Rhododendron, a globally important group of alpine flowering plants, provides an exceptional system for investigating ecological adaptation and stress resistance owing to its high-altitude specialization. Using 18 Rhododendron species, a graph-based pangenome was constructed that captures 72,089 nonredundant structural variants. The findings support the integration of subgenus Azaleastrum into subgenus Tsutsusi, with their comparatively smaller genome sizes likely resulting from the contraction of multiple gene families during lineage differentiation. Gene families specific to high-altitude Rhododendron species were significantly enriched in pathways associated with stress resistance. High-altitude-specific long terminal repeat retrotransposons operate through similar regulatory mechanisms, predominantly influencing stress-responsive genes and promoting adaptive evolution. Through an integrated analysis of population genetics (389 re-sequenced samples with a mean coverage of 50.2×), transcriptomics, and real-time quantitative polymerase chain reaction, conserved genes and gene families linked to alpine adaptation in Rhododendron were identified. These include genes implicated in cold-stress responses and ultraviolet (UV) tolerance, such as CML18, CPK1, DREB1E, LPAT2, GPC1, and UVR8. Structural variant profiles within several of these genes offer insights into divergent adaptive mechanisms between high- and low-altitude Rhododendron species. The rapid induction of cold-sensing genes and CBF/DREB1-centered cold-stress signaling pathways indicates an evolutionary adaptation of alpine Rhododendron species to low-temperature habitats. Furthermore, transgenic analyses indicate that cold-resistance genes, such as GPC1 derived from high-altitude Rhododendron, markedly improve cold tolerance in Arabidopsis thaliana and tobacco. Collectively, this study advances insights into high-altitude adaptation in ornamental plants and underscores the value of super-pangenome resources for evolutionary and functional genomics research.

Telling species apart using DNA sequence data plays a key role in understanding, monitoring, and managing biodiversity. However, plant species discrimination is often difficult due to the complex nature of plant species boundaries. To inform future strategies for DNA-based identification of plants using the nuclear genome and to gain fundamental insights into the genomic nature of differences between plant species, we conducted a large-scale analysis mining data from 151 studies. Of the 1713 multiple-sampled species evaluated, 1202 resolved as monophyletic (70.2%). We then assessed the density of species-specific SNPs (SSSNPs) in the DNA sequence data - of the 462 species from 27 genera assessed in detail, there was a median density of 193 SSSNPs per Mb and 412 species (89.2%) had at least one SSSNP. Randomly sub-sampling the SNP data showed an asymptote in species discrimination with around 3000 randomly selected SNPs. Finally, we undertook a resampling of 6 target-capture datasets and showed that 1-9 pre-selected loci provided equivalent levels of species discrimination compared to hundreds of nuclear loci. These findings provide an important quantitative assessment of the genomic nature of differences between plant species and provide foundations for the development of enhanced approaches for high-resolution DNA-based plant species discrimination.

Chelonopsis is a small genus endemic to East Asia. In this study, a new species, C. guchengensis , from Nanhe National Nature Reserve, Gucheng County, Hubei Province is described and illustrated. Molecular phylogenetic analyses based on two nuclear ribosomal DNA regions (ETS and ITS) and five plastid DNA markers ( trnL intron, trnL - trnF , trnS - trnG , psbA - trnH , and rps16 ) were carried out to explore the phylogenetic position of the new species. A close relationship between the new species and C. giraldii is supported by molecular phylogenetic and morphological evidence. However, the two species can be easily distinguished from each other by mostly leaf and inflorescence morphology.

Chelonopsis is a small genus endemic to East Asia. In this study, a new species, C. guchengensis, from Nanhe National Nature Reserve, Gucheng County, Hubei Province is described and illustrated. Molecular phylogenetic analyses based on two nuclear ribosomal DNA regions (ETS and ITS) and five plastid DNA markers (trnL intron, trnL-trnF, trnS-trnG, psbA-trnH, and rps16) were carried out to explore the phylogenetic position of the new species. A close relationship between the new species and C. giraldii is supported by molecular phylogenetic and morphological evidence. However, the two species can be easily distinguished from each other by mostly leaf and inflorescence morphology.

