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.

A high-quality Actinidia chinensis(kiwifruit)genome

Actinidia chinensis(kiwifruit)is a perennial horticultural crop species of the Actinidiaceae family with high nutritional and economic value.Two versions of the A.chinensis genomes have been previously assembled,based mainly on relatively short reads.Here,we report an improved chromosome-level reference genome of A.chinensis(v3.0),based mainly on PacBio long reads and Hi-C data.The high-quality assembled genome is 653 Mb long,with 0.76%heterozygosity.At least 43%of the genome consists of repetitive sequences,and the most abundant long terminal repeats were further identified and account for 23.38%of our novel genome.It has clear improvements in contiguity,accuracy,and gene annotation over the two previous versions and contains 40,464 annotated protein-coding genes,of which 94.41%are functionally annotated.Moreover,further analyses of genetic collinearity revealed that the kiwifruit genome has undergone two whole-genome duplications:one affecting all Ericales families near the K-T extinction event and a recent genus-specific duplication.The reference genome presented here will be highly useful for further molecular elucidation of diverse traits and for the breeding of this horticultural crop,as well as evolutionary studies with related taxa.

A chromosome-scale genome assembly of Isatis indigotica,an important medicinal plant used in traditional Chinese medicine

Isatis indigotica(2n=14)is an important medicinal plant in China.Its dried leaves and roots(called Isatidis Folium and Isatidis Radix,respectively)are broadly used in traditional Chinese medicine for curing diseases caused by bacteria and viruses such as influenza and viral pneumonia.Various classes of compounds isolated from this species have been identified as effective ingredients.Previous studies based on transcriptomes revealed only a few candidate genes for the biosynthesis of these active compounds in this medicinal plant.Here,we report a high-quality chromosome-scale genome assembly of I.indigotica with a total size of 293.88 Mb and scaffold N50=36.16 Mb using single-molecule real-time long reads and high-throughput chromosome conformation capture techniques.We annotated 30,323 highconfidence protein-coding genes.Based on homolog searching and functional annotations,we identified many candidate genes involved in the biosynthesis of main active components such as indoles,terpenoids,and phenylpropanoids.In addition,we found that some key enzyme-coding gene families related to the biosynthesis of these components were expanded due to tandem duplications,which likely drove the production of these major active compounds and explained why I.indigotica has excellent antibacterial and antiviral activities.Our results highlighted the importance of genome sequencing in identifying candidate genes for metabolite synthesis in medicinal plants.

Bioinformatic analysis of chromatin organization and biased expression of duplicated genes between two poplars with a common whole-genome duplication

The nonrandom three-dimensional organization of chromatin plays an important role in the regulation of gene expression.However,it remains unclear whether this organization is conserved and whether it is involved in regulating gene expression during speciation after whole-genome duplication(WGD)in plants.In this study,high-resolution interaction maps were generated using high-throughput chromatin conformation capture(Hi-C)techniques for two poplar species,Populus euphratica and Populus alba var.pyramidalis,which diverged~14 Mya after a common WGD.We examined the similarities and differences in the hierarchical chromatin organization between the two species,including A/B compartment regions and topologically associating domains(TADs),as well as in their DNA methylation and gene expression patterns.We found that chromatin status was strongly associated with epigenetic modifications and gene transcriptional activity,yet the conservation of hierarchical chromatin organization across the two species was low.The divergence of gene expression between WGD-derived paralogs was associated with the strength of chromatin interactions,and colocalized paralogs exhibited strong similarities in epigenetic modifications and expression levels.Thus,the spatial localization of duplicated genes is highly correlated with biased expression during the diploidization process.This study provides new insights into the evolution of chromatin organization and transcriptional regulation during the speciation process of poplars after WGD.

