Leea is a small group of plants belonging to the family Leeaceae (Vitales) with a wide distribution in the Old World tropics. Several species within this genus have been broadly circumscribed, making them species complexes. One of these complexes includes Leea guineensis, a red-flowered species, resulting in more than 30 synonyms across Africa and Southeast Asia. Leea cumingii described from the Philippines has long been considered a synonym of L. guineensis. However, a thorough analysis of the protologue, type specimen, and other herbarium materials revealed that this species is distinct and is therefore reinstated here. The present study provides the description, distribution map, photo plates, and assessment of the conservation status of L. cumingii. In addition, a lectotype is designated for the name, L. cumingii, to stabilize its nomenclatural status.

Amphi-Pacific tropical disjunctions constitute one of the major disjunction patterns in angiosperms, but have been rarely explored. Dendropanax Decne. & Planch. is one of the most diverse genera of Araliaceae and constitutes a typical example of this pattern, with two main clades distributed in Asia and the Neotropics. The evolutionary history of the genus and the factors explaining its disjunct pattern remain mostly unknown, with previous research based on limited species and genetic sampling. Here, we aim to disentangle the evolutionary relationships and understand the factors explaining the disjunct distribution of Dendropanax. We sampled 122 specimens representing Dendropanax (55% of the species) and its closely related genera to obtain highly resolved nuclear and plastid phylogenies used to perform time calibration, biogeographic, and hybridization analyses. Our results support the monophyly of core Dendropanax and polyphyly of several Neotropical taxa. Five main geographic clades were recovered by nuclear and plastid analyses, with low internal resolution in the Neotropics that may be associated with early hybridization. We inferred an early Eocene Asian origin for Dendropanax, with an Eocene-Oligocene colonization of Mesoamerica and genetic isolation between Asia and the Neotropics during the Oligocene global cooling. The Caribbean and South America were colonized from Mesoamerica during the early Miocene, with the differentiation of Eastern and Western South America lineages during the middle Miocene associated with aridification. In summary, our study improved the knowledge on the evolutionary history of Dendropanax and demonstrated an influence of global geographic patterns and hybridization in the evolution of the genus.

The staghorn sumac Rhus typhina is native to North America but has been introduced into China, where it has become widely established owing to its high adaptability and ecological and economic importance. In this study, a chromosome-level and haplotype-resolved genome of R. typhina was generated using PacBio HiFi, Illumina, and Hi-C sequencing technologies. The two haplotypes, Hap1 and Hap2, were assembled to sizes of 333.98 Mb (scaffold N50 = 21.27 Mb) and 332.18 Mb (scaffold N50 = 21.23 Mb), respectively. A total of 27,336 protein-coding genes (26,489 functionally annotated, BUSCO completeness = 96.09%) and 27,397 protein-coding genes (26,601 functionally annotated, BUSCO completeness = 96.09%) were identified in Hap1 and Hap2, respectively. The phylogenetic analysis and time estimation indicated that R. typhina clustered with the Pistacia species within the Anacardiaceae, diverging from them approximately 31.68 million years ago. This study presents the first high-quality haplotype-resolved genome of R. typhina, providing a valuable resource for its functional and evolutionary studies and insights into its coevolution with Melaphis insects.

The distribution patterns of plants in the Northern Hemisphere are closely linked to their evolutionary history. The genus Lonicera, commonly referred to as honeysuckle, is widely distributed across the northern temperate zone, making it an ideal model for exploring the distribution patterns and driving factors of plants in the Northern Hemisphere. This study, based on 108 globally distributed Lonicera samples (57 species), covered 22 of the 25 subsections of Lonicera recognized by Rehder (1903) and Nakai (1938), analyzed 485 orthologous loci and plastid genomes to investigate phylogenetic relationships, and observed phylogenetic incongruence. QuIBL and f-branch analyses revealed that incomplete lineage sorting (ILS) is the primary driver of phylogenetic discordance, accompanied by widespread but weak introgression, with only a small proportion of triplets showing strong support for introgression with relatively high mixture weights. Biogeographic and diversity distribution analyses suggest that Lonicera originated in the Qinghai-Xizang Plateau (QXP) and/or East Asia, spread to North America and Europe, and established diversity centers in East Asia, Central Europe, and western North America. Our results support the hypothesis that the uplift of the QXP and global climate shift of the Eocene-Oligocene transition (EOT) were both evolutionary drivers, with varied ecological adaptability among various Lonicera lineages. This study provides new insights into the phylogeny and biogeographic evolution of Lonicera, while also serving as a reference for studies on the evolutionary history of plant and animal lineages.

