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One of the challenges when working with the genus Isoeetes is the scarcity of in-depth comparative analyses of its morphological characters. This paucity of analyses relates in part to the long-held conclusion that most of the characteristics associated with the traits of the genus aside from spore morphology, are too variable to be informative. As a result, our understanding of morphological variability among species of Isoeetes is underdeveloped. Recent workers have attempted to address this deficiency by examining the glossopodia of the ligule, a structure unique among living taxa to Isoeetes and its sister genus, Selaginella. The glossopodium is embedded in the adaxial surface of the microphyll, and has shown evidence of interspecific variability in the few studies in which it has been examined. However, these prior works were limited to qualitative comparisons. The present study compares 3D reconstructions of the glossopodia of three species, Isoeetes howellii, I. bolanderi and I. nuttallii, using morphometric analyses in addition to more traditional qualitative comparisons. MANOVA of measurements obtained from 3D reconstructions of the glossopodia show significant differences in size while elliptical Fourier analysis of these reconstructions demonstrates differences in shape among the species. These analyses provide a repeatable, statistical framework for future work on the glossopodium and potentially other traits in Isoeetes.

Strigolactones (SLs) are a class of plant hormones which regulate shoot branching and function as host recognition signals for symbionts and parasites in the rhizosphere. However, steps in SL biosynthesis after carlactone (CL) formation remain elusive. This study elucidated the common and diverse functions of MAX1 homologs which catalyze CL oxidation. We have reported previously that Arabidopsis MAX1 converts CL to carlactonoic acid (CLA), whereas a rice MAX1 homolog has been shown to catalyze the conversion of CL to 4-deoxyorobanchol (4DO). To determine which reaction is conserved in the plant kingdom, we investigated the enzymatic function of MAX1 homologs in Arabidopsis, rice, maize, tomato, poplar and Selaginella moellendorffii. The conversion of CL to CLA was found to be a common reaction catalyzed by MAX1 homologs, and MAX1s can be classified into three types: A1-type, converting CL to CLA; A2-type, converting CL to 4DO via CLA; and A3-type, converting CL to CLA and 4DO to orobanchol. CLA was detected in root exudates from poplar and Selaginella, but not ubiquitously in other plants examined in this study, suggesting its role as a species-specific signal in the rhizosphere. This study provides new insights into the roles of MAX1 in endogenous and rhizosphere signaling.

Lycophytes are a key group for understanding vascular plant evolution. Lycophyte plastomes are highly distinct, indicating a dynamic evolutionary history, but detailed evaluation is hindered by the limited availability of sequences. Eight diverse plastomes were sequenced to assess variation in structure and functional content across lycophytes. Lycopodiaceae plastomes have remained largely unchanged compared with the common ancestor of land plants, whereas plastome evolution in Isoetes and especially Selaginella is highly dynamic. Selaginella plastomes have the highest GC content and fewest genes and introns of any photosynthetic land plant. Uniquely, the canonical inverted repeat was converted into a direct repeat (DR) via large-scale inversion in some Selaginella species. Ancestral reconstruction identified additional putative transitions between an inverted and DR orientation in Selaginella and Isoetes plastomes. A DR orientation does not disrupt the activity of copy-dependent repair to suppress substitution rates within repeats. Lycophyte plastomes include the most archaic examples among vascular plants and the most reconfigured among land plants. These evolutionary trends correlate with the mitochondrial genome, suggesting shared underlying mechanisms. Copy-dependent repair for DR localized genes indicates that recombination and gene conversion are not inhibited by the DR orientation. Gene relocation in lycophyte plastomes occurs via overlapping inversions rather than transposase/recombinase-mediated processes.

Flavonoids ubiquitously distribute to the terrestrial plants and chalcone isomerase (CHI)-catalyzed intramolecular and stereospecific cyclization of chalcones is a committed step in the production of flavonoids. However, so far the bona fide CHIs are found only in vascular plants, and their origin and evolution remains elusive. We conducted transcriptomic and/or genomic sequence search, subsequent phylogenetic analysis, and detailed biochemical and genetic characterization to explore the potential existence of CHI proteins in the basal bryophyte liverwort species and the lycophyte Selaginella moellendorffii. We found that both liverwort and Selaginella species possess canonical CHI-fold proteins that cluster with their corresponding higher plant counterparts. Among them, some members exhibited bona fide CHI activity, which catalyze stereospecific cyclization of both 6′-hydroxychalcone and 6′-deoxychalcone, yielding corresponding 5-hydroxy and 5-deoxyflavanones, resembling the typical type II CHIs currently known to be ‘specific’ for legume plants. Expressing those primitive bona fide CHIs in the Arabidopsis chi mutant restores the seed coat transparent testa phenotype and the accumulation of flavonoids. These findings, in contrast to our current understanding of the evolution of enzymatic CHIs, suggest that emergence of the bona fide type II CHIs is an ancient evolution event that occurred before the divergence of liverwort lineages.

