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Summary Dipterocarpaceae are typical tropical plants (dipterocarp forests) that are famous for their high economic value because of their production of fragrant oleoresins, top‐quality timber and usage in traditional Chinese medicine. Currently, the lack of Dipterocarpaceae genomes has been a limiting factor to decipher the fragrant oleoresin biosynthesis and gain evolutionary insights into high‐quality wood formation in Dipterocarpaceae. We generated chromosome‐level genome assemblies for two representative Dipterocarpaceae species viz. Dipterocarpus turbinatus Gaertn. f. and Hopea hainanensis Merr. et Chun. Our whole‐genome duplication (WGD) analysis revealed that Dipterocarpaceae underwent a shared WGD event, which showed significant impacts on increased copy numbers of genes related to the biosynthesis of terpene, BAHD acyltransferases, fatty acid and benzenoid/phenylpropanoid, which probably confer to the formation of their characteristic fragrant oleoresin. Additionally, compared with common soft wood plants, the expansion of gene families was also found to be associated with wood formation, such as in CESA (cellulose synthase), CSLE (cellulose synthase‐like protein E), laccase and peroxidase in Dipterocarpaceae genomes, which might also contribute to the formation of harder, stronger and high‐density timbers. Finally, an integrative analysis on a combination of genomic, transcriptomic and metabolic data from different tissues provided further insights into the molecular basis of fragrant oleoresins biosynthesis and high‐quality wood formation of Dipterocarpaceae. Our study contributes the first two representative genomes for Dipterocarpaceae, which are valuable genetic resources for further researches on the fragrant oleoresins and superior‐quality timber, genome‐assisted breeding and improvement, and conservation biology of this family.

[This corrects the article DOI: 10.3389/fpls.2022.1075102.].

Hopea hainanensis Merrill & Chun (Dipterocarpaceae) is an endangered tree species restricted to Hainan Island, China and a small part of Northern Vietnam. On Hainan Island, it is an important indicator species for tropical forests. However, because of its highly valued timber, H . hainanensis has suffered from overexploitation, leading to a sharp population decline. To facilitate the conservation of this species, genetic diversity and population structure were assessed using 12 SSR markers for 10 populations sampled across Hainan Island. Compared to non-threatened Hopea species, H . hainanensis exhibited reduced overall genetic diversity and increased population differentiation (AMOVA: F ST = 0.23). Bayesian model-based clustering and principal coordinate analysis consistently assigned H . hainanensis individuals into three genetic groups, which were found to be widespread and overlapping geographically. A Mantel test found no correlation between genetic and geographical distances ( r = 0.040, p = 0.418). The observed genetic structure suggests that long-distance gene flow occurred among H . hainanensis populations prior to habitat fragmentation. A recent population bottleneck was revealed, which may cause rapid loss of genetic diversity and increased differentiation across populations. Based on these findings, appropriate strategies for the long-term conservation of the endangered species H . hainanensis are proposed.

Merrill & Chun is considered a keystone and indicator species in the tropical lowland rainforests of Hainan Island. Owing to its high-quality timber, has been heavily exploited, leading to its classification as a first-class national protected plant in China and a plant species with extremely small populations (PSESPs). This study analyzed genome-wide single nucleotide polymorphisms obtained through restriction site-associated DNA sequencing from 78 adult trees across 10 populations on Hainan Island. The nucleotide diversity of the sampled populations ranged from 0.00096 to 0.00138, which is lower than that observed in several other PSESPs and endangered tree species. Bayesian unsupervised clustering, principal component analysis, and neighbor-joining tree reconstruction identified three to five genetic clusters in , most of which were geographically widespread and shared by multiple populations. Demographic history analysis based on pooled samples indicated that the decline in the population began approximately 20,000 years ago, starting from an ancestral population size of approximately 10,000 individuals. The reduction in population size accelerated approximately 4,000 years ago and has continued to the present, resulting in a severely reduced population on Hainan Island. Intensified genetic drift in small and isolated populations may contribute to moderate differentiation between some of them, as revealed by pairwise . In conclusion, our conservation genomic study confirms a severe population decline and an extremely low level of nucleotide variation in on Hainan Island. These findings provide critical insights for the sustainable management and genetic restoration of on Hainan Island.

