Genomic analyses of a “living fossil”: The endangered dove‐tree

Genomic signatures of inbreeding and mutation load in tree ferns

Ferns (Pteridophyta), as the second largest group of vascular plants, play important roles in ecosystem functioning. Homosporous ferns exhibit a remarkable range of mating systems, from extreme inbreeding to obligate outcrossing, which may have significant evolutionary and ecological implications. Despite their significance, the impact of genome-wide inbreeding on genetic diversity and mutation load within the fern lineage remain largely unexplored. In this study, we utilized whole-genome sequencing to investigate the genomic signatures of inbreeding and genetic load in three Alsophila tree fern species. Our analysis revealed extremely high inbreeding in A. spinulosa, in contrast to the predominantly outcrossing observed in A. costularis and A. latebrosa. This difference likely reflects divergent mating systems and demographic histories. Consistent with its extreme inbreeding propensity, A. spinulosa exhibits reduced genetic diversity and a pronounced decline in effective population size. Comparison of genetic load revealed an overall reduction in deleterious mutations in the highly inbred A. spinulosa, highlighting that long-term inbreeding may have contributed to the purging of strongly deleterious mutations, thereby prolonging the survival of A. spinulosa. Despite this, however, A. spinulosa carries a substantive realized genetic load that may potentially instigate future fitness decline. Our findings illuminate the complex evolutionary interplay between inbreeding and mutation load in homosporous ferns, yielding insights with important implications for the conservation and management of these species.

The 'queen of the Andes' (Puya raimondii) is genetically fragile and fragmented: a consequence of long generation time and semelparity?

Understanding how life history shapes genetic diversity is a fundamental issue in evolutionary biology, with important consequences for conservation. However, we still have an incomplete picture of the impact of life history on genome-wide patterns of diversity, especially in long-lived semelparous plants. Puya raimondii is a high-altitude semelparous species from the Andes that flowers at 40-100 years of age. We sequenced the whole genome and estimated the nucleotide diversity of 200 individuals sampled from nine populations. Coalescent-based approaches were then used to infer past population dynamics. Finally, these results were compared with results obtained for the iteroparous species, Puya macrura. The nine populations of P. raimondii were highly divergent, highly inbred, and carried an exceptionally high genetic load. They are genetically depauperate, although, locally in the genome, balancing selection contributed to the maintenance of genetic polymorphism. While both P. raimondii and P. macrura went through a severe bottleneck during the Pleistocene, P. raimondii did not recover from it and continuously declined, while P. macrura managed to bounce back. Our results demonstrate the importance of life history, in particular generation time and reproductive strategy, in affecting population dynamics and genomic variation, and illustrate the genetic fragility of long-lived semelparous plants.

A genome assembly of decaploid Houttuynia cordata provides insights into the evolution of Houttuynia and the biosynthesis of alkaloids

Houttuynia cordata Thunb., commonly known as yuxingcao in China, is known for its characteristic fishy smell and is widely recognized as an important herb and vegetable in many parts of Asia. However, the lack of genomic information on H. cordata limits the understanding of its population structure, genetic diversity, and biosynthesis of medicinal compounds. Here we used single-molecule sequencing, Illumina paired-end sequencing, and chromosome conformation capture technology to construct the first chromosome-scale decaploid H. cordata reference genome. The genome assembly was 2.63 Gb in size, with 1348 contigs and a contig N50 of 21.94 Mb further clustered and ordered into 88 pseudochromosomes based on Hi-C analysis. The results of genome evolution analysis showed that H. cordata underwent a whole-genome duplication (WGD) event ~17 million years ago, and an additional WGD event occurred 3.3 million years ago, which may be the main factor leading to the high abundance of multiple copies of orthologous genes. Here, transcriptome sequencing across five different tissues revealed significant expansion and distinct expression patterns of key gene families, such as l-amino acid/l-tryptophan decarboxylase and strictosidine synthase, which are essential for the biosynthesis of isoquinoline and indole alkaloids, along with the identification of genes such as TTM3, which is critical for root development. This study constructed the first decaploid medicinal plant genome and revealed the genome evolution and polyploidization events of H. cordata .

