Transcriptome dataset of gall-rust infected Sengon (Falcataria falcata) seedlings using long-read PCR-cDNA sequencing.

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.

Effects of two contrasting potting media on the leaf development index, photosynthetic rate, and metabolite profile of camphor (Dryobalanops aromatica) seedlings.

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.

Integrative taxonomy using the plant core DNA barcodes in Sumatra's Burseraceae.

The high diversity and limited floral information in tropical forests often pose a challenge for species identification. However, over the past decade, DNA barcoding has been employed in tropical forests, including Sumatran forests, to enhance floristic surveys. This technique facilitates the discrimination of morphologically similar species and addresses the limitations of conventional species identification, which relies on short-lived reproductive structures. This study aimed to evaluate the efficiency of matK, rbcL, and the combination of both chloroplast markers for species identification in Burseraceae by employing genetic distance and species tree inference. In this study, we collected 197 specimens representing 20 species from five genera of Burseraceae. The highest percentage of specimens' identification (36%) at the species level was obtained using matK + rbcL, followed by matK (31%), and rbcL (7%). The matK dataset presented the highest interspecific divergence with a mean of 0.008. In addition, a lack of barcode gap was observed in both markers, suggesting potential limitations of the core barcodes for distinguishing Sumatran species within Burseraceae. The monophyly test confirmed five species as monophyletic using Bayesian species tree inferences for matK. Overall, our results demonstrate that matK outperforms rbcL in species identification of Burseraceae, whereas their combination did not enhance species delimitation. To improve the molecular species assignments of this family, future studies may consider including more DNA markers in conjuction with matK, and broadening the availability of reference sequences for species that have not yet been included in the databases. The outcomes of molecular species identification vary depending on the taxonomic group under investigation. Implementation of phylogenomics for species delimitation and diagnostic marker development is strongly recommended for tropical biodiversity assessments, especially for poorly studied clades.

Molecular and morphological survey of Lamiaceae species in converted landscapes in Sumatra.

Molecular biodiversity surveys have been increasingly applied in hyperdiverse tropical regions as an efficient tool for rapid species assessment of partially undiscovered fauna and flora. This is done by overcoming shortfalls in knowledge or availability of reproductive structures during the sampling period, which often represents a bottleneck for accurate specimens' identification. DNA sequencing technology is intensifying species discovery, and in combination with morphological identification, has been filling gaps in taxonomic knowledge and facilitating species inventories of tropical ecosystems. This study aimed to apply morphological taxonomy and DNA barcoding to assess the occurrence of Lamiaceae species in converted land-use systems (old-growth forest, jungle rubber, rubber, and oil palm) in Sumatra, Indonesia. In this species inventory, we detected 89 specimens of Lamiaceae from 18 species distributed in seven subfamilies from the Lamiaceae group. One third of the species identified in this study lacked sequences in the reference database for at least one of the markers used (matK, rbcL, and ITS). The three loci species-tree recovered a total of 12 out of the 18 species as monophyletic lineages and can be employed as a suitable approach for molecular species assignment in Lamiaceae. However, for taxa with a low level of interspecific genetic distance in the barcode regions used in this study, such as Vitex gamosepala Griff. and V. vestita Wall. ex Walp., or Callicarpa pentandra Roxb. and C. candidans (Burm.f.) Hochr., the use of traditional taxonomy remains indispensable. A change in species composition and decline in abundance is associated with an increase in land-use intensification at the family level (i.e., Lamiaceae), and this tendency might be constant across other plant families. For this reason, the maintenance of forest genetic resources needs to be considered for sustainable agricultural production, especially in hyperdiverse tropical regions. Additionally, with this change in species composition, accurate species identification throughout molecular assignments will become more important for conservation planning.

Collecting wood core samples from Macassar ebony (Diospyros celebica Bakh.) for multi-purpose analysis using pickering punch.

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).

Generating long-read sequences using Oxford Nanopore Technology from Diospyros celebica genomic DNA.

