Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations.

Accurate subgenome phasing is crucial for understanding the origin, evolution and adaptive potential of polyploid genomes. SubPhaser and WGDI software are two common methodologies for subgenome phasing in allopolyploids, particularly in scenarios lacking known diploid progenitors. Triggered by a recent debate over the subgenomic origins of the cultivated octoploid strawberry, we examined four well-documented complex allopolyploidy cases as benchmarks, to evaluate and compare the accuracy of the two software. Our analysis demonstrates that the subgenomic structure phased by both software is in line with prior research, effectively tracing complex allopolyploid evolutionary trajectories despite the limitations of each software. Furthermore, using these validated methodologies, we revisited the controversial issue regarding the progenitors of the octoploid strawberry. The results of both methodologies reaffirm Fragaria vesca and Fragaria iinumae as progenitors of the octoploid strawberry. Finally, we propose recommendations for enhancing the accuracy of subgenome phasing in future studies, recognizing the potential of integrated tools for advanced complex allopolyploidy research and offering a new roadmap for robust subgenome-based phylogenetic analysis.

Chromosome-level genome assembly and population genetic analysis of a critically endangered rhododendron provide insights into its conservation.

Rhododendrons are woody plants, famous throughout the world as having high horticultural value. However, many wild species are currently threatened with extinction. Here, we report for the first time a high-quality, chromosome-level genome of Rhododendron griersonianum, which has contributed to approximately 10% of all horticultural rhododendron varieties but which in its wild form has been evaluated as critically endangered. The final genome assembly, which has a contig N50 size of approximately 34 M and a total length of 677 M, is the highest-quality genome sequenced within the genus to date, in part due to its low heterozygosity (0.18%). Identified repeats constitute approximately 57% of the genome, and 38 280 protein-coding genes were predicted with high support. We further resequenced 31 individuals of R. griersonianum as well as 30 individuals of its widespread relative R. delavayi, and performed additional conservation genomic analysis. The results showed that R. griersonianum had lower genetic diversity (θ = 2.58e-3; π = 1.94e-3) when compared not only to R. delavayi (θ = 11.61e-3, π = 12.97e-3), but also to most other woody plants. Furthermore, three severe genetic bottlenecks were detected using both the Stairway plot and fastsimcoal2 analysis, which are thought to have occurred in the late Middle Pleistocene and the Last Glacial Maximum (LGM) period. After these bottlenecks, R. griersonianum recovered and maintained a constant effective population size (>25 000) until now. Intriguingly, R. griersonianum has accumulated significantly more deleterious mutations in the homozygous state than R. delavayi, and several deleterious mutations (e.g., in genes involved in the response to heat stress) are likely to have harmed the adaptation of this plant to its surroundings. This high-quality, chromosome-level genome and the population genomic analysis of the critically endangered R. griersonianum will provide an invaluable resource as well as insights for future study in this species to facilitate conservation and in the genus Rhododendron in general.

SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome-specific k-mers.

With advanced sequencing technology, dozens of complex polyploid plant genomes have been characterized. However, for many polyploid species, their diploid ancestors are unknown or extinct, making it impossible to unravel the subgenomes and genome evolution directly. We developed a novel subgenome-phasing algorithm, SubPhaser, specifically designed for a neoallopolyploid or a homoploid hybrid. SubPhaser first searches for the subgenome-specific sequence (k-mer), then assigns homoeologous chromosomes into subgenomes, and further provides tools to annotate and investigate specific sequences. SubPhaser works well on neoallopolyploids and homoploid hybrids containing subgenome-specific sequences like wheat, but fails on autopolyploids lacking subgenome-specific sequences like alfalfa, indicating that SubPhaser can phase neoallopolyploid/homoploid hybrids with high accuracy, sensitivity and performance. This highly accurate, highly sensitive, ancestral data free chromosome phasing algorithm, SubPhaser, offers significant application value for subgenome phasing in neoallopolyploids and homoploid hybrids, and for the subsequent exploration of genome evolution and related genetic/epigenetic mechanisms.

Demographic history and identification of threats revealed by population genomic analysis provide insights into conservation for an endangered maple.