Whole-genome sequencing of allotetraploid bermudagrass reveals the origin of Cynodon and candidate genes for salt tolerance

Bermudagrass (Cynodon dactylon) is a globally distributed, extensively used warm-season turf and forage grass with high tolerance to salinity and drought stress in alkaline environments. However, the origin of the species and genetic mechanisms for salinity tolerance in the species are basically unknown. Accordingly, we set out to study evolution divergence events in the Cynodon genome and to identify genes for salinity tolerance. We developed a 604.0 Mb chromosome-level polyploid genome sequence for bermudagrass 'A12359' (n = 18). The C. dactylon genome comprises 2 complete sets of homoeologous chromosomes, each with approximately 30 000 genes, and most genes are conserved as syntenic pairs. Phylogenetic study showed that the initial Cynodon species diverged from Oropetium thomaeum approximately 19.7-25.4 million years ago (Mya), the A and B subgenomes of C. dactylon diverged approximately 6.3-9.1 Mya, and the bermudagrass polyploidization event occurred 1.5 Mya on the African continent. Moreover, we identified 82 candidate genes associated with seven agronomic traits using a genome-wide association study, and three single-nucleotide polymorphisms were strongly associated with three salt resistance genes: RAP2-2, CNG channels, and F14D7.1. These genes may be associated with enhanced bermudagrass salt tolerance. These bermudagrass genomic resources, when integrated, may provide fundamental insights into evolution of diploid and tetraploid genomes and enhance the efficacy of comparative genomics in studying salt tolerance in Cynodon.

Cryptic divergences and repeated hybridizations within the endangered "living fossil" dove tree (Davidia involucrata) revealed by whole genome resequencing

The identification and understanding of cryptic intraspecific evolutionary units (lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species. However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a "living fossil" dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range. Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.

Regional environmental differences significantly affect the genetic structure and genetic differentiation of Carpinus tientaiensis Cheng, an endemic and extremely endangered species from China

Differences in topography and environment greatly affect the genetic structure and genetic differentiation of species, and endemic or endangered species with limited geographic ranges seem to be more sensitive to changes in climate and other environmental factors. The complex topography of eastern China is likely to affect genetic differentiation of plants there. Carpinus tientaiensis Cheng is a native and endangered plants from China, and exploring its genetic diversity has profound significance for protection and the collection of germplasm resources. Based on AFLP markers, this study found that C. tientaiensis has low genetic diversity, which mainly came from within populations, while Shangshantou and Tiantai Mountain populations have relatively high genetic diversity. The Nei genetic distance was closely related to geographical distance, and temperature and precipitation notablely affected the genetic variation and genetic differentiation of C. tientaiensis. Based on cpDNA, this study indicated that C. tientaiensis exhibits a moderate level of genetic diversity, and which mainly came from among populations, while Tiantai Mountain population have the highest genetic diversity. It demonstrated that there was genetic differentiation between populations, which can be divided into two independent geographical groups, but there was no significant phylogeographic structure between them. The MaxEnt model showed that climate change significantly affects its distribution, and the suitable distribution areas in Zhejiang were primarily divided into two regions, eastern Zhejiang and southern Zhejiang, and there was niche differentiation in its suitable distribution areas. Therefore, this study speculated that the climate and the terrain of mountains and hills in East China jointly shape the genetic structure of C. tientaiensis, which gived rise to an obvious north-south differentiation trend of these species, and the populations located in the hilly areas of eastern Zhejiang and the mountainous areas of southern Zhejiang formed two genetic branches respectively.

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.