Wintersweet (Chimonanthus praecox) is a traditional Chinese ornamental plant that produces showy yellow flowers in winter. In addition to the common yellow-flowered variety group, there is a wintersweet group that produces unusual yellow-green tepals. Up to now, the mechanisms underlying the coloration of the yellow-green tepals are unknown. In this study, the results of chlorophyll content determination experiment showed that the chlorophyll content in wintersweet 'H37' (yellow-green variety) was significantly higher than that in 'H25' (yellow variety); the cellular ultrastructural observations suggested that the chloroplasts within 'H37' tepals cells could maintain their structure and function over a longer period during flower development. Moreover, the differentially expressed CpSGR1 gene and CpCHLD gene were screened by comparing the transcriptomes of 'H25' and 'H37'. Finally, the gene function verification experiments showed that, in chlorophyll metabolic pathway, CpSGR1 degraded chlorophyll, resulting in significant de-greening phenotypes, whereas CpCHLD could keep the leaves and flowers green. The findings provide new insights into the formation of the yellow-green tepal phenotype, as well as provide a research foundation for flower color breeding in wintersweet.

East Asian wild grapes show a high level of species diversity and have been widely recognized as important germplasm resources of wine, table grapes, and resistance to biotic and abiotic stresses for the grape industry. However, the deeper phylogenetic relationships and drivers of diversification of East Asian Vitis remain poorly understood. Hybridization and introgression events of East Asian Vitis are not well investigated, particularly at the genome-wide scale. The phylogenetic relationships of East Asian Vitis are herein explored using nuclear and plastid genome data based on target enrichment (Hyb-Seq). Seven major clades are recognized for East Asian Vitis based on the nuclear phylogenetic trees, but there is topological incongruence between concatenated and coalescent analyses. Furthermore, significant cytonuclear discordance is observed within East Asian Vitis. Species network analyses identified several hybridization events within East Asian Vitis. These interspecific hybridization events may have caused the topological discordances and relatively low support detected in our analyses. Ecological niche modeling shows that most of the diversification of East Asian Vitis species is driven by temperature and precipitation environmental variables. Sympatric parallel diversifications of major clades also may have facilitated the rich diversity in East Asian Vitis.

The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on genomic data from the New World Vitis, a charismatic component of the temperate North American flora with known and suspected gene flow among species. Biogeographic inference and fossil evidence suggest that the grapes were widely distributed from North America to Europe during the Paleocene to the Eocene, followed by widespread extinction and survival of relicts in the tropical New World. During the climate warming in the early Miocene, a Vitis ancestor migrated northward from the refugia with subsequent diversification in the North American region. We found strong evidence for widespread incongruence and reticulate evolution among nuclear genes within both recent and ancient lineages of the New World Vitis. Furthermore, the organellar genomes showed strong conflicts with the inferred species tree from the nuclear genomes. Our phylogenomic analyses provided an important assessment of the wide occurrence of reticulate introgression in the New World Vitis, which potentially represents one of the most important mechanisms for the diversification of Vitis species in temperate North America and even the entire temperate Northern Hemisphere. The scenario we report here may be a common model of temperate diversification of flowering plants adapted to the global climate cooling and fluctuation in the Neogene.

Members of the AP2 subfamily were identified at the whole genome level in Chimonanthus praecox,and their expression patterns during flower development were analyzed. The expression profile of CpAP2-L11 was investigated,and 35S::CpAP2-L11 was introduced into Arabidopsis thaliana Columbia-0（Col-0）to analyze its function. A total of 20 AP2 subfamily transcription factors were identified,including five,six,and nine members from the euAP2,basalANT,and euANT groups,respectively,and all members of the euAP2 group have no miR172 binding sites. Synteny analysis revealed that 12members form 16 pairs of duplicated genes,which were subject to purifying selection during the evolutionary process. Most AP2 subfamily members are highly expressed in April and May flower buds（FBs）,with low expression during the entire or later stage of the chilling requirement（CR）accumulation;the expression level of CpAP2-L11 increased significantly in FBs initiating blooming when CR accumulation reached 570 CU. qRT-PCR analysis indicated CpAP2-L11 was highly expressed in the young fruit,outer tepals,and stamens,but a low expression level was detected in stems and leaves in C.praecox. The expression level of CpAP2-L11 was downregulated by high-or low-temperature. Ectopic expression of CpAP2-L11 in Arabidopsis showed earlier bolting time and the relative expression of FT,SOC1,LFY and AP1 genes increased significantly. CpAP2-L11 probably participates in chilling-induced dormancy breaking and blooming in winter and FBs differentiation in spring in C. praecox,also promoting flowering in ectopic overexpression Arabidopsis.