Recent advancements in whole genome sequencing techniques capable of covering nearly all the nucleotide variations of a genome would make it possible to set up a conservation framework for threatened plants at the genomic level. Here we applied a whole genome resequencing approach to obtain genome-wide data from 105 individuals sampled from the 10 currently known extant populations of Acer yangbiense, an endangered species with fragmented habitats and restricted distribution in Yunnan, China. To inform meaningful conservation action, we investigated what factors might have contributed to the formation of its extremely small population sizes and what threats it currently suffers at a genomic level. Our results revealed that A. yangbiense has low genetic diversity and comprises different numbers of genetic groups based on neutral (seven) and selected loci (13), with frequent gene flow between populations. Repeated bottleneck events, particularly the most recent one occurring within ~10,000 years before present, which decreased its effective population size (Ne ) < 200, and severe habitat fragmentation resulting from anthropogenic activities as well as a biased gender ratio of mature individuals in its natural habitat, might have together contributed to the currently fragmented and endangered status of A. yangbiense. The species has suffered from inbreeding and deleterious mutation load, both of which varied among populations but had similar patterns; that is, populations with higher FROH (frequency of runs of homozygosity) always carried a larger number of deleterious mutations in the homozygous state than in populations with lower FROH. In addition, based on our genetic differentiation results, and the distribution patterns of homozygous deleterious mutations in individuals, we recommend certain conservation actions regarding the genetic rescue of A. yangbiense. Overall, our study provides meaningful insights into the conservation genetics and a framework for the further conservation for the endangered A. yangbiense.

When tropical and subtropical congeners met: Multiple ancient hybridization events within Eriobotrya in the Yunnan-Guizhou Plateau, a tropical-subtropical transition area in China.

Global climate changes during the Miocene may have created ample opportunities for hybridization between members of tropical and subtropical biomes at the boundary between these zones. Yet, very few studies have explored this possibility. The Yunnan-Guizhou Plateau (YGP) in Southwest China is a biodiversity hotspot for vascular plants, located in a transitional area between the floristic regions of tropical Southeast Asia and subtropical East Asia. The genus Eriobotrya (Rosaceae) comprises both tropical and subtropical taxa, with 12 species recorded in the YGP, making it a suitable basis for testing the hypothesis of between-biome hybridization. Therefore, we surveyed the evolutionary history of Eriobotrya by examining three chloroplast regions and five nuclear genes for 817 individuals (47 populations) of 23 Eriobotrya species (including 19 populations of 12 species in the YGP), plus genome re-sequencing of 33 representative samples. We concluded that: (1) phylogenetic positions for 16 species exhibited strong cytonuclear conflicts, most probably due to ancient hybridization; (2) the YGP is a hotspot for hybridization, with 11 species showing clear evidence of chloroplast capture; and (3) Eriobotrya probably originated in tropical Asia during the Eocene. From the Miocene onwards, the intensification of the Eastern Asia monsoon and global cooling may have shifted the tropical-subtropical boundary and caused secondary contact between species, thus providing ample opportunity for hybridization and diversification of Eriobotrya, especially in the YGP. Our study highlights the significant role that paleoclimate changes probably played in driving hybridization and generating rich species diversity in climate transition zones.

The Rhododendron Plant Genome Database (RPGD): a comprehensive online omics database for Rhododendron.

BACKGROUND: The genus Rhododendron L. has been widely cultivated for hundreds of years around the world. Members of this genus are known for great ornamental and medicinal value. Owing to advances in sequencing technology, genomes and transcriptomes of members of the Rhododendron genus have been sequenced and published by various laboratories. With increasing amounts of omics data available, a centralized platform is necessary for effective storage, analysis, and integration of these large-scale datasets to ensure consistency, independence, and maintainability. RESULTS: Here, we report our development of the Rhododendron Plant Genome Database (RPGD; http://bioinfor.kib.ac.cn/RPGD/ ), which represents the first comprehensive database of Rhododendron genomics information. It includes large amounts of omics data, including genome sequence assemblies for R. delavayi, R. williamsianum, and R. simsii, gene expression profiles derived from public RNA-Seq data, functional annotations, gene families, transcription factor identification, gene homology, simple sequence repeats, and chloroplast genome. Additionally, many useful tools, including BLAST, JBrowse, Orthologous Groups, Genome Synteny Browser, Flanking Sequence Finder, Expression Heatmap, and Batch Download were integrated into the platform. CONCLUSIONS: RPGD is designed to be a comprehensive and helpful platform for all Rhododendron researchers. Believe that RPGD will be an indispensable hub for Rhododendron studies.

Natural hybridization between two butterfly bushes in Tibet: dominance of F1 hybrids promotes strong reproductive isolation.