The Development of Plant Genome Sequencing Technology and Its Conservation and Application in Endangered Gymnosperms

Genome sequencing is widely recognized as a fundamental pillar in genetic research and legal studies of biological phenomena, providing essential insights for genetic investigations and legal analyses of biological events. The field of genome sequencing has experienced significant progress due to rapid improvements in scientific and technological developments. These advancements encompass not only significant improvements in the speed and quality of sequencing but also provide an unparalleled opportunity to explore the subtle complexities of genomes, particularly in the context of rare species. Such a wide range of possibilities has successfully supported the validation of plant gene functions and the refinement of precision breeding methodologies. This expanded scope now includes a comprehensive exploration of the current state and conservation efforts of gymnosperm gene sequencing, offering invaluable insights into their genomic landscapes. This comprehensive review elucidates the trajectory of development and the diverse applications of genome sequencing. It encompasses various domains, including crop breeding, responses to abiotic stress, species evolutionary dynamics, biodiversity, and the unique challenges faced in the conservation and utilization of gymnosperms. It highlights both ongoing challenges and the unveiling of forthcoming developmental trajectories.

A chromosome-level genome assembly provides insights into Cornus wilsoniana evolution, oil biosynthesis, and floral bud development

Cornus wilsoniana W. is a woody oil plant with high oil content and strong hypolipidemic effects, making it a valuable species for medicinal, landscaping, and ecological purposes in China. To advance genetic research on this species, we employed PacBio together with Hi-C data to create a draft genome assembly for C. wilsoniana. Based on an 11-chromosome anchored chromosome-level assembly, the estimated genome size was determined to be 843.51 Mb. The N50 contig size and N50 scaffold size were calculated to be 4.49 and 78.00 Mb, respectively. Furthermore, 30 474 protein-coding genes were annotated. Comparative genomics analysis revealed that C. wilsoniana diverged from its closest species ~12.46 million years ago (Mya). Furthermore, the divergence between Cornaceae and Nyssaceae occurred >62.22 Mya. We also found evidence of whole-genome duplication events and whole-genome triplication γ, occurring at ~44.90 and 115.86 Mya. We further inferred the origins of chromosomes, which sheds light on the complex evolutionary history of the karyotype of C. wilsoniana. Through transcriptional and metabolic analysis, we identified two FAD2 homologous genes that may play a crucial role in controlling the oleic to linoleic acid ratio. We further investigated the correlation between metabolites and genes and identified 33 MADS-TF homologous genes that may affect flower morphology in C. wilsoniana. Overall, this study lays the groundwork for future research aimed at identifying the genetic basis of crucial traits in C. wilsoniana.

Overexpression of a laccase gene, DiLAC17, from Davidia involucrata causes severe seed abortion in Arabidopsis

Seed abortion is a common phenomenon in woody plants, especially in rare and endangered species. Serious seed abortion occurs in the dove tree and largely restricts its natural reproduction. A number of differentially expressed genes (DEGs) between normal and aborted seeds of the dove tree have been previously identified through transcriptome profiling. Among these, most DEGs encoding laccase showed significant upregulation in the aborted seeds. In this study, the laccase gene with the highest expression level in aborted seeds, DiLAC17, was cloned from the dove tree genome and further verified. Overexpression of the DiLAC17 gene in Arabidopsis resulted in retarded growth, deformed siliques, and severe seed abortion. Most Arabidopsis genes involved in seed development, such as AtLEC2, AtANT1, and AtRGE1, were suppressed in the transgenic lines. Laccase activity and lignin content were significantly improved in transgenic lines under ectopic overexpression of the DiLAC17 gene. Excessive lignin accumulation in the early developmental stage was assumed to be a key cause of restricting silique growth and seed expansion, which ultimately led to seed abortion. These results indicate a laccase-mediated pathway for seed abortion, which might be a strategy adopted by this rare and endangered species to reduce the reproductive load.

Karyotype evolution of the Asterids insights from the first genome sequences of the family Cornaceae

Cornaceae is a core representative family in Cornales, the earliest branching lineage in the Asterids on the life tree of angiosperms. This family includes the only genus Cornus, a group of ~55 species. These species occur widely in Northern Hemisphere and have been used as resources for horticultural ornaments, medicinal and industrial manufacturing. However, no any genome sequences are available for this family. Here, we reported a chromosome-level genome for Cornus controversa. This was generated using high-fidelity plus Hi-C sequencing, and totally ~771.80 Mb assembled sequences and 39,886 protein-coding genes were obtained. We provided evidence for a whole-genome duplication event (WGD) unique to C. controversa. The evolutionary features of this genome indicated that the expanded and unique genes might have contributed to response to stress, stimulus and defense. By using chromosome-level syntenic blocks shared between eight living genomes, we found high degrees of genomic diversification from the ancestral core-eudicot genome to the present-day genomes, suggesting an important role of WGD in genomic plasticity that leads to speciation and diversification. These results provide foundational insights on the evolutionary history of Cornaceae, as well as on the Asterids diversification.