Euonymus maackii Rupr. is a small deciduous tree belonging to family Celastraceae. It is an important ornamental tree and a potential medicinal plant resource. Here, we assembled and annotated the chloroplast (cp) genome of E. maackii. By combining this genome with seven available cp genomes from Euonymus species, we performed plastome variation analysis of E. maackii and Euonymus. Furthermore, we reconstructed a phylogenetic tree and estimated the differentiation time of E. maackii. The newly assembled cp genome of E. maackii was 157,551 bp in size and had a typical quadripartite structure, which consisted of one large single-copy (LSC 86,524 bp) region, one small single-copy (SSC 18,337 bp) region, and a pair of inverted repeat regions (26,345 bp). A total of 652 single nucleotide polymorphisms (SNPs) and 65 insertions/deletions (indels) were detected between the two cp genomes of E. maackii, with overall genetic variation of 4.1 SNPs per kb or a π value of 0.00443, reflecting a high level of intraspecific variation. Some coding and noncoding regions with higher variation were identified, including trnV-UAC, petN, ycf1-ndhF, trnM-CAU-atpE, rpl2-rpl23, psbZ-trnG-GCC, trnY-GUA-trnE-UUC, trnW-CCA-trnP-UGG, rps16-trnQ-UUG, and psbC-trnS-UGA. The hypervariable coding and noncoding regions in E. maackii were not the same as those in Euonymus. The phylogenetic tree and divergence time based on the whole cp genomes showed that the seven Euonymus species formed a clade, which was sister to that formed with Catha edulis and Maytenus guangxiensis, and they separated 24.74 million years ago. E. maackii and E. hamiltonianus were most closely related, having separated from each other only approximately 2.68 million years ago. Our study provides important genetic information for further studies of E. maackii, such as studies on its phylogeography, population genetics and molecular ecology, and provides new insights into the evolution of the cp genome in Euonymus.

采用实地调查与文献查阅相结合的方法,对西藏杜鹃花属植物资源进行了统计和分析.西藏杜鹃花属植物共有180种(不包括种下分类等级),隶属于常绿杜鹃亚属、杜鹃亚属、马银花亚属、毛枝杜鹃亚属和糙叶杜鹃亚属5个亚属,以常绿杜鹃亚属(58.89％)和杜鹃亚属(38.33％)为主.从生活型来看,西藏杜鹃花属植物可分为灌木型(123种),乔木型(12种),灌木和乔木兼有型(45种).从垂直分布来看,西藏杜鹃花属植物在海拔1000～5800 m的范围内均有分布,在海拔3000～4000 m范围内分布的种类最多(143种).从水平分布来看,西藏除阿里地区之外的其他6市34县(区)均有分布,主要集中在西藏东南部和南部.还从树型、花色、花型、花期等方面分析了西藏杜鹃花属植物的观赏价值和应用潜力,并讨论了其在稳定整个西藏高寒地区脆弱生态方面的重要价值.