A gene that underwent adaptive evolution, LAC2 (LACCASE), in Populus euphratica improves drought tolerance by improving water transport capacity

Drought severely limits plant development and growth;accordingly,plants have evolved strategies to prevent water loss and adapt to water deficit conditions.However,experimental cases that corroborate these evolutionary processes are limited.The LACCASEs(LACs)family is involved in various plant development and growth processes.Here,we performed an evolutionary analysis of LACs from Populus euphratica and characterized the functions of LACs in Arabidopsis and poplar.The results showed that in PeuLACs,multiple gene duplications led to apparent functional redundancy as the result of various selective pressures.Among them,PeuLAC2 underwent strong positive selection.Heterologous expression analyses showed that the overexpression of PeuLAC2 alters the xylem structure of plants,including thickening the secondary cell wall(SCW)and increasing the fiber cell length and stem tensile strength.Altogether,these changes improve the water transport capacity of plants.The analysis of the physiological experimental results showed that PeuLAC2-OE lines exhibited a stronger antioxidant response and greater drought tolerance than WT.Three genes screened by transcriptome analysis,NAC025,BG1,and UGT,that are associated with SCW synthesis and drought stress were all upregulated in the PeuLAC2-OE lines,implying that the overexpression of PeuLAC2 thickened the SCW,improved the water transport capacity of the plant,and further enhanced its drought tolerance.Our study highlights that genes that have undergone adaptive evolution may participate in the development of adaptive traits in P.euphratica and that PeuLAC2 could be a candidate gene for molecular genetic breeding in trees.

Plastome and phylogenetic relationship of the woody buckwheat Fagopyrum tibeticum in the Qinghai-Tibet Plateau

The phylogenetic position of the monotypic woody Parapteropyrum(Polygonaceae)remains controversial.Parapteropyrum has been thought to be closely related to the woody genera of the tribe Atraphaxideae,although some evidence indicates that it nests within the herbal buckwheat genus Fagopyrum of tribe Polygoneae.In this study,we used plastome data to determine the phylogenetic position of Parapteropyrum(Fagopyrum)tibeticum.Different reference species were used to assemble plastomes of three species currently placed in the tribe Ataphaxideae:Parapteropyrum(Fagopyrum)tibeticum,Atraphaxis bracteata and Calligonum ebinuricum.Once assembled,plastomes were characterized and compared to plastomes of 12 species across the family Polygonaceae.Phylogenetic analyses of Polygonaceae were performed using whole plastome,all plastome genes,and single-copy genes.Plastomes assembled using different reference plastomes did not differ;however,annotations showed small variation.Plastomes of Parapteropyrum(Fagopyrum)tibeticum,A.bracteata and C.ebinuricum have the typical quadripartite structure with lengths between 159,265 bp and 164,270 bp,and a total number of plastome genes of about 130.Plastome microsatellites(SSR)ranged in number from 48 to 77.Maximum Likelihood and Bayesian analyses of three plastome data sets consistently nested Parapteropyrum within the genus Fagopyrum.Furthermore,our analyses indicated that sampled woody genera of the family Polygonaceae are polyphyletic.Our study provides strong evidence that the woody Parapteropyrum tibeticum,which is distantly related to woody genera sampled here,should be taxonomically placed under Fagopyrum as Fagopyrum tibeticum.

The Corylus mandshurica genome provides insights into the evolution of Betulaceae genomes and hazelnut breeding

Hazelnut is popular for its flavor,and it has also been suggested that hazelnut is beneficial to cardiovascular health because it is rich in oleic acid.Here,we report the first high-quality chromosome-scale genome for the hazelnut species Corylus mandshurica(2n=22),which has a high concentration of oleic acid in its nuts.The assembled genome is 367.67Mb in length,and the contig N50 is 14.85 Mb.All contigs were assembled into 11 chromosomes,and 28,409 protein-coding genes were annotated.We reconstructed the evolutionary trajectories of the genomes of Betulaceae species and revealed that the 11 chromosomes of the hazelnut genus were derived from the most ancestral karyotype in Betula pendula,which has 14 protochromosomes,by inferring homology among five Betulaceae genomes.We identified 96 candidate genes involved in oleic acid biosynthesis,and 10 showed rapid evolution or positive selection.These findings will help us to understand the mechanisms of lipid synthesis and storage in hazelnuts.Several gene families related to salicylic acid metabolism and stress responses experienced rapid expansion in this hazelnut species,which may have increased its stress tolerance.The reference genome presented here constitutes a valuable resource for molecular breeding and genetic improvement of the important agronomic properties of hazelnut.

