and 100 µg/mL. The results showed that the IC50 values of polysaccharides of Glagah, Spirulina sp. and East Java microalgae were 3.18 µg/mL, 5.43µg/mL, and 9.87 µg/mL, respectively. In Conclusion, polysaccharides of Indonesian mixed microalgae can be promoted as anti-malarial.

Endophytic fungi have been reported to promote plant growth and resistance to biotic and abiotic stresses. This study aimed to determine the effect of endophytic fungi application isolated from the sengon (Falcataria moluccana) seeds on the growth of sengon. The seed-borne endophytic fungi were applied when the session was three weeks old by sprinkling each suspension of endophytic fungi (103 to 106 spores/ml) on the soil around the plant roots. The experimental parameters evaluated were height, diameter, and total wet and dry weight. This study showed that endophytic fungi treatment has no significant effect on the stem diameter, total wet weight, and water content; but significantly affected the height and total dry weight. Cladophialophora sp. and Ascotricha sp. fungi increased the height growth of sengon, while Aspergillus sp. fungi increased the total dry weight against the control. Ochroconis sp. treatment was not significantly different from the control. The shoot-root ratio values range from 1.13-1.43, indicating that the seeds already have roots supporting plant growth. The Dickson quality index range from 0.65-1.03 suggested that the seedlings have good biomass distribution. Consequently, endophytic fungi have the potential to increase the growth of sengon seedlings. Keywords: endophytic fungi, Falcataria moluccana, seedling growth, sengon

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.

Initial evaluation of phenotypic variability and genetic diversity was conducted on the progeny test of 2 years-old sengon from Solomon provenance, which derived from nine families of mother tree and were then planted in 4 blocks in the Cirangsad Experimental Forest. Phenotypic assessment on eight traits was conducted on 36 trees using a scoring system, while genetic diversity of 15 selected individuals which represented high and low-score phenotypic traits was analyzed using 5 selected RAPD primers. The result on phenotypic assessment showed that family 3 (57.25 points) has the highest average score of phenotypic quality and family 4 has the lowest average score (7.50 points). Furthermore, genetic analysis showed that the low-scoring sengon population had a greater mean genetic diversity (He = 0.2535) than the high-score population (He = 0.2345). The analysis of molecular variance (AMOVA) revealed a significant genetic differences (p-value < 0.001) among high and low-score populations and the dendrogram of genetic distance revealed clustering of individuals having similar superior phenotypic against those having non-superior, indicating the selection based on phenotypes in this study had succeeded in pooling the good quantitative alleles in the selected population. This evaluation results can be used as a reference in determining the best families to produce superior sengon (from Solomon provenance) offspring in the future that have desired adaptability, productivity, and diversity.

Climate change has forced human being to adapt in fulfilling their energy needs sustainably. In Indonesia, forestry activities has been considered as an emission rather than carbon sink. This study aims to analyze the inputs, outputs, and potential environmental impacts of wood pellet production in a forest company using life cycle assessment (LCA). The wood pellet is made from Eucalyptus pellita plantation. Analysis was made for 1 planting cycle or 6 years, and allometric equations were used to estimate the ability of industrial timber plantation forest to absorb CO2. Production of wood pellet starting from plantation requires inputs as follows: diesel fuel, electricity, NPK and other fertilizers, pesticides, and electrical energy. Those inputs produced emissions, of which the largest was N2O of 551.2927 kg, followed by NH3 of 7.5275 kg generated from NPK fertilizer. Another was PO43- amounted at 0.1792–0.2229 kg from liquid fertilizers and pesticides. Potential acidification came from 13.3675 kg SO2 eq, and eutrophication of 0.4021 kg PO43- eq. The greenhouse gas (GHG) emission was 678.0270 kg CO2 eq from the plantation activities, especially from diesel-based energy consumption, while wood pellet mills only released 0.1053 kg CO2 eq of GHG emissions. Thus, total emissions from 6 years' time of wood pellet production are much lower compared to the average CO2 absorbed by the plantation forest, of which annually is 36.34–67.69 ton ha-1year-1.

This experimental research was performed to observe the influence of an agricultural liquid organic fertilizer called Bio Ferti on the growth and biomass of Spirulina platensis, aiming at replacing inorganic fertilizer with the liquid organic one. The cultivation of the microalgae was conducted over seven days at Nogotirto Algae Park. The liquid organic fertilizer, namely Bio Ferti, was obtained from the Faculty of Biology, Universitas Gadjah Mada, and prepared to have doses of 2, 4, 6, 8, and 10 mL. For comparison, an inorganic fertilizer with the same doses was also prepared. The variables to be observed were cell density, dry cell weight, and growth kinetics. The culture medium conditions observed were temperature, pH, and salinity (the optimum salinity was 20 ppt). The growth kinetic analysis was performed mathematically using numerical simulations using the Contois and the Haldane models. This research’s results showed that Bio Ferti affected the growth rate of Spirulina platensis. With a dose of 2 mL, it became the optimum medium which produced the highest density and dry weight of 1.78x106 cells/mL and 160 mg/mL, respectively. Meanwhile, the inorganic fertilizer with a dose of 10 mL produced the highest density and dry weight of 2,13x105 and 80 mg/mL, respectively. The temperature ranged from 28 to 31°C, while the pH ranged from 8.01 to 9.02 for each medium. The suitable model to describe the growth kinetics of Spirulina platensis was the Haldane model.