OBJECTIVES: Development of sequencing technology has opened up vast opportunities for tree genomic research in the tropics. One of the aforesaid technologies named ONT (Oxford Nanopore Technology) has attracted researchers in undertaking testings and experiments due to its affordability and accessibility. To the best of our knowledge, there has been no published reports on the use of ONT for genomic analysis of Indonesian tree species. This progress is promising for further improvement in order to acquire more genomic data for research purposes. Therefore, the present study was carried out to determine the effectiveness of ONT in generating long-read DNA sequences using DNA isolated from leaves and wood cores of Macassar ebony (Diospyros celebica Bakh.). DATA DESCRIPTION: Long-read sequences data of leaves and wood cores of Macassar ebony were generated by using the MinION device and MinKnow v3.6.5 (ONT). The obtained data, as the first long-read sequence dataset for Macassar ebony, is of great importance to conserve the genetic diversity, understanding the molecular mechanism, and sustainable use of plant genetic resources for downstream applications.

DNA isolation success rates from dried and fresh wood samples of selected 20 tropical wood tree species for possible consideration in forensic forestry.

The successful isolation of DNA (Deoxyribonucleic Acid) is essential for the investigation process of forestry molecular genetics. Samples used are usually retrieved either from soft or juvenile plant organs because of their excellent DNA source. However, in certain cases, aforesaid samples are hard to obtain, as for forensic purposes. Alternatively, woods possess potential as alternative source of DNA whose extraction method has been developed with varying degrees of success. However, to date, effectiveness on tropical wood grown in Indonesia has not been widely reported. Therefore, objective of this study was to compare the results of DNA isolation of various dried and fresh wood samples by using two isolation methods: Cetyl Trimethyl Ammonium Bromide (CTAB) and Qiagen DNeasy Plant Mini Kit (QDPMK). Extraction results were visualized in agarose gels and quantified using Nanophotometer NP80 Implen which were then amplified using two universal primers: ITS and rbcL for detecting DNA signals. Extraction results from dried wood indicated no visualization in the gel, while fresh wood samples showed thick smeared bands on both extraction methods. Quantity test results denoted higher concentration in CTAB-extracted samples compared to samples extracted using QDPMK, in both types of samples, even though both resulted in optical density ratios outside the range of purity (λ260/280: 1,8-2,0 and λ260/230: 2,0, respectively). Success rates of ITS and rbcL primary amplification in dried wood samples were quite low yet outputs from the two methods did not differ significantly. Meanwhile, outcome of ITS and rbcL amplification on fresh wood samples had a fairly high success.

The genetic variation and relationship among the natural hybrids of Mangifera casturi Kosterm.

Mangifera casturi Kosterm., a mango plant from Kalimantan Selatan, Indonesia, has limited genetic information, severely limiting the research on its genetic variation and phylogeny. We collected M. casturi's genomic information using next-generation sequencing, developed microsatellite markers and performed Sanger sequencing for DNA barcoding analysis. These markers were used to confirm parental origin and genetic diversity of M. casturi hybrids. The clean reads of the Kasturi accession were assembled de novo, producing 259 872 scaffolds (N50 = 1 445 bp). Fourteen polymorphic microsatellite markers were developed from 11 040 microsatellite motif-containing sequences. In total, 58 alleles were produced with a mean of 4.14 alleles per locus. Microsatellite marker analysis revealed broad genetic variation in M. casturi. Phylogenetic analysis was performed using internal transcribed spacers (ITS), matK, rbcL, and trnH-psbA. The phylogenetic tree of chloroplast markers placed Kasturi, Cuban, Pelipisan, Pinari, and Hambawang in one group, with M. indica as the female ancestor. Meanwhile, the phylogenetic tree of ITS markers indicated several Mangifera species as ancestors of M. casturi. Thus, M. casturi very likely originated from the cross-hybridization of multiple ancestors. Furthermore, crossing the F1 hybrids of M. indica and M. quadrifida with other Mangifera spp. may have generated much genetic variation. The genetic information for M. casturi will be a resource for breeding improvement, and conservation studies.

The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests.

Hyperdiverse tropical rainforests, such as the aseasonal forests in Southeast Asia, are supported by high annual rainfall. Its canopy is dominated by the species-rich tree family of Dipterocarpaceae (Asian dipterocarps), which has both ecological (e.g., supports flora and fauna) and economical (e.g., timber production) importance. Recent ecological studies suggested that rare irregular drought events may be an environmental stress and signal for the tropical trees. We assembled the genome of a widespread but near threatened dipterocarp, Shorea leprosula, and analyzed the transcriptome sequences of ten dipterocarp species representing seven genera. Comparative genomic and molecular dating analyses suggested a whole-genome duplication close to the Cretaceous-Paleogene extinction event followed by the diversification of major dipterocarp lineages (i.e. Dipterocarpoideae). Interestingly, the retained duplicated genes were enriched for genes upregulated by no-irrigation treatment. These findings provide molecular support for the relevance of drought for tropical trees despite the lack of an annual dry season.