Chimonanthusof Calycanthaceae is a small endemic genus in China, with unusual winter-blooming sweet flowers widely cultivated for ornamentals and medicinal uses. The evolution ofChimonanthusplastomes and its phylogenetic relationships remain unresolved due to limited availability of genetic resources. Here, we report fully assembled and annotated chloroplast genomes of fiveChimonanthusspecies. The chloroplast genomes of the genus (size range 153,010 – 153,299 bp) reveal high similarities in gene content, gene order, GC content, codon usage, amino acid frequency, simple sequence repeats, oligonucleotide repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions. Signatures of positive selection are detected inatpFandrpoBgenes inC. campanulatus. The correlations among substitutions, InDels, and oligonucleotide repeats reveal weak to strong correlations in distantly related species at the intergeneric levels, and very weak to weak correlations among closely relatedChimonanthusspecies. Chloroplast genomes are used to reconstruct a well-resolved phylogenetic tree, which supports the monophyly ofChimonanthus. WithinChimonanthus,C. praecoxandC. campanulatusform one clade, whileC. grammatus,C. salicifolius,C. zhejiangensis, andC. nitensconstitute another clade.Chimonanthus nitensappears paraphyletic and is closely related toC. salicifoliusandC. zhejiangensis, suggesting the need to reevaluate the species delimitation ofC. nitens.ChimonanthusandCalycanthusdiverged in mid-Oligocene; the radiation of extantChimonanthusspecies was dated to the mid-Miocene, whileC. grammatusdiverged from otherChimonanthusspecies in the late Miocene.C. salicifolius,C. nitens(a), andC. zhejiangensisare inferred to have diverged in the Pleistocene of the Quaternary period, suggesting recent speciation of a relict lineage in the subtropical forest regions in eastern China. This study provides important insights into the chloroplast genome features and evolutionary history ofChimonanthusand family Calycanthaceae.

Vitisshizishanensis (Vitaceae), a new species from Hubei, China, is described and illustrated. It is morphologically similar to V.flexuosa and V.bryoniifolia, but differs in leaf lobing and pubescence. It can be easily distinguished from the two species based on its glabrous or with very sparse arachnoid tomentum on the abaxial mature leaf surface, and its unlobed to 3-7 lobed leaves. A detailed description, along with photographs for the new species, and a table for morphological comparisons with similar Vitis species, are also provided.

With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and generating 10 datasets with different sequencing coverage in silico . We tested the performance of the four datasets (plastome, nrDNA, mtDNA, and SCNs) obtained from genome skimming based on phylogenetic analyses of the Vitis clade at the genus-level and Vitaceae at the family-level, respectively. Our results showed that optimal minimum sequencing depth for high-quality SCNs assembly via genome skimming was about 10× coverage. Without the steps of synthesizing baits and enrichment experiments, we showcase that deep genome skimming (DGS) is effective for capturing large datasets of SCNs, in addition to plastomes, mtDNA, and entire nrDNA repeats, and may serve as an economical alternative to the widely used target enrichment Hyb-Seq approach.

The grape family consists of 16 genera and ca. 950 species. It is best known for the economically important fruit crop - the grape Vitis vinifera. The deep phylogenetic relationships and character evolution of the grape family have attracted the attention of researchers in recent years. We herein reconstruct the phylogenomic relationships within Vitaceae using nuclear and plastid genes based on the Hyb-Seq approach and test the newly proposed classification system of the family. The five tribes of the grape family, including Ampelopsideae, Cayratieae, Cisseae, Parthenocisseae, and Viteae, are each robustly supported by both nuclear and chloroplast genomic data and the backbone relationships are congruent with previous reports. The cupular floral disc (raised above and free from ovary at the upper part) is an ancestral state of Vitaceae, with the inconspicuous floral disc as derived in the tribe Parthenocisseae, and the state of adnate to the ovary as derived in the tribe Viteae. The 5-merous floral pattern was inferred to be the ancestral in Vitaceae, with the 4-merous flowers evolved at least two times in the family. The compound dichasial cyme (cymose with two secondary axes) is ancestral in Vitaceae and the thyrse inflorescence (a combination of racemose and cymose branching) in tribe Viteae is derived. The ribbonlike trichome only evolved once in Vitaceae, as a synapomorphy for the tribe Viteae.