A chromosome-scale reference genome of Lobularia maritima,an ornamental plant with high stress tolerance

Lobularia maritima(L.)Desv.is an ornamental plant cultivated across the world.It belongs to the family Brassicaceae and can tolerate dry,poor and contaminated habitats.Here,we present a chromosome-scale,high-quality genome assembly of L.maritima based on integrated approaches combining Illumina short reads and Hi–C chromosome conformation data.The genome was assembled into 12 pseudochromosomes with a 197.70 Mb length,and it includes 25,813 protein-coding genes.Approximately 41.94%of the genome consists of repetitive sequences,with abundant long terminal repeat transposable elements.Comparative genomic analysis confirmed that L.maritima underwent a species-specific whole-genome duplication(WGD)event~22.99 million years ago.We identified~1900 species-specific genes,25 expanded gene families,and 50 positively selected genes in L.maritima.Functional annotations of these genes indicated that they are mainly related to stress tolerance.These results provide new insights into the stress tolerance of L.maritima,and this genomic resource will be valuable for further genetic improvement of this important ornamental plant.

The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies.Poplars,among the world’s most widely distributed and cultivated trees,exhibit extensive phenotypic diversity and environmental adaptability.In this study,we present a genus-level super-pangenome comprising 19 Populus genomes,revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation.Through the integration of pangenomes with transcriptomes,methylomes,and chromatin accessibility mapping,we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures,notably CG methylation in gene-body regions.Further comparative genomic analyses have enabled the identification of 142202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence.We have experimentally validated a∼180-bp presence/absence variant affecting the expression of the CUC2 gene,crucial for leaf serration formation.Finally,we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome(http://www.populus-superpangenome.com).Together,the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.

Phylotranscriptomics of Swertiinae(Gentianaceae)reveals that key floral traits are not phylogenetically correlated

Establishing how lineages with similar traits are phylogenetically related remains critical for understanding the origin of biodiversity on Earth.Floral traits in plants are widely used to explore phylogenetic relationships and to delineate taxonomic groups.The subtribe Swertiinae(Gentianaceae)comprises more than 350 species with high floral diversity ranging from rotate to tubular corollas and possessing diverse nectaries.Here we performed phylogenetic analysis of 60 species from all 15 genera of the subtribe Swertiinae sensu Ho and Liu,representing the range of floral diversity,using data from the nuclear and plastid genomes.Extensive topological conflicts were present between the nuclear and plastome trees.Three of the 15 genera represented by multiple species are polyphyletic in both trees.Key floral traits including corolla type,absence or presence of lobe scales,nectary type,nectary position,and stigma type are randomly distributed in the nuclear and plastome trees without phylogenetic correlation.We also revealed the likely ancient hybrid origin of one large clade comprising 10 genera with diverse floral traits.These results highlight the complex evolutionary history of this subtribe.The phylogenies constructed here provide a basic framework for further exploring the ecological and genetic mechanisms underlying both species diversification and floral diversity.

Natural variation in the SVP contributes to the pleiotropic adaption of Arabidopsis thaliana across contrasted habitats

Coordinated plant adaptation involves the interplay of multiple traits driven by habitat-specific selection pressures. Pleiotropic effects, wherein genetic variants of a single gene control multiple traits, can expedite such adaptations. Until present, only a limited number of genes have been reported to exhibit pleiotropy. Here, we create a recombinant inbred line (RIL) population derived from two Arabidopsis thaliana (A. thaliana) ecotypes originating from divergent habitats. Using this RIL population, we identify an allelic variation in a MADS-box transcription factor, SHORT VEGETATIVE PHASE (SVP), which exerts a pleiotropic effect on leaf size and drought-versus-humidity tolerance. Further investigation reveals that a natural null variant of the SVP protein disrupts its normal regulatory interactions with target genes, including GRF3, CYP707A1/3, and AtBG1, leading to increased leaf size, enhanced tolerance to humid conditions, and changes in flowering time of humid conditions in A. thaliana. Remarkably, polymorphic variations in this gene have been traced back to early A. thaliana populations, providing a genetic foundation and plasticity for subsequent colonization of diverse habitats by influencing multiple traits. These findings advance our understanding of how plants rapidly adapt to changing environments by virtue of the pleiotropic effects of individual genes on multiple trait alterations.