Giam Malut Hopea ferrea Laness (Dipterocarpaceae) is a woody species that has become endangered due to its habitat destruction and overexploitation. In an effort to support and provide conservation and management of this species, we utilized eight microsatellite loci to investigate the genetic diversity and structure of 234 adult trees across eight populations, encompassing its geographic distribution in Vietnam. The genetic diversity of H. ferrea was found to be low in comparison to other dipterocarps, suggesting a reduction in the number of alleles due to anthropogenic activities. Heterozygosity deficits were identified across all studied populations. Interestingly, the coastal populations exhibited higher genetic diversity compared to the Highlands and southeast populations. Bottleneck effects were detected in the majority of populations, with the exception of the two Highlands populations of Chu Mon Ray and York Don. These effects indicated a reduction in the population sizes. The results of genetic differentiation mirrored the genetic structure and revealed three major clusters corresponding to the three distribution areas of the species. A low level of genetic differentiation among populations (FST=0.146) was detected, consistent with the AMOVA analysis. Geographic distance and anthropogenic activities emerged as the major factors limiting gene exchange among populations. Based on these findings, we propose conservation measures for this endangered species.

The complete chloroplast genome of Hopea rudiformis, a critically endangered species on the IUCN Red List, was sequenced and analyzed to uncover its genomic structure, gene content, and evolutionary context, contributing essential resources for conservation and phylogenetics. Assembled using GetOrganelle with 146.3× coverage, the plastome spans 151,323 bp and follows the typical quadripartite structure of angiosperms, comprising an LSC, SSC, and two IR regions, with an overall GC content of 37.39%, highest in the IRs due to rRNA gene enrichment. A total of 126 genes were annotated, including 83 protein-coding genes, 35 tRNAs, and 8 rRNAs, with gene losses (infA, ycf15, atpF), intron reductions (clpP, rps12), and the presence of cis- and trans-splicing genes (notably trans-spliced rps12) highlighting structural and functional plastome modifications. Codon usage and amino acid profiles showed biases favoring translational efficiency, while 191 SSRs—primarily trinucleotides—were identified, offering potential for marker development. Comparative genome analysis with other Hopea species (H. odorata, H. hainanensis, and H. dryobalanoides) revealed high synteny and conserved IR boundaries, with minor lineage-specific shifts. Phylogenomic analysis positioned H. rudiformis within a well-supported clade alongside these congeners, confirming its evolutionary placement in the core Hopea lineage. This study not only clarifies the plastid genome architecture of H. rudiformis but also provides a foundation for its genetic conservation, phylogenetic refinement within Dipterocarpaceae, and future biodiversity research.

Reasonable cultivation is an important part of the protection work of endangered species. The timely and nondestructive monitoring of chlorophyll can provide a basis for the accurate management and intelligent development of cultivation. The image analysis method has been applied in the nutrient estimation of many economic crops, but information on endangered tree species is seldom reported. Moreover, shade control, as the common seedling management measure, has a significant impact on chlorophyll, but shade levels are rarely discussed in chlorophyll estimation and are used as variables to improve model accuracy. In this study, 2-year-old seedlings of tropical and endangered Hopea hainanensis were taken as the research object, and the SPAD value was used to represent the relative chlorophyll content. Based on the performance comparison of RGB and multispectral (MS) images using different algorithms, a low-cost SPAD estimation method combined with a machine learning algorithm that is adaptable to different shade conditions was proposed. The SPAD values changed significantly at different shade levels ( p  < 0.01), and 50% shade in the orthographic direction was conducive to chlorophyll accumulation in seedling leaves. The coefficient of determination ( R 2 ), root mean square error (RMSE), and average absolute percent error (MAPE) were used as indicators, and the models with dummy variables or random effects of shade greatly improved the goodness of fit, allowing better adaption to monitoring under different shade conditions. Most of the RGB and MS vegetation indices (VIs) were significantly correlated with the SPAD values, but some VIs exhibited multicollinearity (variance inflation factor (VIF) > 10). Among RGB VIs, RGRI had the strongest correlation, but multiple VIs filtered by the Lasso algorithm had a stronger ability to interpret the SPAD data, and there was no multicollinearity (VIF < 10). A comparison of the use of multiple VIs to estimate SPAD indicated that Random forest (RF) had the highest fitting ability, followed by Support vector regression (SVR), linear mixed effect model (LMM), and ordinary least squares regression (OLR). In addition, the performance of MS VIs was superior to that of RGB VIs. The R 2 of the optimal model reached 0.9389 for the modeling samples and 0.8013 for the test samples. These findings reinforce the effectiveness of using VIs to estimate the SPAD value of H. hainanensis under different shade conditions based on machine learning and provide a reference for the selection of image data sources.

