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Gagea kotuchovii (Liliaceae) a new narrow endemic species growing exclusively in the Karatau Mountains in South Kazakhstan, is here described and illustrated. It is a unique species within the section Gagea, differing from closely related taxa by the presence of several stolons of different lengths (0.5-8 cm), formed on a single vegetative individual, as well as a unique bulb with a densely woolly sheath. Morphological characteristics, distribution map, and illustrations of the habit and habitats of the new species are presented. We also present phylogenetic analyses based on the internal transcribed spacer (ITS) of nuclear DNA and SNPs obtained from DArT genome-wide sequencing (Diversity Arrays Technology sequencing), which confirmed the isolated position of G. kotuchovii but also revealed its phylogenetic relation with morphologically similar species. Additionally, our results reveal phylogenetic intergeneric organization of Gagea representatives occurring in Kazakhstan and/or Middle Asia. To facilitate morphological identification of Asian Gagea with stolons, and similar to G. kotuchovii, we present an identification key.

Key message Oxidative stress and apoptosis-like programmed cell death, induced in part by H 2 O 2 , are two key factors that damage cells during plant cryopreservation. Their inhibition can improve cell viability. We hypothesized that oxidative stress and apoptosis-like event induced by ROS seriously impact plant cell viability during cryopreservation. This study documented changes in cell morphology and ultrastructure, and detected dynamic changes in ROS components (O 2 ·− , H 2 O 2 and OH·), antioxidant systems, and programmed cell death (PCD) events during embryonic callus cryopreservation of Agapanthus praecox . Plasmolysis, organelle ultrastructure changes, and increases in malondialdehyde (a membrane lipid peroxidation product) suggested that oxidative damage and PCD events occurred at several early cryopreservation steps. PCD events including autophagy, apoptosis-like, and necrosis also occurred at later stages of cryopreservation, and most were apoptosis. H 2 O 2 is the most important ROS molecule mediating oxidative damage and affecting cell viability, and catalase and AsA–GSH cycle are involved in scavenging the intracellular H 2 O 2 and protecting the cells against stress damage in the whole process. Gene expression studies verified changes of antioxidant system and PCD-related genes at the main steps of the cryopreservation process that correlated with improved cell viability. Reducing oxidative stress or inhibition of apoptosis-like event by deactivating proteases improved cryopreserved cell viability from 49.14 to 86.85 % and 89.91 %, respectively. These results verify our model of ROS-induced oxidative stress and apoptosis-like event in plant cryopreservation. This study provided a novel insight into cell stress response mechanisms in cryopreservation.

Background  Cardiocrinum giganteum , belonging to genus Cardiocrinum of family Liliaceae, is a genus endemic to East Asia and is considered one of the more primitive groups within the Liliaceae family. C. giganteum is the largest one among all the lily species in plant and flower size, and possesses high ornamental, medicinal, and scientific research value. However, due to its long-term wild status, its value has not been fully exploited and utilized, especially regarding the mitochondrial genome, which is crucial for plant growth activities, there have been no relevant studies and reports so far. Results In this study, we sequenced and assembled the complete mitochondrial genome of C. giganteum and elucidated its evolutionary trajectory and phylogenetic relationships. The C. giganteum mitogenome has a multi-chromosomal structure containing 19 circular molecules. The assembled mitogenome has a total length of 2,066,679 bp and a GC content of 44.54%. A total of 37 unique protein-coding genes (PCGs), 16 tRNA, and three rRNA genes were annotated. Several repetitive sequences and sequence fragments homologous to chloroplasts have also been found in the C. giganteum mitogenome. To determine the evolutionary and taxonomic positions of C. giganteum , we constructed a phylogenetic tree using C. giganteum mitochondrial PCGs. Additionally, we analyzed the relatively synonymous codon usage of PCGs, identified RNA editing events, and conducted syntenic analysis with closely related species. Conclusions This study presents the first comprehensive mitochondrial genome (mtDNA) characterization of C. giganteum (Liliaceae), revealing its unique multi-chromosomal configuration. Our findings address the knowledge gap in mitochondrial research within the Cardiocrinum genus while enriching the mitochondrial genome database of Liliaceae. The assembled mtDNA provides critical insights into the phylogenetic relationships between Cardiocrinum and its allied genera, establishing essential genomic resources for evolutionary analyses, species identification, and genetic diversity studies across Liliaceae.