BACKGROUND: It has been recognized that a certain amount of habitat disturbance is a facilitating factor for the occurrence of natural hybridization, yet to date we are unaware of any studies exploring hybridization and reproductive barriers in those plants preferentially occupying disturbed habitats. Buddleja plants (also called butterfly bush) generally do grow in disturbed habitats, and several species with hybrid origin have been proposed, based solely on morphological evidence. RESULTS: In the present study, we test the hypothesis that B. × wardii is of natural hybridization origin in two sympatric populations of three taxa including B. × wardii and its parents (B. alternifolia and B. crispa) plus 4 referenced parental populations, using four nuclear genes and three chloroplast intergenic spacers, as well as with 10 morphological characters. Our results suggest that at both sites B. × wardii is likely to be a hybrid between B. alternifolia and B. crispa, and moreover, we confirm that most of the hybrids examined are F1s. That these plants are F1s is further supported by morphology, as no transgressive characters were detected. B. crispa was found to be the maternal parent in the Bahe (BH) population, from cpDNA evidence. However, in the Taji (TJ) population, the direction of hybridization was difficult to establish due to the shared cpDNA haplotypes between B. alternifolia and B. crispa, however we still predicted a similar unidirectional hybridization pattern due to results from cross-specific pollination treatments which supported the "SI × SC rule". CONCLUSIONS: The presence of mainly F1 hybrids can successfully impede gene flow and thus maintain species boundaries in parental species in a typical distribution of Buddleja, i.e. in disturbed habitats.

Genome-wide analysis of butterfly bush (Buddleja alternifolia) in three uplands provides insights into biogeography, demography and speciation.

Understanding processes that generate and maintain large disjunctions within plant species can provide valuable insights into plant diversity and speciation. The butterfly bush Buddleja alternifolia has an unusual disjunct distribution, occurring in the Himalaya, Hengduan Mountains (HDM) and the Loess Plateau (LP) in China. We generated a high-quality, chromosome-level genome assembly of B. alternifolia, the first within the family Scrophulariaceae. Whole-genome re-sequencing data from 48 populations plus morphological and petal colour reflectance data covering its full distribution range were collected. Three distinct genetic lineages of B. alternifolia were uncovered, corresponding to Himalayan, HDM and LP populations, with the last also differentiated morphologically and phenologically, indicating occurrence of allopatric speciation likely to be facilitated by geographic isolation and divergent adaptation to distinct ecological niches. Moreover, speciation with gene flow between populations from either side of a mountain barrier could be under way within LP. The current disjunctions within B. alternifolia might result from vicariance of a once widespread distribution, followed by several past contraction and expansion events, possibly linked to climate fluctuations promoted by the Kunlun-Yellow river tectonic movement. Several adaptive genes are likely to be either uniformly or diversely selected among regions, providing a footprint of local adaptations. These findings provide new insights into plant biogeography, adaptation and different processes of allopatric speciation.

Acceleration of Hg0 Adsorption onto Natural Sphalerite by Cu2+ Activation during Flotation: Mechanism and Applications in Hg0 Recovery.

The rate of gaseous Hg0 adsorption onto natural sphalerite increased by approximately 1.9-7.7 times after Cu2+ activation during flotation of the natural sphalerite to remove impurities. Via a new pathway involving CuS, physically adsorbed Hg0 was oxidized by CuS to HgS on natural sphalerite after Cu2+ activation. In a similar intrinsic ZnS pathway, physically adsorbed Hg0 was oxidized by ZnS to HgS. The rate of the CuS pathway for Hg0 capture was generally significantly larger than that of the intrinsic ZnS pathway. Thus, Hg0 adsorption onto natural sphalerite was notably accelerated after Cu2+ activation. However, the kinetic analysis indicated that the capacity of natural sphalerite for Hg0 capture did not vary. Because the properties of the activated sphalerite for Zn smelting were barely degraded after Hg0 capture, the spent activated sphalerite for Hg0 capture can be reused for Zn smelting. Moreover, most of the gaseous Hg0 captured by activated sphalerite can be recovered eventually as liquid Hg0 in the condenser unit of Zn smelters. Thus, Hg0 recovery by activated sphalerite is a cost-effective and environmentally friendly technology to recover Hg0 from Zn smelting flue gas, thus replacing the complex and dangerous Boliden-Norzink process.

Conservation implications of asymmetric introgression and reproductive barriers in a rare primrose species.