Hopea bilitonensis is a rare, endemic Dipterocarp species in the Malesian Region. It has a disjunct distribution pattern, where main populations occur on the sandy soils of Bangka Belitung Islands of Indonesia and some on limestone forest in Perak, Peninsular Malaysia. Current global status of this species based on the IUCN Red List is Critically Endangered (CR) A1c+2c, B1+2c (1998) whilst in Malaysia it is assessed as CR A4c, B1ab(iii) (2010). A reassessment of the conservation status of this species is needed to provide the most current population status and its extinction risk, especially in Indonesia using the IUCN Red List Categories and Criteria version 3.1. This study was conducted to survey and assess the current populations of this species in Belitung Island where most population occurred and subsequently to recommend its current conservation status. The species is in fact still common in the island, stretching along the main roads and surrounding forests. Using the purposive sampling method, we developed a total of 16 plots of 20x20m each in 10 different locations across the Belitung Island. A total of 730 individuals were found with stem diameter at breast height ranged from 2cm to more than 30cm. For global reassessment, based on the current distribution and herbarium records, the calculated extent of occurrence (EOO) is 108,128.642km2, whilst the area of occupancy (AOO) is 84 km2. However, the species clearly has a restricted distribution and is facing high threats due to frequent timber harvesting and continuing decline of the EOO and AOO. The species extinction risk was then assessed by using five quantitative criteria of the IUCN. Therefore, we propose H. bilitonensis category is considered to be Endangered (EN) based on A2c, B2ab(i,ii,iii,iv,v) and C2a(i) criteria.

The national capital of Indonesia is in the early stages of relocation from the island of Java to East Kalimantan; Indonesia’s new capital city (Ibu Kota Negara; IKN) will be called Nusantara. The development of IKN will utilise the concept of a forest city representing the lowland forest of Borneo containing its rich biodiversity. To realize this concept, sufficient data and information regarding the status of tree diversity in this area is required. To provide this information, research was conducted in sample plots totaling 20.75 ha spread over eight locations in East Kalimantan. The selection of priority tree species for rehabilitation was carried out by using the Analytical Hierarchy Process (AHP) method with the criteria of conservation status, endemicity, climax species, distribution, food potential, ethnobotanical potential, animal food, and tree growth rates. In the sample plots, we found 5,745 trees representing 571 species with the family Dipterocarpaceae dominating, followed by Euphorbiaceae, Phyllanthaceae, Malvaceae and Annonaceae. Based on the priority categories of restoration, most of the species proposed for planting belong to the Dipterocarpaceae, in the genera Anisoptera (2 species), Anthoshorea (2 species), Cotylelobium (1 species), Dipterocarpus (3 species), Dryobalanops (1 species), Hopea (3 species), Richetia (3 species), Rubroshorea (7 species), Shorea (4 species), and Vatica (4 species). Hopea rudiformis is a Critically Endangered and Borneo endemic species with the highest score, and the only species included in 1 st priority, followed by 14 species in 2 nd priority, 62 species in 3 rd priority, and the remainder in 4 th priority. About 18% of tree species with potential food sources can be planted to meet the 10% target of forest cover to contribute to food security in IKN. Samboja Research Forest, Sungai Wain Protection Forest, and Bangkirai Hill are forested areas with high tree species diversity and can act as a source of seeds for the IKN nursery.

Microsatellite markers were isolated and characterized for Hopea hainanensis Merrill & Chun, an endangered tree species with scattered distribution in Hainan Island and northern Vietnam. Twenty‐six microsatellite markers were developed based on next‐generation sequencing data and were genotyped by capillary electrophoresis on an ABI 3730xl DNA Analyzer. Twelve markers were found to be polymorphic in H. hainanensis. GENODIVE analyses indicated that the number of alleles ranged from 2 to 6 per locus, and the observed and expected heterozygosity varied from 0 to 0.755 and from 0.259 to 0.779, respectively. Primer transferability was tested with Hopea chinensis Hand.‐Mazz. and Hopea reticulata Tardieu, in which 3 and 7 microsatellite markers were found to be polymorphic, separately. The results showed that H. reticulata and H. hainanensis had similar levels of genetic diversity. A neighbor joining dendrogram clustered all individuals into two major groups, one of which was exclusively constituted by H. hainanensis, while the other consisted of two subgroups, corresponding to H. reticulata and H. chinensis, respectively. The 12 polymorphic microsatellite markers could be applied to study genetic diversity, population differentiation, mating system, and fine‐scale spatial genetic structures of H. hainanensis as well as its close relatives, facilitating the conservation and restoration of these endangered but valuable Hopea species. We reported, for the first time, twelve polymorphic microsatellite markers for an endangered tree species Hopea hainanensis Merrill & Chun. These newly developed microsatellite markers could be applied to study genetic diversity, population structure, and mating system of H. hainanensis, as well as its close relatives, facilitating the conservation and restoration of these endangered and valuable Hopea species.