BACKGROUND AND AIMS:Mexico constitutes a biotic transition zone between Nearctic and Neotropical floras, which alongside its complex geography and climatic variability makes it an especially diverse region. Cissus, the largest genus of Vitaceae, has ∼70 species in the Neotropics, with 20-25 species in Mexico and Central America, occupying diverse environments from tropical forests to deserts. Despite their ecological relevance in the area, Neotropical Cissus species have been barely studied. Here we aim to address the phylogenetic history, taxonomic delimitation, biogeography and ecological preferences of Cissus in the biotic transition zone of Mexico and Central America. METHODS:We obtained nuclear and plastid phylogenies of Neotropical Cissus using target enrichment Hyb-Seq, sampling ∼50 % of the Neotropical species and most Mexican species. We performed time calibration and biogeographic analyses to assess the colonization history, performed ancestral reconstructions of relevant taxonomic traits, and studied geographic and climatic differences between clades and species in Mexico and Central America using climatic principal component analyses. KEY RESULTS:Four main clades were retrieved in Neotropical Cissus via phylogenomics, with putative early hybridization detected between clades. Morphological examination and phylogenetic data provided support for taxonomic reassessment in Mexico. Biogeographic analyses pointed to several colonization events to Mexico during the Oligocene and the Miocene, with xeric species from western Mexico clustering in a single mid-Miocene lineage. Climatic and geographic analyses supported differences between clades, and mountain ranges were suggested to have acted as geographic and climatic barriers for some lineages. CONCLUSIONS:Our research recovered four main clades with significantly distinct geographic and climatic preferences in Neotropical Cissus. Mexico was colonized several times and geographic and climatic isolations were crucial for speciation. Our results highlighted the presence of hidden species diversity in Mexico, underscoring the need for integrative biodiversity discovery in the Mexico transition zone.

Glehnia littoralis, a critically endangered coastal plant endemic to sandy beach habitats, plays a unique role in the ecology of fragile coastal ecosystems. Its genome was characterized using an integrated approach combining flow cytometry, high-throughput sequencing, k-mer analysis, Smudgeplot, and cytogenetic validation. Flow cytometry estimated the genome size at ~2,913 Mb, while k-mer analysis under a diploid model (p = 2) revealed low heterozygosity (1.15%) and a high repeat content (80.87%), reflecting a relatively homogeneous yet highly repetitive genome shaped by historical whole-genome duplication events and transposon expansion. Smudgeplot patterns and cytogenetic analysis further confirmed the diploid status (2n = 22, x = 11) with a karyotype of 2n = 2x = 18m + 4sm (type 2A). These findings not only illuminate the evolutionary history and genomic architecture of this rare Apiaceae species but also offer critical insights into its adaptation to extreme coastal environments, providing valuable information for conservation strategies aimed at preserving this highly vulnerable, ecologically significant plant.

Genome size, the total amount of DNA content in the cell nucleus, varies greatly among flowering plants. One factor underlying this variation is the environment under which plants evolve. Given this premise, harsh environmental conditions in arid regions may profoundly influence genome evolution. However, the specific impact of aridification on genome size evolution, particularly for African lineages, remains largely unexplored. Here, we investigate linkages between genome size evolution and ecological adaptation using the genus Cyphostemma in the grape family (Vitaceae) as a model. Cyphostemma species exhibit genome size expansion and remarkable morphological traits in arid environments, including succulent stems or leaves and loss of tendrils. Our biogeographic reconstruction, based on substantial taxon sampling (112 of 200 species), reveals that Cyphostemma originated in continental Africa during the late Eocene to Oligocene and has undergone rapid radiation since the middle Miocene, coinciding with intensified aridification and geological activity in eastern Africa. Incorporating extensive data on traits, habitats, genome size, and chromosome numbers, we show that Cyphostemma species with the largest genomes are succulent polyploids restricted to nutrient-rich limestone outcrops. Broad-scale analyses across eudicots further confirm that larger genomes are significantly associated with both succulence and arid habitats. Our findings reveal a strong association between genome size expansion, polyploidy, and adaptive traits, indicating that genome size is a hitherto neglected trait associated with the radiation of succulent plants during the African aridification in the Cenozoic.