BACKGROUND: Primula is a large genus of flowering herbs well known for their heterostyly. Currently few natural hybrids are known and reproductive barriers in this genus in the wild have received little attention. However, there is instance of hybridization between rare and widely-spread species, and conservation implications of such situation is poorly understood. In the present study, we investigated hybridization patterns and reproductive barriers between a wide spread species, Primula poissonii and a rare species P. anisodora, of which only three populations are currently known. RESULTS: Pollinator-mediated reproductive isolation was strong between parental species but not significant between hybrids and parental species. Hand pollination experiments showed significant reduction of both fruit- and seed-set for heterospecific pollination as compared with conspecific pollination for both parental species. Furthermore, hybrids had higher fruit- and seed-set when pollinated with P. anisodora pollen as opposed to P. poissonii pollen. Microsatellites identified backcrosses to P. anisodora in two of the three populations of P. anisodora, and additionally more individuals of P. anisodora showed introgression from P. poissonii than vice versa. CONCLUSIONS: These results provide evidence for potential genetic swamping of the P. anisodora populations, which could pose a serious threat for this locally endemic species.

Hierarchical Ag-SiO2@Fe3O4 magnetic composites for elemental mercury removal from non-ferrous metal smelting flue gas.

Hierarchical Ag-SiO2@Fe3O4 magnetic composites were selected for elemental mercury (Hg0) removal from non-ferrous metal smelting flue gas in this study. Results showed that the hierarchical Ag-SiO2@Fe3O4 magnetic composites had favorable Hg0 removal ability at low temperature. Moreover, the adsorption capacity of hierarchical magnetic composite is much larger than that of pure Fe3O4 and SiO2@Fe3O4. The Hg0 removal efficiency reached the highest value as approximately 92% under the reaction temperature of 150°C, while the removal efficiency sharply reduced in the absence of O2. The characterization results indicated that Ag nanoparticles grew on the surface of SiO2@Fe3O4 support. The large surface area of SiO2 supplied efficient reaction room for Hg and Ag atoms. Ag-Hg amalgam is generated on the surface of the composites. In addition, this magnetic material could be easily separated from fly ashes when adopted for treating real flue gas, and the spent materials could be regenerated using a simple thermal-desorption method.

Maintenance of species boundaries in three sympatric Ligularia (Senecioneae, Asteraceae) species.

The key process in speciation concerns the formation and maintenance of reproductive isolating barriers between diverging lineages. Although species boundaries are frequently investigated between two species across many taxa, reproductive isolating barriers among multiple species (>2) that would represent the most common phenomenon in nature, remain to be clarified. Here, we use double digest restriction-site associated DNA (ddRAD) sequencing to examine patterns of hybridization at a sympatric site where three Ligularia species grow together and verify whether those patterns contribute to the maintenance of boundaries among species. The results based on the RAD SNP datasets indicated hybridization Ligularia cyathiceps × L. duciformis and L. duciformis × L. yunnanensis were both restricted to F1 s plus a few first-generation backcrosses and no gene introgression were identified, giving rise to strong reproductive isolation among hybridizing species. Moreover, hybrid swarm simulation, using HYBRIDLAB, indicated the RAD SNP datasets had sufficient discriminatory power for accurate hybrid detection. We conclude that parental species show strong reproductive isolation and they still maintain species boundaries, which may be the key mechanism to maintain species diversity of Ligularia in the eastern Qinghai-Tibetan Plateau and adjacent areas. Moreover, this study highlights the effectiveness of RAD sequencing in hybridization studies.

Natural hybridization and reproductive isolation between two Primula species.

Natural hybridization frequently occurs in plants and can facilitate gene flow between species, possibly resulting in species refusion. However, various reproductive barriers block the formation of hybrids and maintain species integrity. Here, we conducted a field survey to examine natural hybridization and reproductive isolation (RI) between sympatric populations of Primula secundiflora and P. poissonii using ten nuclear simple sequence repeat (SSR) loci. Although introgressive hybridization occurred, species boundaries between P. secundiflora and P. poissonii were maintained through nearly complete reproductive isolation. These interfertile species provide an excellent model for studying the RI mechanisms and evolutionary forces that maintain species boundaries.

Natural hybridization and asymmetric introgression at the distribution margin of two Buddleja species with a large overlap.