Genome-scale angiosperm phylogenies based on nuclear,plastome,and mitochondrial datasets

Angiosperms dominate the Earth’s ecosystems and provide most of the basic necessities for human life.The major angiosperm clades comprise 64 orders,as recognized by the APGⅣclassification.However,the phylogenetic relationships of angiosperms remain unclear,as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized,from targeted genes to transcriptomes.Here,we used currently available de novo genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear,plastid,and mitochondrial genomes of the same species with compatible datasets.The phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome type.However,there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were examined.We discuss ways to address these inconsistencies,which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of life.The angiosperm phylogenies presented here provide a basic framework for further updates and comparisons.These phylogenies can also be used as guides to examine the evolutionary trajectories among the three genome types during lineage radiation.

不同生活型被子植物功能性状与基因组大小的关系

基因组大小在被子植物物种之间存在着巨大的变异,但目前对不同生活型被子植物功能性状与基因组大小的关系缺乏统一的认识。本研究基于被子植物245科2,226属11,215个物种的基因组大小数据,探讨了不同生活型物种种子重量、最大植株高度和叶片氮、磷含量4个功能性状与基因组大小之间的关系。结果表明,被子植物最大植株高度和种子重量与基因组大小间的关系在草本和木本植物中存在显著差异。草本植物最大植株高度与基因组大小的关系不显著,但种子重量与其呈极显著的正相关关系。木本植物最大植株高度与基因组大小显著负相关,但种子重量与其关系不显著。木本植物叶片氮含量与基因组大小呈显著正相关,但其他生活型植物的叶片氮、磷含量与基因组大小均无显著相关性。本研究表明被子植物功能性状与基因组大小的相关性在不同生活型间存在差异,这为深入研究植物多种功能性状和植物生活型与基因组大小的权衡关系在植物演化和生态适应中的作用提供了重要依据。

WGDI:A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

Evidence of whole-genome duplications(WGDs)and subsequent karyotype changes has been detected in most major lineages of living organisms on Earth.To clarify the complex resulting multi-layered patterns of gene collinearity in genome analyses,there is a need for convenient and accurate toolkits.To meet this need,we developed WGDI(Whole-Genome Duplication Integrated analysis),a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidization events and cross-species genome alignments.WGDI supports three main workflows(polyploid inference,hierarchical inference of genomic homology,and ancestral chromosome karyotyping)that can improve the detection of WGD and characterization of WGD-related events based on high-quality chromosome-level genomes.Significantly,it can extract complete synteny blocks and facilitate reconstruction of detailed karyotype evolution.This toolkit is freely available at GitHub(https://github.com/SunPengChuan/wgdi).As an example of its application,WGDI convincingly clarified karyotype evolution in Aquilegia coerulea and Vitis vinifera following WGDs and rejected the hypothesis that Aquilegia contributed as a parental lineage to the allopolyploid origin of core dicots.

Co-occurrence prediction in a large location-based social network

Location-based social network （LBSN） is at the forefront of emerging trends in social network services （SNS） since the users in LBSN are allowed to ＂check-in＂ the places （locations） when they visit them. The accurate geographi- cal and temporal information of these check-in actions are provided by the end-user GPS-enabled mobile devices, and recorded by the LBSN system. In this paper, we analyze and mine a big LBSN data, Gowalla, collected by us. First, we investigate the relationship between the spatio-temporal co- occurrences and social ties, and the results show that the co- occurrences are strongly correlative with the social ties. Sec- ond, we present a study of predicting two users whether or not they will meet （co-occur） at a place in a given future time, by exploring their check-in habits. In particular, we first intro- duce two new concepts, bag-of-location and bag-of-time-lag, to characterize user＇s check-in habits. Based on such bag rep- resentations, we define a similarity metric called habits sim- ilarity to measure the similarity between two users＇ check-in habits. Then we propose a machine !earning formula for pre- dicting co-occurrence based on the social ties and habits sim- ilarities. Finally, we conduct extensive experiments on our dataset, and the results demonstrate the effectiveness of the proposed method.