Genome-wide identification, characterization and expression of HSP 20 gene family in dove

Davidia involucrata is a significant living fossil with high abiotic stress tolerance. Although heat shock protein 20 (HSP20) has already been linked to heat stress, nothing is known about HSP20 family protein activities in D. involucrata. The functional dynamics of the D. involucrata HSP20 (DiHSP20) gene family were identified and characterized using a thorough genome-wide investigation. From the genome of D. involucrata, a total of 42 HSP20 genes were identified, which are distributed across 16 chromosomes. The DiHSP20 proteins were grouped into seven separate subfamilies by our phylogenetic analysis, which was validated by the conserved motif composition and gene structure studies. Segmental duplication events were shown to play a crucial role in the expansion of the DiHSP20 gene family. Synteny analysis revealed that 19 DiHSP20 genes of D. involucrata shared a syntenic connection with Arabidopsis genes, 39 with C. acuminata genes, and just 6 with O. sativa genes. Additionally, heat stress differently enhanced the expression levels of D. involucrata HSP20 genes. After 1 hour of heat treatment, the expression levels of most DiHSP20 genes, particularly DiHSP20-7, DiHSP20-29, DiHSP20-30, DiHSP20-32, and DiHSP20-34, were dramatically increased, suggestted that they might be employed as heat tolerance candidate genes. Overall, these findings add to our knowledge of the HSP20 family genes and provide helpful information for breeding heat stress resistance in D. involucrata.

Human follicular mites: Ectoparasites becoming symbionts

Most humans carry mites in the hair follicles of their skin for their entire lives. Follicular mites are the only metazoans tha continuously live on humans. We propose that Demodex folliculorum (Acari) represents a transitional stage from a host-injuring obligate parasite to an obligate symbiont. Here, we describe the profound impact of this transition on the genome and physiology of the mite. Genome sequencing revealed that the permanent host association of D. folliculorum led to an extensive genome reduction through relaxed selection and genetic drift, resulting in the smallest number of protein-coding genes yet identified among panarthropods. Confocal microscopy revealed that this gene loss coincided with an extreme reduction in the number of cells. Single uninucleate muscle cells are sufficient to operate each of the three segments that form each walking leg. While it has been assumed that the reduction of the cell number in parasites starts early in development, we identified a greater total number of cells in the last developmental stage (nymph) than in the terminal adult stage, suggesting that reduction starts at the adult or ultimate stage of development. This is the first evolutionary step in an arthropod species adopting a reductive, parasitic or endosymbiotic lifestyle. Somatic nuclei show underreplication at the diploid stage. Novel eye structures or photoreceptors as well as a unique human host melatonin-guided day/night rhythm are proposed for the first time. The loss of DNA repair genes coupled with extreme endogamy might have set this mite species on an evolutionary dead-end trajectory.

Genomes and demographic histories of the endangered Bretschneidera sinensis (Akaniaceae)

BACKGROUND

Bretschneidera sinensis is an endangered relic tree species in the Akaniaceae family and is sporadically distributed in eastern Asia. As opposed to its current narrow and rare distribution, the fossil pollen of B. sinensis has been found to be frequent and widespread in the Northern Hemisphere during the Late Miocene. B. sinensis is also a typical mycorrhizal plant, and its annual seedlings exhibit high mortality rates in absence of mycorrhizal development. The chromosome-level high-quality genome of B. sinensis will help us to more deeply understand the survival and demographic histories of this relic species.

