Introduction Plant development is shaped by environmental conditions, and its adaptation to climate change is crucial for biodiversity conservation. The extreme climate of the Qinghai-Tibet Plateau makes it an ideal system for studying plant adaptive strategies. Rosa sericea, a dominant alpine shrub, exhibits remarkable morphological plasticity, but its molecular and cellular adaptation mechanisms are still unclear. In this study, we integrated single-nucleus RNA sequencing (snRNA-seq) with high-dimensional weighted gene co-expression network analysis (hdWGCNA), gene ontology (GO) enrichment, gene set enrichment analysis (GSEA), pseudotime trajectory inference, and gene overexpression techniques to profile 31,796 cells from R. sericea leaves.Methods We constructed a draft single-cell transcriptional atlas with putative annotation of 11 leaf cell types and identified eight co-expression gene modules linked to key cell types.Results The leaf development spatiotemporal dynamics uncovered a developmental continuum from cell proliferation to photosynthetically specialized maturation. Furthermore, we identified several developmental and physiological features potentially associated with high-altitude adaptation, including presence of transcriptionally active nuclear-encoded genes involved in chloroplast function in epidermal pavement cells, the potential role of SPL7-mediated copper homeostasis, and a putative RO6G37307-TTG2-TCP4 regulatory module associated with trichome development.Discussion Together, this study provides the first single-cell-resolved transcriptional framework for R. sericea leaves and suggests adaptive developmental mechanisms at the cellular and genetic levels, enhancing our understanding of how alpine plants respond to climate change.

Background and Aims Chinese old garden roses are major contributors to the genetic development of modern roses. The RoKSN gene is associated with continuous flowering in roses and is proposed to have originated from Chinese wild roses. However, the wild roses that are implicated in the breeding of Chinese old garden roses and the origin of the RoKSN locus remain unidentified. We collected 25 of the most renowned and classic diploid Chinese old garden roses along with all related wild roses from East Asia. These roses were analysed with the aim of identifying the wild species that contributed to the genetic composition of Chinese old garden roses. In addition, we aimed to infer the geographical origin of the RoKSN gene and to develop a schematic overview of hybrid domestication of Chinese old garden roses.Methods We compared the haplotypes of internal transcribed spacers (nrITS), six nuclear single-copy genes and three chloroplast genes between Chinese old garden roses and wild roses. Additionally, we assessed genetic organization using 21 expressed sequence tag-simple sequence repeats to identify potential donor species that contributed to the emergence of these cultivars. Primers were designed for RoKSN to allow comparison of the gene across the entire distribution range of Rosa sect. Chinenses.Key Results Our findings confirmed that the majority of rose cultivars are descendants of early hybridization events. Rosa chinensis var. spontanea, R. odorata var. gigantea and R. multiflora var. cathayensis were the primary donors for the 25 cultivar roses. Chinese old garden roses were categorized into four groups. Ten cultivars were hybrids between R. chinensis var. spontanea and R. multiflora var. cathayensis, thereby forming the 'Old Blush' group. Five cultivars were hybrids between 'Old Blush' and the R. kwangtungensis species complex, thereby forming the 'Slater's crimson' group. Six cultivars were hybrids between 'Old Blush' and R. odorata var. gigantea, thereby forming the 'Tea Rose' group, and three cultivars were hybrids that evolved from more than three donors. Moreover, we observed relatively close genetic proximity among Chinese old garden roses with an identical RoKSN-copia gene that is responsible for continuous flowering, which indicates a single origin for this retrotransposon-containing allele. Additionally, we determined that the haplotypes of the RoKSN-copia gene predominantly occurred in the Sichuan Basin region. In contrast, R. chinensis cultivated in the Ya'an region showed no markers of hybridization and displayed a genetic composition that was close to that of the wild species R. chinensis var. spontanea. This cultivar may represent the earliest mutated individual that bears the RoKSN-copia gene and may have served as a bridge from wild species to continuous-flowering old rose cultivars.Conclusions The study provides crucial evidence that elucidates the origin of cultivated roses and lays the groundwork for further analysis of the breeding history of Chinese old garden roses using genomic data.