Understanding how a lineage originates, diversifies, and adapts through interactions between intrinsic traits and the environment is a central question in evolutionary biology and ecology. Prunus L., one of the morphologically diverse genera in the Rosaceae, holds considerable ornamental and economic importance. However, the factors associated with its remarkable diversity and its responses to environmental change throughout its diversification history remain poorly understood. Here, we reconstruct a comprehensive nuclear phylogeny of Prunus by integrating universal Angiosperms353 genes and lineage-specific orthologous genes, providing a robust framework for investigating the spatiotemporal dynamics of diversification and their correlations with trait variation and environmental conditions. Our comparative analyses date the crown age of Prunus to the early Paleocene (∼63 million years ago, Ma) and identify increased diversification rates, including at least one major rate shift. Pronounced diversification pulses were associated with variation in paleotemperature, as well as interactions between climatic variables and intrinsic traits, particularly ploidy level and inflorescence types. These associations are consistent with patterns of ecological expansion and lineage radiation. Ancestral state reconstructions indicate that the most recent common ancestor of Prunus was deciduous, racemose, polyploid, and possessed a glabrous ovary. Together, these results show that the evolutionary trajectory of Prunus has been shaped by both climatic change and key biological traits, providing a robust macroevolutionary framework for future evolutionary, and comparative studies in Rosaceae.

Abstract Rafflesiaceae, including Rafflesia, Sapria, and Rhizanthes , are some of the rarest flowering plants in the world, known for producing the largest blooms on Earth. These holoparasites depend exclusively on Tetrastigma (Vitaceae) vines, yet the chemical basis for this host specificity is poorly understood, complicating conservation efforts. Untargeted negative-ion LC- MS metabolomics was used to profile Rafflesiaceae buds and seeds, infected Tetrastigma hosts associated with Rafflesia lagascae, R. speciosa, and Sapria himalayana , uninfected Tetrastigma hosts, and corresponding non-host species from the Philippines and Thailand. Python scripts used for data processing and visualization were developed with generative AI assistance and validated by the authors. Principal component analysis revealed distinct metabolomic profiles across samples, with significant shifts in host metabolites upon infection. Infected Tetrastigma tissues showed nominal enrichment in phenylpropanoid and gibberellin-related metabolites, suggestive of defense and hormonal pathway activation during Rafflesia infection, as well as citric acid, suggesting increased energy demand to support the parasite. Non-host Tetrastigma species showed nominal enrichment in metabolites putatively annotated as stilbenoids, resveratrol diglucosides, and condensed tannins such as procyanidin B2, compounds broadly associated with plant defense. Rafflesia seeds harbored fatty acids/oxylipins, while Rafflesia buds accumulated gallic acid derivatives, compounds also reported in galls. These findings support a chemically mediated model of host compatibility and parasitism, with implications for the ex-situ conservation of these endangered plants.

Amur grape (Vitis amurensis Rupr.) is widely recognized for its cold tolerance traits and serves as a valuable genetic resource for breeding climate-resilient grape cultivars. Here, we construct a graph pangenome reference (Vampan_V1.0) and generate a variant map comprising 48,308,434 short variants and 127,094 TE-associated structural variants (TEVs) using deep resequencing data from 330 samples across 31 natural populations covering the species' distribution range. We discover a biased accumulation of SNPs around TEVs and identify 823 candidate adaptive genes associated with environmental variables. Using machine learning-based genetic offset models, we further show that putative adaptive TEVs significantly reduce genetic offsets by 7.3% to 8.2% under future climate scenarios. Our study shows the power of a graph-based pangenome to resolve complex variation and highlights the impact of TEVs on genetic diversity, local adaptation, and resilience to future climate change, providing insights into utilizing crop wild relatives in climate-resilient crop breeding.

Anaphalis is the largest genus in tribe Gnaphalieae of Asteraceae in Asia, with more than 110 species distributed mainly in tropical to temperate Asia. The interspecific relationships and evolution within Anaphalis are complex and remain controversial, with little attention for their chloroplast evolution at the genomic level. In this study, we sequenced and assembled chloroplast genomes, performing comparative and phylogenetic analyses on 32 representative species of Anaphalis. Our results revealed that these chloroplast genomes exhibit a typically circular quadripartite structure ranging in length from 152,396 to 153,573 bp with a total of 131 to 132 genes, including 87 protein-coding, 36-37 tRNA, and 8 rRNA genes. The phylogenetic analyses suggested that Anaphalis is polyphyletic and nested with Helichrysum and Pseudognaphalium, which are clustered into two groups as clades I and II. The overall genome length of clade I was relatively smaller than that of clade II, possibly due to less insertion with more deletions in intergenic regions of the former. The trnT-GGU gene is presented as pseudogene in clade II but is absent in clade I. The rpl22 gene shows significantly higher positive selection from most species of clade I than those in clade II, probably related to environmental adaptations of species from clade I survived in high-altitude mountains. The results of the comparative and phylogenetic analyses provide valuable references for further research studies of classification, phylogenetic relationships and genomic adaptation of Anaphalis species.