BACKGROUND: Natural hybridization in plants is universal and plays an important role in evolution. Based on morphology it has been presumed that hybridization occurred in the genus Buddleja, though genetic studies confirming this assumption have not been conducted to date. The two species B. crispa and B. officinalis overlap in their distributions over a wide range in South-West China, and we aimed to provide genetic evidence for ongoing hybridization in this study. RESULTS: We investigated the occurrence of hybrids between the two species at the southern-most edge of the distribution of B. crispa using five nuclear loci and pollination experiments. The genetic data suggest substantial differentiation between the two species as species-specific alleles are separated by at least 7-28 mutations. The natural hybrids found were nearly all F1s (21 of 23), but backcrosses were detected, and some individuals, morphologically indistinguishable from the parental species, showed introgression. Pollen viability test shows that the percentage of viable pollen grains was 50 ± 4% for B. crispa, and 81 ± 2% for B. officinalis. This difference is highly significant (t = 7.382, p < 0.0001). Hand cross-pollination experiments showed that B. crispa is not successful as pollen-parent, but B. officinalis is able to pollinate B. crispa to produce viable hybrid seed. Inter-specific seed-set is low (8 seeds per fruit, as opposed to about 65 for intra-specific pollinations), suggesting post-zygotic reproductive barriers. In addition, one of the reference populations also suggests a history of introgression at other localities. CONCLUSIONS: The occurrence of morphologically intermediate individuals between B. crispa and B. officinalis at Xishan Mountain is unequivocally linked to hybridization and almost all examined individuals of the putative hybrids were likely F1s. Despite pollination experiments indicating higher chances for introgression into B. officinalis (hybrids only produced viable seed when crossed with B. officinalis), observed introgression was asymmetrical into B. crispa. This could be due to seeds produced by hybrids not contributing to seedlings, or other factors favoring the establishment of backcrosses towards B. crispa. However, further research will be needed to confirm these observations, as the small number of plants used for the pollination experiments could have introduced an artifact, for example if used individuals were more or less compatible than the species average, and also the small number of loci used could convey a picture of introgression that is not representative for the whole genome.

Investigation of Compton profiles of molecular methane and ethane.

The Compton profiles of methane and ethane molecules have been determined at an incident photon energy of 20 keV based on the third generation synchrotron radiation, and the statistical accuracy of 0.2% is achieved near pz = 0. The density functional theory with aug-cc-pVTZ basis set was used to calculate the Compton profiles of methane and ethane. The present experimental Compton profiles are in better agreement with the theoretical calculations in the whole pz region than the previous experimental results, which indicates that the present experimental Compton profiles are accurate enough to serve as the benchmark data for methane and ethane molecules.

Unidirectional hybridization and reproductive barriers between two heterostylous primrose species in north-west Yunnan, China.

BACKGROUND AND AIMS: Heteromorphy in flowers has a profound effect on breeding patterns within a species, but little is known about how it affects reproductive barriers between species. The heterostylous genus Primula is very diverse in the Himalaya region, but hybrids there have been little researched. This study examines in detail a natural hybrid zone between P. beesiana and P. bulleyana. METHODS: Chloroplast sequencing, AFLP (amplified fragment length polymorphism) markers and morphological comparisons were employed to characterize putative hybrids in the field, using synthetic F1s from hand pollination as controls. Pollinator visits to parent species and hybrids were observed in the field. Hand pollinations were conducted to compare pollen tube growth, seed production and seed viability for crosses involving different morphs, species and directions of crossing. KEY RESULTS: Molecular data revealed all hybrid derivatives examined to be backcrosses of first or later generations towards P. bulleyana: all had the chloroplast DNA (cpDNA) of this species. Some individuals had morphological traits suggesting they were hybrids, but they were genetically similar to P. bulleyana; they might have been advanced generation backcrosses. Viable F1s could not be produced with P. bulleyana pollen on P. beesiana females, irrespective of the flower morphs used. Within-morph crosses for each species had very low (<10 %) seed viability, whereas crosses between pin P. bulleyana (female) and pin P. beesiana had a higher seed viability of 30 %. Thus genetic incompatibility mechanisms back up mechanical barriers to within-morph crosses in each species, but are not the same between the two species. The two species share their main pollinators, and pollinators were observed to fly between P. bulleyana and hybrids, suggesting that pollinator behaviour may not be an important isolating factor. CONCLUSIONS: Hybridization is strongly asymmetric, with P. bulleyana the only possible mother and all detected hybrids being backcrosses in this direction. Partial ecological isolation and inhibition of heterospecific pollen, and possibly complete barriers to F1 formation on P. beesiana, may be enough to make F1 formation very rare in these species. Therefore, with no F1 detected, this hybrid zone may have a finite life span as successive generations become more similar to P. bulleyana.

Mechanism of the selective catalytic oxidation of slip ammonia over Ru-modified Ce-Zr complexes determined by in situ diffuse reflectance infrared Fourier transform spectroscopy.