RESULTS

A total of 25.39 Gb HiFi reads and 109.17 Gb Hi-C reads were used to construct the chromosome-level genome of B. sinensis, which is 1.21 Gb in length with the contig N50 of 64.13 Mb and chromosome N50 of 146.54 Mb. The identified transposable elements account for 55.21% of the genome. A total of 45,839 protein-coding genes were predicted in B. sinensis. A lineage-specific whole-genome duplication was detected, and 7,283 lineage-specific expanded gene families with functions related to the specialized endotrophic mycorrhizal adaptation were identified. The historical effective population size (Ne) of B. sinensis was found to oscillate greatly in response to Quaternary climatic changes. The Ne of B. sinensis has decreased rapidly in the recent past, making its extant Ne extremely lower. Our additional evolutionary genomic analyses suggested that the developed mycorrhizal adaption might have been repeatedly disrupted by environmental changes caused by Quaternary climatic oscillations. The environmental changes and an already decreased population size during the Holocene may have led to the current rarity of B. sinensis.

CONCLUSION

This is a detailed report of the genome sequences for the family Akaniaceae distributed in evergreen forests in eastern Asia. Such a high-quality genomic resource may provide critical clues for comparative genomics studies of this family in the future.

The genome sequence provides insights into salt tolerance of Achnatherum splendens (Gramineae), a constructive species of alkaline grassland

Achnatherum splendens Trin. (Gramineae) is a constructive species of the arid grassland ecosystem in Northwest China and is a major forage grass. It has good tolerance of salt and drought stress in alkaline habitats. Here, we report its chromosome-level genome, determined through a combination of Illumina HiSeq sequencing, PacBio sequencing and Hi-C technology. The final assembly of the ~1.17 Gb genome sequence had a super-scaffold N50 of 40.3 Mb. A total of 57 374 protein-coding genes were annotated, of which 54 426 (94.5%) genes have functional protein annotations. Approximately 735 Mb (62.37%) of the assembly were identified as repetitive elements, and among these, LTRs (40.53%) constitute the highest proportion, having made a major contribution to the expansion of genome size in A. splendens. Phylogenetic analysis revealed that A. splendens diverged from the Brachypodium distachyon-Hordeum vulgare-Aegilops tauschii subclade around 37 million years ago (Ma) and that a clade comprising these four species diverged from the Phyllostachys edulis clade ~47 Ma. Genomic synteny indicates that A. splendens underwent an additional species-specific whole-genome duplication (WGD) 18-20 Ma, which further promoted an increase in copies of numerous saline-alkali-related gene families in the A. splendens genome. By transcriptomic analysis, we further found that many of these duplicated genes from this extra WGD exhibited distinct functional divergence in response to salt stress. This WGD, therefore, contributed to the strong resistance to salt stress and widespread arid adaptation of A. splendens.

Pan-genome of Raphanus highlights genetic variation and introgression among domesticated, wild, and weedy radishes

Post-polyploid diploidization associated with descending dysploidy and interspecific introgression drives plant genome evolution by unclear mechanisms. Raphanus is an economically and ecologically important Brassiceae genus and model system for studying post-polyploidization genome evolution and introgression. Here, we report the de novo sequence assemblies for 11 genomes covering most of the typical sub-species and varieties of domesticated, wild and weedy radishes from East Asia, South Asia, Europe, and America. Divergence among the species, sub-species, and South/East Asian types coincided with Quaternary glaciations. A genus-level pan-genome was constructed with family-based, locus-based, and graph-based methods, and whole-genome comparisons revealed genetic variations ranging from single-nucleotide polymorphisms (SNPs) to inversions and translocations of whole ancestral karyotype (AK) blocks. Extensive gene flow occurred between wild, weedy, and domesticated radishes. High frequencies of genome reshuffling, biased retention, and large-fragment translocation have shaped the genomic diversity. Most variety-specific gene-rich blocks showed large structural variations. Extensive translocation and tandem duplication of dispensable genes were revealed in two large rearrangement-rich islands. Disease resistance genes mostly resided on specific and dispensable loci. Variations causing the loss of function of enzymes modulating gibberellin deactivation were identified and could play an important role in phenotype divergence and adaptive evolution. This study provides new insights into the genomic evolution underlying post-polyploid diploidization and lays the foundation for genetic improvement of radish crops, biological control of weeds, and protection of wild species' germplasms.