Rosa laevigata Michx., a member of the genus Rosa in Rosaceae, has large, pure white flowers with a pleasant floral scent, making it a valuable ornamental and aromatic plant. However, the composition and dynamic changes in the abundance of its volatile organic compounds (VOCs) at different developmental stages, as well as the molecular mechanisms regulating floral scent biosynthesis, remain unclear. In this study, we conducted metabolomic and transcriptomic analyses to investigate the composition and abundance changes of VOCs in R. laevigata flowers at three developmental stages. Additionally, we identified key structural genes involved in the floral scent biosynthesis pathways. The results showed that a total of 330 VOCs were identified during the three developmental stages, of which 192 were differential volatile organic compounds (DVOCs), mainly benzenoids/phenylpropanoids and esters. Transcriptomic analysis further identified 8,585 differentially expressed genes, of which 67 were key structural genes related to floral scent biosynthesis. The regulatory network of transcription factors and structural genes revealed that 20 transcription factors were highly associated with floral scent biosynthesis. These findings provide a theoretical basis for the molecular breeding of fragrant germplasm in R. laevigata and contribute to the development of its aromatic industry.

We investigated the function of the white trichome tufts on and within labellum and the pollination mechanism of Cypripedium wardii. We conducted field observations on a large population over four years analyzing its floral epidermis, breeding system, and trichome consumption by its visitors. Flowers bear two tufts of white, clustered, moniliform, trichomes located on the infolded entrance to the labellum, and a third tuft is located on the floor of the labellum. These trichomes are lipid-rich and are collected by bees and consumed by hoverflies. Although self-compatible, these flowers require pollen vectors for fruit set. Trichomes of C. wardii provide a pollen surrogate potentially rewarding polylectic/polyphagic pollinators. This results into an unusually high fruit set (76%-82%) contrasting with a lower-level of fruit set in other deceptive orchids. Our findings provide new insights on the gradation between reward and deception in the evolution of orchid flowers.

Rosa hugonis is widely distributed in the Hengduan Mountains, Qinling Mountains, and northern China. It is an important candidate species for ecological restoration, given its good adaptability. Here, we present the first high-quality chromosome-level assembly of R. hugonis based on HiFi reads and Hi-C data. The sequencing data were then assembled onto seven pseudochromosomes of R. hugonis. The genome sizes of R. hugonis is 337.92 Mb, with contig N50 length of 26.84 Mb. We annotated 36,218 protein-coding genes in R. hugonis. In summary, the high-quality genome sequences of R. hugonis provide a genetic roadmap for the study of its genetics and species relationships. This will facilitate future genomic comparative studies across more species within Rosa.

Although considerable progress has recently been made in the phylogeny of Hymenasplenium, the genus remains poorly investigated; specifically, the diversification and historical biogeography of the genus have been little studied. Here, we infer an updated plastid DNA phylogeny and the first large-scale nuclear DNA phylogeny to understand the biogeography of the genus. The plastid phylogeny includes 312 accessions from across the genus ' distribution range (ca. 121% increase of the latest sampling), with special attention paid to island accessions from 14 Indian Ocean and Pacific islands, whereas the nuclear phylogeny includes 161 accessions of the Afro-Eurasian species. We identify one new major clade and two new subclades. Reticulate evolution was revealed both among subclades and among species in the Afro-Eurasian. Our divergence-time analyses show that most of the extant species diversity has arisen from diversification after the Oligocene despite a Cretaceous origin of the genus. Ancestral area reconstruction revealed that vicariance likely played a major role in building biogeographic patterns at deep evolutionary scales (the Afro-Eurasian clade and the American clade) in Hymenasplenium, while the intercontinental disjunctions within the Afro-Eurasian clade among Asia, Africa, and Oceania might have resulted from frequent long-distance dispersal events from Asia to Oceania and Africa.

The genus Rosa presents significant challenges in species identification and phylogenetic research due to phenotypic similarities, rapid diversification, hybridization, and incomplete lineage sorting. This study investigates the phylogenetic relationships and morphological evolution of 56 taxa (53 Synstylae and three Chinenses) using six nuclear regions and 126 chloroplast genomes, resulting in 1142 sequences. We found that these taxa, including 15 newly sampled, were assigned to 12 species complexes based on molecular, morphological, and geographical features. Nuclear markers offer a more reliable phylogenetic backbone than chloroplast genomes, aligning more closely with morphological classifications. A new species, Rosa austrotibetana sp. nov., from Tibet, China, is described, and R. mulliganii is identified as a hybrid of R. luciae and R. filipes; six morphological characters were analysed in identifying synapomorphic traits among species complexes; leaflet evolution exhibits homoplasy; and stipule margin shape, petal hairs, and style hairs are key traits for circumscribing species series and complexes, whereas leaflet texture, leaflet number, and abaxial leaflet hairs are key for species delimitation within complexes.