The slip ammonia from selective catalytic reduction (SCR) of NOx in coal-fired flue gas can result in deterioration of the utilities or even the environmental issues. To achieve selective catalytic oxidation (SCO) of slip ammonia, Ru-modified Ce-Zr solid solution catalysts were prepared and evaluated under various conditions. It was found that the Ru/Ce(0.6)Zr(0.4)O2(polyvinylpyrrolidone (PVP)) catalyst displayed significant catalytic activity and the slip ammonia was almost completely removed with the coexistence of NOx and SO2. Interestingly, the effect of SO2 on NH3 oxidation was bifacial, and the N2 selectivity of the resulting products was as high as 100% in the presence of SO2 and NH3. The mechanism of the SCO of NH3 over Ru/Ce(0.6)Zr(0.4)O2(PVP) was studied using various techniques, and the results showed that NH3 oxidation follows an internal SCR (iSCR) mechanism. The adsorbed ammonia was first activated and reacted with lattice oxygen atoms to form an -HNO intermediate. Then, the -HNO mainly reacted with atomic oxygen from O2 to form NO. Meanwhile, the formed NO interacted with -NH2 to N2 with N2O as the byproduct, but the presence of SO2 can effectively inhibit the production of N2O.

Absorption characteristics of elemental mercury in mercury chloride solutions.

Elemental mercury (Hg(0)) in flue gases can be efficiently captured by mercury chloride (HgCl2) solution. However, the absorption behaviors and the influencing effects are still poorly understood. The mechanism of Hg(0) absorption by HgCl2 and the factors that control the removal were studied in this paper. It was found that when the mole ratio of Cl(-) to HgCl2 is 10:1, the Hg(0) removal efficiency is the highest. Among the main mercury chloride species, HgCl3(-) is the most efficient ion for Hg(0) removal in the HgCl2 absorption system when moderate concentrations of chloride ions exist. The Hg(0) absorption reactions in the aqueous phase were investigated computationally using Moller-Plesset perturbation theory. The calculated Gibbs free energies and energy barriers are in excellent agreement with the results obtained from experiments. In the presence of SO3(2-) and SO2, Hg(2+) reduction occurred and Hg(0) removal efficiency decreased. The reduced Hg(0) removal can be controlled through increased chloride concentration to some degree. Low pH value in HgCl2 solution enhanced the Hg(0) removal efficiency, and the effect was more significant in dilute HgCl2 solutions. The presence of SO4(2-) and NO3(-) did not affect Hg(0) removal by HgCl2.

Plant species with extremely small populations conservation program: achieving Kunming-Montreal global biodiversity targets.

Conservation programs for plant species with extremely small populations (PSESP) have been successfully implemented for several decades in China. Here we highlight how their inclusion in several national conservation policies helps meet targets of the Kunming-Montreal Global Biodiversity Framework (KMGBF) and show how lessons from these programs can be applied more widely.

The chromosome-scale genome of Magnolia sinica (Magnoliaceae) provides insights into the conservation of plant species with extremely small populations (PSESP).

Magnolia sinica (Magnoliaceae) is a highly threatened tree endemic to southeast Yunnan, China. In this study, we generated for the first time a high-quality chromosome-scale genome sequence from M. sinica, by combining Illumina and ONT data with Hi-C scaffolding methods. The final assembled genome size of M. sinica was 1.84 Gb, with a contig N50 of ca. 45 Mb and scaffold N50 of 92 Mb. Identified repeats constituted approximately 57% of the genome, and 43,473 protein-coding genes were predicted. Phylogenetic analysis shows that the magnolias form a sister clade with the eudicots and the order Ceratophyllales, while the monocots are sister to the other core angiosperms. In our study, a total of 21 individuals from the 5 remnant populations of M. sinica, as well as 22 specimens belonging to 8 related Magnoliaceae species, were resequenced. The results showed that M. sinica had higher genetic diversity (θw = 0.01126 and θπ = 0.01158) than other related species in the Magnoliaceae. However, population structure analysis suggested that the genetic differentiation among the 5 M. sinica populations was very low. Analyses of the demographic history of the species using different models consistently revealed that 2 bottleneck events occurred. The contemporary effective population size of M. sinica was estimated to be 10.9. The different patterns of genetic loads (inbreeding and numbers of deleterious mutations) suggested constructive strategies for the conservation of these 5 different populations of M. sinica. Overall, this high-quality genome will be a valuable genomic resource for conservation of M. sinica.