Chromosome-scale genome assembly of Castanopsis tibetana provides a powerful comparative framework to study the evolution and adaptation of Fagaceae trees

Fagaceae species are increasingly used as models to elucidate the process and mechanism of adaptation and speciation by integrating ecology, evolution and genomics. The genus Castanopsis belongs to the family Fagaceae and is mainly distributed across subtropical and tropical Asia. In the present study, we reported the first chromosome-scale genome assembly of Castanopsis tibetana, a common species of evergreen broadleaved forests in subtropical China. The combination of Nanopore sequencing and Hi-C technologies enabled a high-quality genome assembly. The final assembled genome size of C. tibetana was 878.6 Mb (97.6% of the estimated genome size), consisting of 477 contigs with an N50 length of 3.3 Mb. The benchmarking universal single-copy orthologue (BUSCO) assessment indicated a completeness of 93.0%. Hi-C scaffolding generated 12 pseudochromosomes, representing 98.7% of the assembled genome. Subsequently, 40,937 protein-coding genes were predicted and 90.04% of them were functionally annotated. More than 476.9 Mb of repetitive sequences (54.3% of the genome) were identified, and the percentage of the genome covered by TE elements was 39.98%. Comparative genomics analysis revealed that C. tibetana was most closely related to Castanea mollissima and diverged at 18.48 Ma, and that C. tibetana has undergone considerable gene family expansion and contraction. Evidence of positive selection was detected in 53 genes, which showed different arrangement pattern compared to Quercus robur. The chromosome-scale genome assembly of C. tibetana will expand Fagaceae genome resources across the family and provide a powerful comparative framework to study the adaptation and evolution of Fagaceae trees.

Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species

Speciation is the key evolutionary process for generating biological diversity and has a central place in evolutionary and ecological research. How species diverge and adapt to different habitats is one of the most exciting areas in speciation studies. Here, we sequenced 55 individuals from three closely related species in the genus Carpinus: Carpinus tibetana, Carpinus monbeigiana, and Carpinus mollicoma to understand the strength and direction of gene flow and selection during the speciation process. We found low genetic diversity in C. tibetana, which reflects its extremely small effective population size. The speciation analysis between C. monbeigiana and C. mollicoma revealed that both species diverged ∼1.2 Mya with bidirectional gene flow. A total of 291 highly diverged genes, 223 copy number variants genes, and 269 positive selected genes were recovered from the two species. Genes associated with the diverged and positively selected regions were mainly involved in thermoregulation, plant development, and response to stress, which included adaptations to their habitats. We also found a great population decline and a low genetic divergence of C. tibetana, which suggests that this species is extremely vulnerable. We believe that the current diversification and adaption study and the important genomic resource sequenced herein will facilitate the speciation studies and serve as an important methodological reference for future research.

A chromosome-level genome assembly for the tertiary relict plant Tetracentron sinense oliv. (trochodendraceae)

Tetracentron sinense and Trochodendron aralioides are two Tertiary relict species of large trees in the family Trochodendraceae with narrow distributions on the mainland and islands of eastern Asia. They belong to the order Trochodendrales, which is one of the four early-diverged eudicot lineages. These two relict species provide a good system in which to examine genomic changes that occurred as they survived during repeated climatic oscillations in the Quaternary. We sequenced the genome of Te. sinense and compared it with that of Tr. aralioides. We found that Te. sinense has a smaller genome size (986.3 Mb) than that of Tr. aralioides (1610 Mb). Repetitive elements made the major contribution to the contrasting genome sizes in the two species, with most bursts of repeats occurring within the past four million years when the climate oscillated greatly. These species share two rounds of whole-genome duplications. The mainland species Te. sinense had a larger effective population size than the island species Tr. aralioides after the largest glaciation during the Quaternary climatic oscillation. However, soon after this recovery stage, the effective population sizes of both species continued to decrease, although the current effective population size of Te. sinense is still larger than that of Tr. aralioides. We recovered three distinctly diverged clades through resequencing the genomes of 50 individuals across the distributional range of Te. sinense in China. Our results provide an important genomic resource with which to examine early trait evolution in the core eudicots and assist efforts to conserve this relict tree species.