Background Wintersweet ( Chimonanthus praecox ), an important ornamental plant, has evolved unique fragrant aroma and winter-flowering properties, which are critical for its successful sexual reproduction. However, the molecular mechanisms underlying these traits are largely unknown in this species. In addition, wintersweet is also a typical representative species of the magnoliids, where the phylogenetic position of which relative to eudicots and monocots has not been conclusively resolved. Results Here, we present a chromosome-level wintersweet genome assembly with a total size of 695.36 Mb and a draft genome assembly of Calycanthus chinensis . Phylogenetic analyses of 17 representative angiosperm genomes suggest that Magnoliids and eudicots are sister to monocots. Whole-genome duplication signatures reveal two major duplication events in the evolutionary history of the wintersweet genome, with an ancient one shared by Laurales, and a more recent one shared by the Calycantaceae. Whole-genome duplication and tandem duplication events have significant impacts on copy numbers of genes related to terpene and benzenoid/phenylpropanoid (the main floral scent volatiles) biosynthesis, which may contribute to the characteristic aroma formation. An integrative analysis combining cytology with genomic and transcriptomic data reveals biological characteristics of wintersweet, such as floral transition in spring, floral organ specification, low temperature-mediated floral bud break, early blooming in winter, and strong cold tolerance. Conclusions These findings provide insights into the evolutionary history of wintersweet and the relationships among the Magnoliids, monocots, and eudicots; the molecular basis underlying floral scent biosynthesis; and winter flowering, and highlight the utility of multi-omics data in deciphering important ornamental traits in wintersweet.

The grape genus (Vitis L.) is of great agronomic importance and represents an economically valuable resource. Researchers have explored the phylogenetic relationships of subgenus Vitis for decades. However, the evolutionary patterns of many morphological characters of subgenus Vitis have not yet been explored in the context of a robust phylogenetic framework. Within the East Asian clade, V. bryoniifolia and its closely related taxa form the V. bryoniifolia clade, which is taxonomically complex. The phylogenetic relationships and species delimitation within this clade remain poorly resolved, due to the limited sampling in prior studies. We tested morphological trait evolution based on ancestral character state reconstruction using a phylogenomic framework. With 89 accessions from the East Asian subgenus Vitis sampled, a robust phylogenetic relationship of the V. bryoniifolia clade is reconstructed using the restriction-site associated DNA sequencing (RAD-seq) data, which support the monophyly of most taxa of the V. bryoniifolia clade. Ancestral character state reconstructions suggest that the weak climbing ability and simplified tendrils of Vitis each evolved multiple times. This study provides a reliable phylogenomic framework for the V. bryoniifolia clade. Coupled with morphological analyses, we discuss the taxonomic status of some taxa in the V. bryoniifolia clade and untangle a taxonomic dilemma in the grape genus.

KEY MESSAGE:Overexpression of CpbHLH1 in Arabidopsis and tobacco resulted in a dramatic decrease in anthocyanin accumulation by repressing the expression of late biosynthesis genes in the flavonoid biosynthesis pathway. Many basic helix-loop-helix (bHLH) transcription factors (TFs) of subgroup IIIf have been characterized as anthocyanin-associated activators in higher plants, but information regarding bHLH TFs that inhibit anthocyanin accumulation remains scarce. In this study, the subgroup IIIf bHLH TF CpbHLH1 from Chimonanthus praecox (L.) was identified as a negative regulator of anthocyanin accumulation. Our results showed that overexpression of CpbHLH1 in model plant species, Arabidopsis and tobacco, resulted in a dramatic decrease in anthocyanin content, whereas the content of proanthocyanidin was little affected. Quantitative RT-PCR (qRT-PCR) assays of the structural genes in the flavonoid biosynthesis pathway revealed that CpbHLH1 inhibits anthocyanin accumulation mainly through repressing the expression of late biosynthesis genes (LBGs). Interactions between CpbHLH1 protein and AtPAP1/NtAN2 protein were detected via yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. This is the first bHLH repressor of anthocyanin biosynthesis identified in dicotyledons. These results can help us better understand the anthocyanin regulatory network in plants and may provide insights into the diverse functions of bHLH proteins.