Species delimitation in recently diverged lineages presents significant challenges in plant systematics, particularly in the genus Rosa, where recent radiation, incomplete lineage sorting, and frequent hybridization have created intricate evolutionary patterns. This study presents a comprehensive investigation of a monophyletic complex comprising R. graciliflora, R. tibetica, and R. tsinlingensis, integrating morphological, ecological, and genomic approaches. Morphological analysis of 392 specimens revealed substantial interspecific trait overlap without distinct morphological boundaries, while ecological niche analysis demonstrated significant habitat overlap, both challenging the current taxonomic classification. Phylogenetic analysis, population genetic structure analysis, and principal component analysis (PCA) based on genome-wide SNP data from 190 individuals across 26 populations did not support the monophyly of these three traditionally recognized species, indicating low genetic differentiation and extensively interwoven genetic backgrounds. Population genetic structure primarily reflected geographical distribution patterns, with genetic differentiation mainly driven by geographic distance and environmental factors. Significant gene flow was detected among adjacent populations. Selective sweep analysis identified key genes associated with flower color and flowering time. Correlation analysis suggested that solar radiation is a crucial environmental factor influencing leaflet number and flower color variation. Based on these findings, we propose treating R. tsinlingensis and R. tibetica as synonyms of R. graciliflora. Our findings underscore the limitations of morphological classification in reflecting the genetic and ecological diversity within the R. graciliflora complex, highlighting the importance of multidimensional data in understanding plant evolution and biodiversity conservation in the face of changing environments.

Two environmentally friendly plasticizers with different structures were synthesized based on ricinoleic acid from non-food crop sources with good plasticizing effect, migration, and volatility resistance.

Interspecific hybridization in the genus Rosa (Rosaceae) is a common natural phenomenon. Hybrids often exhibit heterosis and new combinations of traits, which can provide raw materials for horticultural breeding. DNA barcodes and microsatellites have been proposed to facilitate species discrimination and hybrid detection. However, most SSR markers developed for roses have been found unapplicable to Rosa sect. Synstylae because of null alleles or failed amplification. In this study, we designed 15 pairs of microsatellite primers, along with four previously developed primers specifically for Rosa sect. Synstylae; we then analyzed 174 individuals of three closely related and sympatrically distributed Rosa species as a test case to evaluate the consistency between morphological and genetic hybrid identifications and to compare the discrimination efficiency of the DNA barcodes versus SSRs in detecting admixture. Principle coordinate analysis identified several individuals with intermediate phenotypes among the three rose species. Hybridization, intraspecific morphological polymorphism, and sample collection at different growth stages or phenological phases may have hindered species identification based on morphology and distorted the morphological clustering results. The molecular analyses showed that 12 (6.8

A cytotaxonomic study is conducted for Lepisorus from eastern, southern, and southwestern China, involving 120 samples of about 26 species in seven sections. The chromosome numbers of 10 species are reported for the first time. The basic chromosome numbers, x = 19 and x = 22 discovered in L. cespitosus and L. lineariformis, respectively, are found to be new base numbers in Lepisorus. The taxonomic implications of the chromosome information of some species and the evolution of chromosomes in the genus are discussed.

The pollen morphology of 20 species from Blumea and Cyathocline Cass. was investigated using a light microscope (LM) and scanning electron microscopy (SEM) to explore their taxonomic significance. This study showed that pollen grains of these species were usually tricolporate, rarely tetracolporate (B. sinuata). Nine pollen types were distinguishable through the exine sculpture characters and the number of apertures. It was easily distinguished Cyathocline from species of Blumea s. str. by its much smaller size (15.04 μm × 15.07 μm) and sparse and longer spines (24 spines, spine length 4.23 μm) with acute apex, which suggest that C. purpurea might not belong to the genus Blumea s. str. The palynological characteristics indicated that Section Macrophllae and Section Paniculatae of Blumea were not monophyletic groups. The pollen morphology differentiation of B. lacera clade is consistent with the interspecific relationship revealed by the molecular phylogenetic tree. However, the pollen morphology of the Blumea densiflora clade is inconsistent with the interspecific relationship based on molecular phylogenetic analysis. This palynology research can only partly support the previously published molecular phylogeny of Blumea s. str.