De novo assembly of transcriptome dataset from leaves of Dryobalanops aromatica (Syn. Dryobalanops sumatrensis) seedlings grown in two contrasting potting media.

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.

De novo transcriptome datasets of Shorea balangeran leaves and basal stem in waterlogged and dry soil.

Shorea balangeran Burk locally known as balangeran has been widely used as recommended species for tropical peat swamp forest restoration, due to the capability of these species to grow in waterlogged and dry areas. However, the information concerning genetic basis of adaptation to ecological condition variation is limited and no transcriptome study has been reported in this context. Here we reported two sets of transcriptome data from a sample of leaf and basal stem that were taken from seedlings growing in potted media containing peat and mineral soil. The raw reads are stored in the DDBJ platform with accession number DRA008633.

The dataset of de novo transcriptome assembly of Falcataria moluccana cambium from gall-rust (Uromycladium falcatarium) infected and non-infected tree.

Sengon (Falcataria moluccana), formerly known as Albizia falcataria or Paraserianthes falcataria, is an essential tree species for the development of community-based timber plantation, especially in Indonesia. The plantations nowadays are facing a significant disease threat, namely infection of gall-rust fungi (Uromycladium falcatarium). However, a clear understanding of the molecular mechanisms of the tree response against the disease is still unknown. We carried out transcriptome assembly using BGISEQ-500 technology to provide assembled de novo transcriptome dataset generated from gall-rust infected and non-infected trees. The construction of assembled transcriptome was conducted using Trinity v.2.3.2 The raw reads are available in the DDBJ platform with accession number, DRA007983.

DNA barcoding of flowering plants in Sumatra, Indonesia.

The rapid conversion of Southeast Asian lowland rainforests into monocultures calls for the development of rapid methods for species identification to support ecological research and sustainable land-use management. Here, we investigated the utilization of DNA barcodes for identifying flowering plants from Sumatra, Indonesia. A total of 1,207 matK barcodes (441 species) and 2,376 rbcL barcodes (750 species) were successfully generated. The barcode effectiveness is assessed using four approaches: (a) comparison between morphological and molecular identification results, (b) best-close match analysis with TaxonDNA, (c) barcoding gap analysis, and (d) formation of monophyletic groups. Results show that rbcL has a much higher level of sequence recoverability than matK (95% and 66%). The comparison between morphological and molecular identifications revealed that matK and rbcL worked best assigning a plant specimen to the genus level. Estimates of identification success using best-close match analysis showed that >70% of the investigated species were correctly identified when using single barcode. The use of two-loci barcodes was able to increase the identification success up to 80%. The barcoding gap analysis revealed that neither matK nor rbcL succeeded to create a clear gap between the intraspecific and interspecific divergences. However, these two barcodes were able to discriminate at least 70% of the species from each other. Fifteen genera and twenty-one species were found to be nonmonophyletic with both markers. The two-loci barcodes were sufficient to reconstruct evolutionary relationships among the plant taxa in the study area that are congruent with the broadly accepted APG III phylogeny.

Integrating DNA Barcoding and Traditional Taxonomy for the Identification of Dipterocarps in Remnant Lowland Forests of Sumatra.

DNA barcoding has been used as a universal tool for phylogenetic inferences and diversity assessments, especially in poorly studied species and regions. The aim of this study was to contrast morphological taxonomy and DNA barcoding, using the three frequently used markers matK, rbcL, and trnL-F, to assess the efficiency of DNA barcoding in the identification of dipterocarps in Sumatra, Indonesia. The chloroplast gene matK was the most polymorphic among these three markers with an average interspecific genetic distance of 0.020. The results of the molecular data were mostly in agreement with the morphological identification for the clades of Anthoshorea, Hopea, Richetia, Parashorea, and Anisoptera, nonetheless these markers were inefficient to resolve the relationships within the Rubroshorea group. The maximum likelihood and Bayesian inference phylogenies identified Shorea as a paraphyletic genus, Anthoshorea appeared as sister to Hopea, and Richetia was sister to Parashorea. A better discriminatory power among dipterocarp species provided by matK and observed in our study suggests that this marker has a higher evolutionary rate than the other two markers tested. However, a combination of several different barcoding markers is essential for reliable identification of the species at a lower taxonomic level.