Abstract Background and Aims The role played by the Qinghai–Tibet Plateau (QTP) in the organismal diversification and biogeography of plants in the Northern Hemisphere has attracted much attention from evolutionary biologists. Here we use tribe Lilieae (Liliaceae), including primarily temperate and alpine lineages with disjunct distributions in the North Temperate Zone, as a case study to shed light upon these processes. Methods Using 191 taxa (five outgroup taxa) comprising more than 60 % of extant Lilieae species across the entire geographical range, we analyse phylogenetic relationships based on three plastid markers (matK, rbcL, rpl16) and nuclear ITS. Divergence time estimation and ancestral range reconstruction were further inferred. Key Results The results support a monophyletic Lilieae divided into four clades. Lilium is nested within Fritillaria, which is paraphyletic and partitioned into two clades, New World and Old World, in the chloroplast DNA (cpDNA) analysis. Incongruences between the ITS and cpDNA trees may be explained by divergent ITS paralogues and hybridization. Lilieae originated around 40–49 (28–67) Mya and probably diversified in the QTP region with four major clades that were established during the Oligocene and the Early Miocene. Uplift of the QTP and climatic changes probably drove early diversification of Lilieae in the QTP region. A rapid radiation occurred during the Late Miocene and the Pleistocene, coinciding temporally with recent orogenic process in the QTP region and climatic oscillations. Several lineages dispersed out of the QTP. Conclusions Lineage persistence and explosive radiation were important processes for establishing high species diversity of Lilieae in the QTP region. Both long-distance dispersal and migration across Beringia probably contributed to the modern distribution range of Lilieae. Our study shows that biotic interchanges between the QTP region and Irano-Turanian region and the Mediterranean Basin were bi-directional, suggesting the latter was a secondary centre of diversity.

Summary Amaryllidaceae alkaloids (AAs) are diverse bioactive metabolites with significant pharmaceutical potential, derived from 4′‐O‐methylnorbelladine (4′OM). The biosynthesis of these compounds involves the condensation of tyramine and 3,4‐dihydroxybenzaldehyde by norbelladine synthase (NBS) and/or noroxomaritidine/norcraugsodine reductase (NR), followed by O‐methylation. Cytochrome P450 enzymes, particularly the CYP96T family, introduce further structural diversity through C–C couplings, resulting in lycorine, galanthamine and crinine cores. Despite their importance, the exact biosynthetic pathways remain poorly defined. In this study, we describe key enzymes from Leucojum aestivum (La), providing crucial insight into AA biosynthesis. Transient expression in Nicotiana benthamiana demonstrated that LaNBS and LaNRII catalyse the conversion of tyramine and 3,4‐dihydroxybenzaldehyde to norbelladine, which is subsequently O‐methylated by a norbelladine‐4′‐O‐methyltransferase (LaN4′OMT) in planta. Co‐agroinfiltration of LaNBS, LaNRII, LaN4′OMT and LaCYP96T1 resulted in the production of various phenol‐coupled products, with lycorine as the predominant compound, alongside haemanthamine, crinine/vittatine and norgalanthamine. This study identifies LaCYP96T1 and LaCYP96T2 as the first monocot enzymes capable of catalysing all three regioselective C‐C phenol couplings and also highlights the substrate promiscuity of LaNRII. The findings not only elucidate critical steps in AA biosynthesis but also open new avenues for biotechnological application in producing valuable alkaloids, offering potential for novel drug development. Schematic representation of Amaryllidaceae alkaloid biosynthesis in Leucojum aestivum. Norbelladine synthase (LaNBS) and noroxomaritidine/norcraugsodine reductase (LaNRII) catalyze the condensation of tyramine and 3,4‐dihydroxybenzaldehyde to form norbelladine, which is subsequently O‐methylated by norbelladine‐4′‐O‐methyltransferase (LaN4′OMT). Cytochrome P450 enzymes LaCYP96T1 and LaCYP96T2 mediate C–C phenol couplings, leading to the formation of lycorine, haemanthamine, crinine/vittatine, and norgalanthamine. Transient expression in Nicotiana benthamiana confirms enzymatic activities and alkaloid production, providing new insights into Amaryllidaceae alkaloid biosynthesis and biotechnological applications.