The papilionoid legume genus Sophora (Fabaceae) exhibits a worldwide distribution, but a phylogenetic framework to understand the evolution of this group is lacking to date. Previous studies have demonstrated that Sophora is not monophyletic and might include Ammodendron, Ammothamnus, and Echinosophora, but the relationships among these four genera (defined as Sophora s.l.) are unclear. Here we used a nuclear DNA dataset (ETS, ITS, SQD1) and a plastid DNA dataset (matK, rbcL, rpl32-trnL, trnL-F) of 654 accession sequences to reconstruct the phylogenetic relationships, estimate the divergence times and ancestral range of Sophora s.l., and infer the evolution of chromosome number and morphological characteristics. Our major aim was to reconstruct phylogenetic relationships to test monophyly and elucidate relationships within the genus. Our results indicated that Ammodendron, Ammothamnus, and Echinosophora are embedded within Sophora s.s. and that nine well-supported clades can be recognized within comprise Sophora s.l. Ancestral character state estimation revealed that the most recent common ancestor of Sophora s.l. was a deciduous shrub that lacks rhizome spines and has unwinged legumes. Divergence times estimation and ancestral area reconstruction showed that Sophora s.l. originated in Central Asia and/or adjacent Southeast China in the early Oligocene (ca. 31 Mya) and dispersed from these regions into East and South Asia's adjacent areas and North America via the Bering land bridge. The analyses also supported a South American origin for S. sect. Edwardsia, which experienced rapid radiation with its major lineages diversifying over a relatively narrow timescale (8 Mya).

IntroductionIndigofera L. is the third largest genus in Fabaceae and includes economically important species that are used for indigo dye-producing, medicinal, ornamental, and soil and water conservation. The genus is taxonomically difficult due to the high level of overlap in morphological characters of interspecies, fewer reliability states for classification, and extensive adaptive evolution. Previous characteristic-based taxonomy and nuclear ITS-based phylogenies have contributed to our understanding of Indigofera taxonomy and evolution. However, the lack of chloroplast genomic resources limits our comprehensive understanding of the phylogenetic relationships and evolutionary processes of Indigofera. MethodsHere, we newly assembled 18 chloroplast genomes of Indigofera. We performed a series of analyses of genome structure, nucleotide diversity, phylogenetic analysis, species pairwise Ka/Ks ratios, and positive selection analysis by combining with allied species in Papilionoideae. Results and discussionThe chloroplast genomes of Indigofera exhibited highly conserved structures and ranged in size from 157,918 to 160,040 bp, containing 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Thirteen highly variable regions were identified, of which trnK-rbcL, ndhF-trnL, and ycf1 were considered as candidate DNA barcodes for species identification of Indigofera. Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) methods based on complete chloroplast genome and protein-coding genes (PCGs) generated a well-resolved phylogeny of Indigofera and allied species. Indigofera monophyly was strongly supported, and four monophyletic lineages (i.e., the Pantropical, East Asian, Tethyan, and Palaeotropical clades) were resolved within the genus. The species pairwise Ka/Ks ratios showed values lower than 1, and 13 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis using the branch-site model, eight of which were associated with photosynthesis. Positive selection of accD suggested that Indigofera species have experienced adaptive evolution to selection pressures imposed by their herbivores and pathogens. Our study provided insight into the structural variation of chloroplast genomes, phylogenetic relationships, and adaptive evolution in Indigofera. These results will facilitate future studies on species identification, interspecific and intraspecific delimitation, adaptive evolution, and the phylogenetic relationships of the genus Indigofera.

Plant Volatile components are an ecological adaptation mechanism of plants that can reflect species differences and environment information where it is located. The alpine shrub Rosa sericea complex consists of several allied species, which are morphologically similar and difficult to distinguish, they are typical distribution along the elevation in the Himalayas and the Transverse Ranges. We selected two typical areas to find that the different species could be distinguished by their “green leaf volatile components” (GLV) composition as well as their geographical location, and it was evident that species with glands had higher sesquiterpene content. Correlation analysis revealed the relation between volatile components and ecology factors (climate factors, soil factors, phyllospheric microorganisms). Our study adds a new perspective and basis for the environmental adaptations of different species in the alpine shrub Rosa sericea complex from a chemical ecology perspective.