Characteristics of Surian Flower, Fruit and Seed Productions (Toona sinensis (A. Juss.) M. Roem.) in Sumedang, West Java.

Community forest development requires a constant supply of high-quality seeds. In addition, sound management of Toona sinensis (surian) seed sources requires a deep understanding of factors affecting seed production. This present study investigated the reproduction characteristics of surian, including flower, fruit and seed productions, variations in the productions of fruits and seeds among trees and among branches, and dendrometric factors that influence the productions of fruits and seeds. Flower production characteristics were observed in 99 panicles, fruit production characteristics were observed in 128 panicles, and seed characteristics were evaluated based on 890 fruits. The number of fruits per panicle ranged from 38 to 646. The number of seeds in fruits ranged from 1 to 35. Fruit size was correlated to the number of filled seeds following a quadratic regression equation. The optimal number of filled seeds was 20 per fruit. Stem diameter, crown width, crown base height, and the number of sub-branches positively influenced the production of panicles per tree, while the crown base height (of the tree) negatively affected the fruit set.

Ecological and socio-economic functions across tropical land use systems after rainforest conversion.

Tropical lowland rainforests are increasingly threatened by the expansion of agriculture and the extraction of natural resources. In Jambi Province, Indonesia, the interdisciplinary EFForTS project focuses on the ecological and socio-economic dimensions of rainforest conversion to jungle rubber agroforests and monoculture plantations of rubber and oil palm. Our data confirm that rainforest transformation and land use intensification lead to substantial losses in biodiversity and related ecosystem functions, such as decreased above- and below-ground carbon stocks. Owing to rapid step-wise transformation from forests to agroforests to monoculture plantations and renewal of each plantation type every few decades, the converted land use systems are continuously dynamic, thus hampering the adaptation of animal and plant communities. On the other hand, agricultural rainforest transformation systems provide increased income and access to education, especially for migrant smallholders. Jungle rubber and rubber monocultures are associated with higher financial land productivity but lower financial labour productivity compared to oil palm, which influences crop choice: smallholders that are labour-scarce would prefer oil palm while land-scarce smallholders would prefer rubber. Collecting long-term data in an interdisciplinary context enables us to provide decision-makers and stakeholders with scientific insights to facilitate the reconciliation between economic interests and ecological sustainability in tropical agricultural landscapes.

Population structure and demographic history of a tropical lowland rainforest tree species Shorea parvifolia (Dipterocarpaceae) from Southeastern Asia.

Distribution of tropical rainforests in Southeastern Asia has changed over geo-logical time scale, due to movement of tectonic plates and/or global climatic changes. Shorea parvifolia is one of the most common tropical lowland rainforest tree species in Southeastern Asia. To infer population structure and demographic history of S. parvifolia, as indicators of temporal changes in the distribution and extent of tropical rainforest in this region, we studied levels and patterns of nucleotide polymorphism in the following five nuclear gene regions: GapC, GBSSI, PgiC, SBE2, and SODH. Seven populations from peninsular Malaysia, Sumatra, and eastern Borneo were included in the analyses. STRUCTURE analysis revealed that the investigated populations are divided into two groups: Sumatra-Malay and Borneo. Furthermore, each group contained one admixed population. Under isolation with migration model, divergence of the two groups was estimated to occur between late Pliocene (2.6 MYA) and middle Pleistocene (0.7 MYA). The log-likelihood ratio tests of several demographic models strongly supported model with population expansion and low level of migration after divergence of the Sumatra-Malay and Borneo groups. The inferred demographic history of S. parvifolia suggested the presence of a scarcely forested land bridge on the Sunda Shelf during glacial periods in the Pleistocene and predominance of tropical lowland rainforest at least in Sumatra and eastern Borneo.

Genetic variation at AFLPs for the Dipterocarpaceae and its relation to molecular phylogenies and taxonomic subdivisions.

Genetic differentiation was investigated among 54 Indonesian species of Dipterocarpaceae, a dominant tree family in Asian tropical rainforests, using amplified fragment length polymorphism markers. The tree developed from the resultant unweighted pair group method using arithmetic averages clearly separated all investigated dipterocarps into two major groups that corresponded to tribe Dipterocarpeae and tribe Shoreae, respectively. These results are in accordance with the topology of molecular phylogenetic trees derived from PCR-restriction fragment length polymorphism analysis of chloroplast DNA and generally support the traditional taxonomic assessments. The possibility of interspecific hybridization is also discussed.