Societal Impact Statement Wild grapevines ( Vitis L.) native to the Americas are ecologically and culturally important plants that are also critical to the global cultivated grape industry as sources of traits for crop innovation, but many of these species are poorly documented and insufficiently conserved. We provide new information on the distributions, environmental adaptations, and conservation statuses of 38 wild grapevine taxa native to the Americas. Ranging from southern Canada to northern South America, with the greatest concentration of taxa in the southern and central to eastern United States and in central to southern Mexico, these taxa show wide variations in their adaptations to different environmental conditions. The vast majority of taxa are of urgent or high priority for further conservation action. Summary The wild relatives of cultivated grapevines ( Vitis L.) are ecologically and culturally important plants that provide valuable genetic resources for grape scion and rootstock breeding. The distributions of wild grapevines, local adaptations to environmental conditions of potential interest for crop innovation, and their current degree of representation in conservation systems are insufficiently documented. Here, we compile occurrence records for 38 wild grapevine taxa native to the Americas, predict their distributions at high spatial resolution, use climatic and topographic information to infer their environmental adaptations, and assess their ex situ and in situ conservation representations, including identification of gaps in current conservation. Wild grapevines occur from southeast Canada to southern Mexico, Guatemala, and Belize, with one taxon distributed from Mexico to northern South America as well as the Caribbean and one taxon endemic to Colombia. Taxonomic richness is concentrated in the southern and central to eastern United States and central to southern Mexico, with up to 10 potentially sympatric taxa in central to southern Texas. We find substantial variation among and within Vitis taxa in their adaptations to temperature, precipitation, and topographic characteristics. We categorize 25 of 38 of the taxa as urgent priority and 10 as high priority for improving ex situ conservation representation. Three taxa are assessed as urgent and 29 as high priority for enhancing in situ conservation. Further action, with emphasis on conservation gap hotspots, is needed to more comprehensively conserve wild Vitis native to the Americas.

Ampelocissus Planch. (Vitaceae) comprises c. 95 currently recognized species that are distributed across tropical and subtropical regions in Asia, Australia, continental Africa, Madagascar, and Central America. Ampelocissus has attracted extensive attention for its close relationship with the economically important grape genus Vitis L. Despite their widespread use as food and medicinal plants, only two species have IUCN conservation status. The circumscription of several African species remains unclear due to a lack of integrative molecular and morphological studies. In this study, we conduct a comprehensive investigation of the phylogeny, biogeography, and morphological evolution of Ampelocissus using phylogenomic data with expanded taxon sampling, particularly from Africa. Our phylogenetic analyses resolve four major clades, supporting traditionally defined sections within Ampelocissus. African species of Ampelocissus are shown to be non-monophyletic, forming two lineages with distinct inflorescence types: the paniculate lineage and the cymose lineage. However, each lineage includes species from both Africa and Asia. Our biogeographic reconstruction suggests that African Ampelocissus lineages may have originated in Asia during the Eocene and supports at least two independent dispersal events from Asia to continental Africa and one from Asia to Madagascar. We further demonstrate that inflorescence type, flower-stalk, and tendril-associated inflorescences are well conserved across the phylogeny and serve as key taxonomic characteristics. Finally, we revisit the taxonomy of some controversial African Ampelocissus species and describe three new taxa from Madagascar, integrating molecular, morphological, and geographic evidence.