The genus Sorbus L. in the Rosaceae family is taxonomically challenging due to its morphological variation, polyploidy, and interspecific hybridization. In this study, we used scanning electron microscopy (SEM) to observe the pollen morphology of eighty species, representing six subgenera, in order to assess the differences within the genus Sorbus and its pollen characteristics. We conducted a cluster analysis on three qualitative and four quantitative characteristics. The results demonstrated that the pollen grains of the studied Sorbus species are isopolar and tricolporate. We identified five types of pollen shapes: suboblate, spheroidal, subprolate, prolate, and perprolate. The pollen ornamentation of the investigated species could be classified into five types: striate-perforate, striate, cerebroid-perforate, cerebroid, and foveolate. Interestingly, within the same subgenera, different species exhibited multiple types of characters. The cluster analysis indicated that all 80 species could be divided into six groups, with group B consisting exclusively of species from the subgenus Sorbus. Although pollen micro-morphologies alone do not provide sufficient evidence to establish the taxonomic relationships of the subgenera within Sorbus, they do offer valuable information for species-level taxonomic treatment.

The genera Uraria Desv. and Christia Moench are sister genera belonging to the tribe Desmodieae (Fabaceae), and most species are used as important medicinal or ornamental plants. Evolutionary patterns and intergeneric delimitation of these genera have long been controversial. In the present study, the chromosome numbers and karyotypes of six Uraria species and three Christia species were analyzed via the root tip chromosome squashing method towards a better understanding of karyotype evolution. The chromosome numbers observed in Uraria and Christia were 2n=2x=22 and 2n=2x=20, respectively. Analysis of karyotypes resulted in formulas of 20m+2sm (U. crinita and U. lacei), 18m+4sm (U. lagopodioides), 22m (U. picta, U. rufescens, and U. sinensis), and 20m (C. campanulata, C. obcordata, and C. vespertilionis). Cluster analysis conducted using the UPMGA algorithm based on chromosomal and karyotypic parameters revealed that these nine species were divided into two clades, where species of Uraria and Christia each formed a monophyletic clade. In the Uraria clade, U. picta, U. sinensis, U. crinita, and U. rufescens were divided into a subclade, while U. lacei and U. lagopodioides were divided together, showing their close genetic relationships. The taxonomically controversial species, C. campanulata, nested within the Christia clade and showed a close affinity to C. vespertilionis.

Mazusmotuoensis W.B.Ju, Bo Xu bis & X.F.Gao is a newly described species found in Xizang Autonomous Region, China. Morphologically, this species differs from all the other known Mazus species by having erect perennial herb form with a rhizome, presence of multicellular hairs, without basal leaves, opposite arrangement of stem leaves, and corolla lobes with erose-toothed margins. Molecular phylogenetic analysis using nuclear and cpDNA genes suggests that this new species occupies a basal position within Mazus. In conclusion, both morphological evidence and molecular phylogenetic analyses support that this species belongs to Mazus and represents an as-yet-unreported new species with distinct differences from other species within the genus.

Rubus L. (Rosaceae, Rosoideae) contains around 700 species distributed on all continents except Antarctica, with the highest species diversity in temperate to subtropical regions of the northern hemisphere. The taxonomy of Rubus is challenging due to the frequency of polyploidy, hybridization and apomixis. Previous studies mostly sampled sparsely and used limited DNA sequence data. The evolutionary relationships between infrageneric taxa, therefore, remain to be further clarified. In the present study, genotyping by sequencing (GBS) reduced-representation genome sequencing data from 186 accessions representing 65 species, 1 subspecies and 17 varieties of Rubus, with emphasis on diploid species, were used to infer a phylogeny using maximum likelihood and maximum parsimony methods. The major results were as follows: (1) we confirmed or reconfirmed the polyphyly or paraphyly of some traditionally circumscribed subgenera, sections and subsections; (2) 19 well-supported clades, which differed from one another on molecular, morphological and geographical grounds, were identified for the species sampled; (3) characteristics such as plants with dense bristles or not, leaves leathery or papyraceous, number of carpels, instead of inflorescences paniculate or not, aggregate fruits and leaves abaxially tomentose or not, may be of some use in classifying taxa whose drupelets are united into a thimble-shaped aggregate fruit that falls in its entirety from the dry receptacle; and (4) a preliminary classification scheme of diploid species of Rubus is proposed based on our results combined with those from previous phylogenetic analyses.