Hybrid speciation via inheritance of alternate alleles of parental isolating genes

It is increasingly realized that homoploid hybrid speciation(HHS),which involves no change in chromosome number,is an important mechanism of speciation.HHS will likely increase in frequency as ecological and geographical barriers between species are continuing to be disrupted by human activities.HHS requires the establishment of reproductive isolation between a hybrid and its parents,but the underlying genes and genetic mechanisms remain largely unknown.In this study,we reveal by integrated approaches that reproductive isolation originates in one homoploid hybrid plant species through the inheritance of altemate alleles at genes that determine parental premating isolation.The parent species of this hybrid species are reproductively isolated by differences in flowering time and survivorship on soils containing high concentrations of iron.We found that the hybrid species inherits alleles of parental isolating major genes related to flowering time from one parent and alleles of major genes related to iron tolerance from the other parent.In this way,it became reproductively isolated from one parent by the difference in flowering time and from the other by habitat adaptation(iron tolerance).These findings and further modeling results suggest that HHS may occur relatively easily via the inheritance of alternate parental premating isolating genes and barriers.

北半球高山和极地虎耳草属物种丰富度的地理格局:温度和生境异质性的作用

现代气候、生境异质性和长期气候变化对森林生态系统中分布的木本植物的物种丰富度格局的影响在以往研究中受到广泛关注,但对高寒-极地生态系统中的草本植物物种丰富度格局及其影响因素的研究仍较少。本研究旨在检验以往研究中基于物种丰富度和环境因子关系提出的假说是否能够解释高寒-极地地区典型草本植物-虎耳草属(Saxifraga)的物种丰富度格局。本研究利用全球437种虎耳草属物种分布数据,探讨了全部物种、广域和狭域物种丰富度格局的影响因素。采用广义线性模型和空间自回归模型,评估了现代气候、生境异质性和历史气候对虎耳草属物种丰富度格局的影响。采用偏回归分析了不同变量对物种丰富度的独立解释率和共同解释率,并检验了4种广泛使用的物种丰富度与环境关系模型对物种丰富度格局的解释能力。研究结果表明,温度与虎耳草属所有物种和广域物种的物种丰富度格局呈显著负相关关系,是影响物种丰富度格局最重要的环境因子,这可能反映了虎耳草属对其祖先温带生态位的保守性。生境异质性和末次冰期以来的气候变化是虎耳草属狭域物种丰富度空间变异的最佳预测因子。总体而言,包含5个预测变量的组合模型可以解释大约40%–50%的虎耳草属物种丰富度的空间变异。此外,进化和生物地理过程在虎耳草属物种丰富度格局形成方面可能发挥了重要作用,这有待进一步研究。

Confirmation of natural hybrids between Gentiana straminea and G. siphonantha (Gentianaceae) based on molecular evidence

A few individuals with intermediate morphology always appeared in the sympatric distributions of Gentiana straminea and G.siphonantha.These intermediate individuals were hypothesized to be the hybrids of two species after a careful evaluation of their morphological characteristics.To test this hypothesis,sequence comparison of the internal transcribed spacer(ITS)regions of the nuclear ribosomal and trnS(GCU)-trnG(UCC)intergenic spacer region of the chloroplast DNA from Gentiana straminea,G.siphonantha and the putative hybrids was performed.The results suggest that most intermediate individuals were the natural hybrids between G.straminea and G.siphonantha.In addition,we examined the sequence variation among the individuals of both parent species and analyzed the possibility leading to the incongruent identification in some individuals based on morphologic and molecular evidences,respectively.The intraspecific diversification of DNA fragments within both parent species and their high variability in hybrid swarms probably resulted from chloroplast genome recombination and incomplete lineage sorting during the early stages of speciation origin of the parent species.

Molecular signatures of parallel adaptive divergence causing reproductive isolation and speciation across two genera

Parallel evolution of reproductive isolation(PERI)provides strong evidence for natural selection playing a fundamental role in the origin of species.However,PERI has been rarely demonstrated for well established species drawn from different genera.In particular,parallel molecular signatures for the same genes in response to similar habitat divergence in such different lineages is lacking.Here,based on whole-genome sequencing data.