Molecular cloning and potential role of DiSOC1s in flowering regulation in Davidia involucrata Baill

Davidia involucrata Baill. (dove tree) is unique Tertiary relic plant in China, also known as 'living fossil' and 'giant panda'. The MADS-box family gene SOC1 is involved in the regulatory pathway that integrates flowering signals to promote flowering at the optimal time. In this study, we isolated and identified two dove tree SOC1 homologues, named DiSOC1-a and DiSOC1-b. These two sequences possess highly conserved domains MADS-box and SOC1-motif, as well as the semi-conserved region K-box. DiSOC1-a and DiSOC1-b were expressed at varying levels in all tested tissues of dove tree and shared high levels of expression in the flower buds. The expression tendencies of both genes in bract were initially upward and then downward and were highest in young bracts. Neither DiSOC1-a nor DiSOC1-b was expressed in immature leaves. Proteins encoded by DiSOC1-a and DiSOC1-b were located in the nucleus. In addition, ectopic overexpression of both genes in WT Arabidopsis promoted early flowering and the growth of the main bolt. Taken together, these results suggest that DiSOC1-a and DiSOC1-b are involved in the flowering initiation and the main bolt growth process of dove tree. Our results provide a foundation for horticultural breeding to control flowering time of dove tree.

Population Genetic Diversity and Structure of Ancient Tree Populations of Cryptomeria japonica var. sinensis Based on RAD-seq Data

Research highlights: Our study is the first to explore the genetic composition of ancient Cryptomeria trees across a distribution range in China. Background and objectives: Cryptomeria japonica var. sinensis is a native forest species of China; it is widely planted in the south of the country to create forests and for wood production. Unlike Cryptomeria in Japan, genetic Chinese Cryptomeria has seldom been studied, although there is ample evidence of its great ecological and economic value. Materials and methods: Because of overcutting, natural populations are rare in the wild. In this study, we investigated seven ancient tree populations to explore the genetic composition of Chinese Cryptomeria through ddRAD-seq technology. Results: The results reveal a lower genetic variation but higher genetic differentiation (Ho = 0.143, FST = 0.1204) than Japanese Cryptomeria (Ho = 0.245, FST = 0.0455). The 86% within-population variation is based on an analysis of molecular variance (AMOVA). Significant excess heterozygosity was detected in three populations and some outlier loci were found; these were considered to be the consequence of selection or chance. Structure analysis and dendrogram construction divided the seven ancient tree populations into four groups corresponding to the geographical provinces in which the populations are located, but there was no obvious correlation between genetic distance and geographic distance. A demographic history analysis conducted by a Stairway Plot showed that the effective population size of Chinese Cryptomeria had experienced a continuing decline from the mid-Pleistocene to the present. Our findings suggest that the strong genetic drift caused by climate fluctuation and intense anthropogenic disturbance together contributed to the current low diversity and structure. Considering the species’ unfavorable conservation status, strategies are urgently required to preserve the remaining genetic resources.

The Genome Sequence of Alpine Megacarpaea delavayi Identifies Species-Specific Whole-Genome Duplication

Megacarpaea delavayi (Brassicaceae), a plant found the high mountains of southwest China at high altitudes (3000–4800 m), is used as a vegetable or medicine. Here, we report a draft genome for this species. The assembly genome of M. delavayi is 883 Mb, and 61.59% of the genome is composed of repeat sequences. Annotation of the genome identified a total of 41,114 protein-coding genes. We found that M. delavayi experienced an independent whole-genome duplication (WGD), paralleling those independent WGDs in Iberis, Biscutella, and Anastatica in the early Miocene. Phylogenetic analyses based on the single-copy genes confirmed the position of the genus Megacarpaea within the expanded lineage II of the family and resolved its basal divergence to a subclade consisting of Anastatica, Iberis, and Biscutella. Species-specific and fast-evolving genes in M. delavayi are mainly involved in “DNA repair” and “response to UV-B radiation.” These genetic changes may together help this species survive in high-altitude environments. The reference genome reported here provides a valuable resource for studying adaptation of this and other alpine plants to the high-altitude habitats.