Abstract Objectives Efforts to restore tropical peat swamp forests in Indonesia face huge challenges of potential failures due to socio-economic factors and ecological dynamics attributed to lack of knowledge on the adaptive mechanisms of potential tree species such as Kapur (Dryobalanops aromatica C.F.Gaertn Syn. Dryobalanops sumatrensis J.F. Gmelin A.J.G.H Kostermans). This species is a multi-purpose tree that, commonly grows in mineral soils, but also in peat swamp as previously reported, which raised a fundamental question regarding the molecular mechanism of this adaptation. Therefore, a dataset was created aiming to detect candidates of adaptive genes in D. aromatica seedlings, cultivated in two contrasting potting media, namely mineral soil and peat media, based on RNA Sequencing Transcriptome Analysis. Data description The RNA transcriptome data of D. aromatica’s seedlings derived from young leaves of three one-year-old seedlings, raised in each dry mineral soil media and peat media, were generated by using Illumina HiSeq 4000 platform in NovogenAIT, Singapore. The acquired data, as the first transcriptome dataset for D. aromatica, is of a great importance in understanding molecular mechanism and responses of the involved genes of D. aromatica to the contrasting, growing potting media conditions that could also be useful to generate molecular markers.

Shorea is a genus of the Dipterocarpaceae family which shows high economic and ecological values. Currently, market demand for wood is still met from natural forests that are degrading due to over exploitation. The degraded forests are included in the rehabilitation program that require significant number of planting stocks, mainly from seedlings or wildlings. Correct species identification of planting stocks, particularly wildlings, is an important first step in planting activities and it is relevant with Shorea spp planting stocks due to leaf morphology traits. This study was aimed to examine the traits of leaf morphology of four Shorea species for easy field identification. Samples were taken from five trees for each species. Morphological trait identification was conducted by leaf observation and measurement. The results showed that all four species had the same apex shape. Six of the twelve morphological characteristic of the variable character can influence the morphological characteristics of the leaves, namely the roving leaf, leaf area, leaf length, aspect ratio, form factorand perimeter ratio of diameter. S. leprosula is similar to S. parvifolia, while S. ovalis is similar to S. guiso. Shorea leaf character S. parvifolia differentiated from S. leprosula, while Shorea ovalis similar to Shorea guiso. The LP variable (length from the base of the leaf to the widest point of the leaf) is a variable that can be used as aleaf morphological characteristic of the four Shorea which are compared because each one has a different value. S. ovalis has the highest LP value, followed by S. guiso and S. leprosula, while S. parvifolia has the lowest LP value. Keywords: apex shape, identification, leaf morphology traits, Shorea

Indonesia has a high genetic diversity of tropical fruits. However, studies on genomics are still very limited. In this data article, six underutilized Indonesian fruits were analyzed for the estimated genome size and partial data of genome assembly including Artocarpus nangkadak (Artocarpus heterophyllus x Artocarpus integer), Salacca sumatrana, Flacourtia inermis, Lansium domesticum, Pometia pinnata, and Syzygium samarangense. These genome data may be used to construct molecular markers for plant systematics and breeding program of these species. Our genome data were sequenced paired-end libraries using BGISeq-500 and generated approximately 5 Gb of bases per species. The raw sequences have been deposited in the DNA Data Bank of Japan (DDBJ) under the DDBJ BioProject umbrella with accession number PRJDB7265 and to the DDBJ Read Archive for each species following Artocarpus nangkadak (DRA007398), Salacca sumatrana (DRA007394), Flacourtia inermis (DRA007395), Lansium domesticum (DRA007393), Pometia pinnata (DRA007396), Syzygium samarangense (DRA007397).

Pine woolly adelgid is a recently found exotic pest attacking seedling up to grown plants of Pinus merkusii plantations forest. Since its discovery, there were not much information about it. The objectives of this research were to study pine woolly adelgids distribution, symptoms and indicators, and its scale of infestations on Pinus merkusii plantation in Java, to determine the presence of any specific P. merkusii sites invaded by pine woolly adelgids, considering the pests were native to boreal and temperate areas. Hypothesis was pine woolly adelgids infestation on P. merkusii in Java is consistent with their native distribution. There were 9 Forest Management Unit (KPH) with infested P. merkusii plantations which were located at altitude between 900 to 1,700 m asl. with temperature ranging 16-22 ˚C and air humidity 80-90%. This indicated that Pine Woolly Adelgids required low temperature to survive, which was consistent with their original distribution. Host preference with regard to scale of infestation was closely related to temperature, altitude, and number of trees per hectare. The scale of infestation varied among regions, from light to heavy infested/death of trees.Keywords: pine woolly adelgid, Pinus merkusii, scale of infestation, host preferences

Forest exploitation and conversion to other landuse may cause lost of biodiversity, including most important dipterocarp trees species, i.e. Shorea leprosula and Shorea laevis. The objective of this study was to determine the rarity status of the two important shorea species, i.e. S. laevis and S. leprosula, based on IUCN criteria, their habitat characteristics, and their association with other species, as one of the basis for determining their conservation strategy as a part of forest management. This study was conducted in three types of ecosystem (virgin forest, secondary forest, and fragmented forest) in Muara Teweh, Central Kalimantan. Methodology used in this research includes vegetation and tree diversity analysis. Study results showed that both S. laevis and S. leprosula were included within category of “low risk” in the 3 types of ecosystem in the forest area being studied. Habitat characteristics which determined the absence of S. laevis in the virgin forest habitat was the soil permeability which was too low, whereas other soil chemical and physical properties in the three types of ecosystems were relatively similar. Presence of S. laevis were positively associated with species of S. uliginosa, Dialium platysepalum, Dipterocarpus ibmalatus, Palaquium rostatum, Vatica rasak, Adinandra sp., and Memecyclon steenis. On the other hand, S. leprosula were positively correlated with S. kunstleri, Castanopsis sp., Shorea sp., Quercus bennettii, Castanopsis argentea, and D. hasseltii.Keywords: threatened species, Shorea spp., habitat characteristic, ecosystems type, associated species