Background and Aims The taxonomic arrangement within subfamily Ornithogaloideae (Hyacinthaceae) has been a matter of controversy in recent decades: several new taxonomic treatments have been proposed, based exclusively on plastid DNA sequences, and these have resulted in classifications which are to a great extent contradictory. Some authors have recognized only a single genus Ornithogalum for the whole subfamily, including 250–300 species of variable morphology, whereas others have recognized many genera. In the latter case, the genera are inevitably much smaller and they are better defined morphologically. However, some are not monophyletic as circumscribed. Methods Phylogenetic analyses of Ornithogaloideae were based on nucleotide sequences of four plastid regions (trnL intron, trnL-F spacer, rbcL and matK) and a nuclear region (ITS). Eighty species covering all relevant taxonomic groups previously recognized in the subfamily were sampled. Parsimony and Bayesian analyses were performed. The molecular data were compared with a matrix of 34 morphological characters. Key Results Combinations of plastid and nuclear data yielded phylogenetic trees which are better resolved than those obtained with any plastid region alone or plastid regions in combination. Three main clades are found, corresponding to the previously recognized tribes Albuceae, Dipcadieae and Ornithogaleae. In these, up to 19 clades are described which are definable by morphology and biogeography. These mostly correspond to previously described taxa, though some need recircumscription. Morphological characters are assessed for their diagnostic value for taxonomy in the subfamily. Conclusions On the basis of the phylogenetic analyses, 19 monophyletic genera are accepted within Ornithogaloideae: Albuca, Avonsera, Battandiera, Cathissa, Coilonox, Dipcadi, Eliokarmos, Elsiea, Ethesia, Galtonia, Honorius, Loncomelos, Melomphis, Neopatersonia, Nicipe, Ornithogalum, Pseudogaltonia, Stellarioides and Trimelopter. Each of these has a particular syndrome of morphological characters. As a result, 105 new combinations are made and two new names are proposed to accommodate the taxa studied in the new arrangement. A short morphological diagnosis, synonymy, details of distribution and an identification key are presented.

Aspilia africana (Pers.) C. D. Adams is a valuable medicinal plant, and the expanding therapeutic use of the plant due to explosion of human population is causing depletion of its wild population, thus requiring propagation. This study established an effective method for direct somatic embryogenesis in A. africana using leaf explants. We evaluated the effects of exogenous plant growth regulators (PGRs) and some molecules on induction, development, and maturation of somatic embryos. Murashige and Skoog (MS) medium supplemented with 1.0 mg/L benzylaminopurine (BAP) and 3.472 × 10 −2 mg/L adenosine 5-monophosphate (AMP) optimally induced direct somatic embryogenesis in A. africana leaf explants (100% response and 9.50 ± 0.29 somatic embryos per explant). Differentiation and maturation of somatic embryos was enhanced under osmotic stress induced by using 9 g/L gelrite in MS medium augmented with 0.5 mg/L abscisic acid (ABA) and 6.634 × 10 −2 mg/L nicotinamide adenine dinucleotide (NAD) (6.27 ± 0.36 globular, 3.40 ± 0.35 heart, 2.60 ± 0.51 torpedo, and 4.73 ± 0.41 cotyledonary). Half strength MS medium containing 0.5 mg/L gibberellin (GA) and 0.1 mg/L naphthaleneacetic acid (NAA) optimally supported germination (31 ± 1.73%) of cotyledonary somatic embryos. Pre-germination treatment of cold (stratification at 4 o C) further stimulated somatic embryo germination (60.00%) and their conversion into plantlets (26.67%). After five weeks of acclimatization, the survival rate of somatic embryo derived A. africana plants was 75.00%. Histological observations and flow cytometric analysis confirmed different somatic embryo stages and stability in genome size of regenerated plants, respectively. Moreover, chlorophyll contents and photosynthetic rates were similar between zygotic and somatic embryo derived plants. This method could be employed in mass clonal regeneration, conservation, synthetic seed production, cryopreservation, and genetic improvement of A. africana . Additionally, the system would provide suitable model for investigating molecular, biochemical, and physiological events, which occur at the induction and development of embryogenesis in A. africana .