The genus Oxytropis DC. comprises about 310 species distributed in Asia, Europe, and North America. Previous studies based on evidences from morphology or a few molecular markers are helpful for understanding the classification and systematic evolution of Oxytropis. However, a scarcity of chloroplast genomic resources for Oxytropis has hindered the understanding of the genus’s systematic classification and chloroplast genome evolution. Here comparative genomic analyses were conducted on chloroplast genomes of 24 Oxytropis species. Chloroplast genomes of Oxytropis species showed the triad structure due to the loss of one copy of the IR, with the size range from 121854 bp to 125271 bp. The Oxytropis cp genomes encoded a total of 110 genes, including 76 protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. It was found that the atpF intron, one clpP intron, one rps12 intron, rpl22 gene, rps16 gene, and infA gene were lost in the Oxytropis cp genomes. Seven regions (5’-rps12-clpP, clpP intron, psbM-petN, rpl23-trnI-CAU, ndhJ-trnF-GAA,trnQ-UUG-accD, trnL-UAA-trnT-UGU) were chosen as potential molecular markers, which will contribute to species identification, population genetics and phylogenetic studies of Oxytropis. The phylogenetic relationships among Oxytropis species provided some implications for the classification of Oxytropis. Congruent with studies based on the morphological evidence, the close relationships between O. neimonggolica and O. diversifolia, as well as O. filiformis and O. coerulea were revealed. The results supported the treatment of O. daqingshanica as a separate species and refuted the inclusion of O. daqingshanica in O. ochrantha as conspecific taxa. In addition, it was suggested that O. chiliophylla should be considered as a separate species rather than its inclusion in O. microphylla. The 16 positively selected genes (rps3, rps4, rps7, rps11, rps12, rpl2, rpl20, rpl32, rpoC2, psbC, rbcL, atpF, clpP, accD, ycf1, ycf2) are related to important biological processes for instance self-replication, photosynthesis and metabolite biosynthesis, which may contribute to the adaptation of Oxytropis to its habitats. This study will lay a solid foundation for further studies on species identification, taxonomy, and systematic evolution of Oxytropis.

IntroductionWhole genome duplication events (WGDs) have been recognized as major drivers of evolution in plants, especially when they involve hybridization (allopolyploidization). In this study we evaluated if WGDs acted as evolutionary forces at the origin and early divergence of the Asian Palmate group (AsPG) of the plant family Araliaceae. This clade encompasses most of the generic and species diversity as well as most of the polyploids of the family, and a role of hybridization in its origin has been suggested.MethodsIn order to test this hypothesis, we obtained nuclear and plastid time-calibrated phylogenomic trees including 80% of Araliaceae genera (37 genera, 237 species) using the Hyb-Seq approach. The role of WGDs in the early evolution of the AsPG was tested using ancestral chromosome number reconstructions based on chromosome counts for 62% of the sampled genera, while recent polyploidization events were explored by inferring ploidy of the sequenced species from allelic frequencies.ResultsPhylogenetic analyses of nuclear and plastid sequences provided highly resolved but incongruent topologies consistent with ancient hybridization not only for the origin of the AsPG, but also in the second most highly diverse clade of the family. Our ancestral chromosome number reconstructions supported that one or two WGDs preceded the origin of two of the three main clades of Araliaceae (AsPG and Polyscias-Pseudopanax), which could have acted as background variables necessary for the posterior diversification of these lineages. Ploidy inference based on allelic frequencies provided signal of recent polyploidization in the AsPG and the third main clade of Araliaceae (Aralia-Panax).ConclusionsIn summary, WGDs are linked to the origin of the main clades of the Araliaceae family, but the drivers of the strong diversification of the AsPG remain an open question.

As the largest lineage in the tribe Gnaphalieae of Asteraceae, phylogenetic relationships within the Helichrysum-Anaphalis-Pseudognaphalium (HAP) remain poorly resolved. In this study we sequenced chloroplast genomes from 28 representative species from the HAP clade, performing comparative and phylogenetic analyses. Their chloroplast genomes ranged from 151,69 to 153,603 bp and possessed a typical quadripartite structure encoding 131-134 genes, including 87-89 protein-coding genes, 36-37 tRNA genes and 8 rRNA genes. The plastome data recognized the HAP into an early-diverging lineage and a large core clade. The latter was further separated into two subclades, namely core I and core II. Relatively small genomes with more insertion and fewer deletions were found in the early HAP lineage and Anaphalis taxa from core I. The small chloroplast genomes of the early lineage in the HAP clade potentially linked to their dry environmental adaptation in South Africa. The trnT-GGU gene was presented as pseudogenes in the early lineage and a subclade of core II but completely lost in the whole core I. As a distinct lineage within the HAP clade, Pseudognaphalium was characterized by the presence of an ycf15 pseudogene with only 54 bp and the lack of hexanucleotide repetitions. The findings in this study enhance our understanding of the internal structure of chloroplast genomes in the HAP clade and provide valuable insights on the phylogenetics and plastome evolution of this clade.

Leea trifoliata M.A.Lawson has long been considered conspecific with L. compactiflora Kurz. Detailed examination of live materials and herbarium specimens suggests that both species are distinct, differing in habit, leaf architecture, and inflorescence and bract morphology. This contribution presents morphological evidence for the reinstatement of L. trifoliata, including its taxonomic description, illustration, distribution maps, notes on habitat, and conservation status assessment using the IUCN criteria. In addition, A neotype was selected for L. compactiflora.