Grape hyacinth (Muscari) is an important ornamental bulbous plant with an extraordinary blue colour. Muscari armeniacum, whose flowers can be naturally white, provides an opportunity to unravel the complex metabolic networks underlying certain biochemical traits, especially colour. A blue flower cDNA library of M. armeniacum and a white flower library of M. armeniacum f. album were used for transcriptome sequencing. A total of 89 926 uni-transcripts were isolated, 143 of which could be identified as putative homologues of colour-related genes in other species. Based on a comprehensive analysis relating colour compounds to gene expression profiles, the mechanism of colour biosynthesis was studied in M. armeniacum. Furthermore, a new hypothesis explaining the lack of colour phenotype of the grape hyacinth flower is proposed. Alteration of the substrate competition between flavonol synthase (FLS) and dihydroflavonol 4-reductase (DFR) may lead to elimination of blue pigmentation while the multishunt from the limited flux in the cyanidin (Cy) synthesis pathway seems to be the most likely reason for the colour change in the white flowers of M. armeniacum. Moreover, mass sequence data obtained by the deep sequencing of M. armeniacum and its white variant provided a platform for future function and molecular biological research on M. armeniacum.

Cellular protuberance formation in walled cells requires the local deformation of the wall and its polar expansion. In many cells, protuberance elongation proceeds by tip growth, a growth mechanism shared by pollen tubes, root hairs, and fungal hyphae. We established a biomechanical model of tip growth in walled cells using the finite element technique. We aimed to identify the requirements for spatial distribution of mechanical properties in the cell wall that would allow the generation of cellular shapes that agree with experimental observations. We based our structural model on the parameterized description of a tip-growing cell that allows the manipulation of cell size, shape, cell wall thickness, and local mechanical properties. The mechanical load was applied in the form of hydrostatic pressure. We used two validation methods to compare different simulations based on cellular shape and the displacement of surface markers. We compared the resulting optimal distribution of cell mechanical properties with the spatial distribution of biochemical cell wall components in pollen tubes and found remarkable agreement between the gradient in mechanical properties and the distribution of deesterified pectin. Use of the finite element method for the modeling of nonuniform growth events in walled cells opens future perspectives for its application to complex cellular morphogenesis in plants.

Background  Paris polyphylla Sm. is a precious medicinal plant rich in various active ingredients. In addition to the well-known saponins, the flavonoids it contains have unique pharmacological potential in antioxidant, neuroprotective, and metabolic regulation. However, the flavonoids in Paris polyphylla Sm. have not been fully researched and developed yet. In this work, we conducted a comprehensive metabolomics and transcriptomics analysis to reveal the metabolic differences and biosynthetic mechanisms of flavonoids in the leaves, stems, and roots of Paris polyphylla Sm. Results Non-targeted metabolomics analysis detected a total of 332 metabolites in Paris polyphylla Sm., among which flavonoids accounted for 19.49%. The diversity and abundance of flavonoids in leaves are the highest, followed by stems and roots. By comparing the metabolites of the roots, stems, and leaves in Paris polyphylla Sm., it was found that there were 45 differential metabolites (DMs) between the leaves and roots, of which flavonoids accounted for 35%. There are 38 DMs between leaves and stems, of which flavonoids account for 45.45%. And there are 52 DMs in stems and roots, among which flavonoids account for 25.53%. A total of 62,766 genes were detected by transcriptomics, and pairwise comparison showed that there were tens of thousands of differentially expressed genes (DEGs) between each group. Afterwards, we selected 39 flavonoids and related metabolites (e.g., kaempferol-3-O-glucoside, quercetin 3-β-D-glucoside, rutin) for targeted metabolomics validation and performed RT-qPCR validation on 29 key flavonoid synthesis genes (e.g., C4H, CHS, FLS, F3’H) to verify the reliability of non-targeted metabolomics and transcriptomics. Conclusions This work indicated that leaves are the main site for the biosynthesis of flavonoids in Paris polyphylla Sm. Among them, kaempferol-3-O-glucoside, quercetin 3-β-D-glucoside, rutin, and other flavonoids are present in higher contents in leaves ( P  < 0.05). Further research on its biosynthetic mechanism indicates that naringenin chalcone is converted to naringenin by chalcone isomerase (CHI). Among them, CHI may be the rate-limiting enzyme in the biosynthesis of flavonoids in Paris polyphylla Sm. The expression of FLS is higher in leaves ( P  < 0.05) and tends to promote the synthesis of flavonols. This work promotes the utilization of non-medicinal parts of Paris polyphylla Sm. and enhances the sustainable development of this precious traditional Chinese medicine resource.