Abstract Selaginellaceae, originated in the Carboniferous and survived the Permian–Triassic mass extinction, is the largest family of lycophyte, which is sister to other tracheophytes. It stands out from tracheophytes by exhibiting extraordinary habitat diversity and lacking polyploidization. The organelle genome-based phylogenies confirmed the monophyly of Selaginella, with six or seven subgenera grouped into two superclades, but the phylogenetic positions of the enigmatic Selaginella sanguinolenta clade remained problematic. Here, we conducted a phylogenomic study on Selaginellaceae utilizing large-scale nuclear gene data from RNA-seq to elucidate the phylogeny and explore the causes of the phylogenetic incongruence of the S. sanguinolenta clade. Our phylogenetic analyses resolved three different positions of the S. sanguinolenta clade, which were supported by the sorted three nuclear gene sets, respectively. The results from the gene flow test, species network inference, and plastome-based phylogeny congruently suggested a probable hybrid origin of the S. sanguinolenta clade involving each common ancestor of the two superclades in Selaginellaceae. The hybrid hypothesis is corroborated by the evidence from rhizophore morphology and spore micromorphology. The chromosome observation and Ks distributions further suggested hybridization accompanied by polyploidization. Divergence time estimation based on independent datasets from nuclear gene sets and plastid genome data congruently inferred that allopolyploidization occurred in the Early Triassic. To our best knowledge, the allopolyploidization in the Mesozoic reported here represents the earliest record of tracheophytes. Our study revealed a unique triad of phylogenetic positions for a hybrid-originated group with comprehensive evidence and proposed a hypothesis for retaining both parental alleles through gene conversion.

The genus Selaginella resides in an early branch o f the land plant lineage that possesses a vasculature and roots. The majority of the Selaginella root system is shoot borne and emerges through a distinctive structure known as the rhizophore, the organ identity of which has been a long-debated question. The rhizophore of Selaginella moellendorffii - a model for the lycophytes - shows plasticity to develop into a root or shoot up until 8 d after angle meristem emergence, after which it is committed to root fate. We subsequently use morphology and plasticity to define the stage of rhizophore identity. Transcriptomic analysis of the rhizophore during its plastic stage reveals that, despite some resemblance to the root meristem, rhizophore gene expression patterns are largely distinct from both shoot and root meristems. Based on this transcriptomic analysis and on historical anatomical work, we conclude that the rhizophore is a distinct organ with unique features.

Nasopharyngeal carcinoma (NPC) presents significant treatment challenges due to its complex etiology and late-stage diagnosis. The traditional Chinese medicine Selaginella doederleinii Hieron ( S. doederleinii ) has shown potentiality in NPC treatment due to its multi-target, multi-pathway anti-cancer mechanisms. First, we identified NPC related target genes from databases like GeneCards, OMIM, and DisGeNET, and performed WGCNA analysis on the GSE53819 dataset to identify several important gene modules related to NPC. Active components and their targets in S. doederleinii were screened from the TCMSP and other databases, identifying 32 overlapping genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that these genes are primarily involved in critical biological processes like protein phosphorylation and cell cycle regulation. A protein–protein interaction network was constructed, and cytoHubba identified six key genes (BCL2, MAPK14, ABCB1, PLK1, ATM, HMOX1). Kaplan–Meier analysis and immune infiltration analysis further showed that these key genes are closely related to the prognosis and immune microenvironment of NPC patients. Single-cell RNA sequencing analysis revealed the expression distribution of key genes across different immune cell types and explored their roles in the differentiation process of malignant cells through pseudotime trajectory analysis. Molecular docking and dynamics simulation results indicated that the Berberine-MAPK14 and Matairesinol-PLK1 complexes have high binding affinity and stability. Binding free energy calculations confirmed the stability of these complexes. Based on our comprehensive multi-level analysis, the active components of S. doederleinii may play a significant role in the treatment of NPC through multi-pathway and multi-target synergistic effects.

The emergence of highly drug-resistant fungal strains is the major concern in health care sector. There is an urgent need to develop novel and potent antifungal drugs with minimal side effects to encounter invasive fungal infections. In this study, we have green-synthesized silver nanoparticles (AgNPs) by using leaf extract of Selaginella bryopteris and checked their antifungal activity against different Candida spp. The optimization of parameters involved in the synthesis of AgNPs includes pH, temperature, concentration of silver nitrate, reaction time. The synthesis of NPs was investigated by the UV–Vis spectrophotometric analysis. The physicochemical properties of AgNPs were further analysed by FESEM, TEM, DLS, zeta potential, FTIR and XRD studies. AgNPs were found to be spherical in shape with an average size of 35 nm and were monodispersed in nature without any agglomeration. The results of antifungal susceptibility testing (AFST) and growth curve kinetics revealed that AgNPs displayed significant anticandidal activity with MIC and MFC values of 0.003 and 0.006 ng/mL respectively. Treatment of Candida spp. with AgNPs leads to damage in fungal cell wall, cell membrane along with disruption of mitochondrial enzyme activity and release of nuclear content. The green-synthesized AgNPs not only caused damage and destruction to the morphology of Candida but also affected the ergosterol biosynthetic pathway. The green-synthesized AgNPs were also found to exhibit antibiofilm activity against Candida spp. which was assessed by crystal violet assay and SEM analysis confirming biofilm reduction by 80–82% as compared to control.

Selaginella doederleinii Hieron has been traditionally used as a folk antitumor herbal medicine in China. In this paper, the phytochemical components of the total biflavonoids extract from S. doederleinii were studied by using high-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry (HPLC-ESI-QTOF MS/MS) in negative ion mode, and their in vitro and in vivo anticancer effects were evaluated. Four types of biflavonoids from S. doederleinii, including IC3′–IIC8′′, IC3′–IIC6′′, IC3′–IIC3′′′, and C–O linked biflavonoids were examined originally using QTOF MS/MS. The fragmentation behavior of IC3′–IIC3′′′ linked biflavonoids was reported for the first time. A total of twenty biflavonoids were identified or tentatively characterized and eight biflavonoids were found from S. doederleinii for the first time. Furthermore, the 3-(4,5-Dimethyl-2-thizolyl)-2,5-diphenyltertazolium bromide (MTT) assay and xenograft model of mouse lewis lung cancer(LLC) in male C57BL/6 mice revealed favorable anticancer properties of the total biflavonoids extracts from S. doederleinii. The results of this work could provide useful knowledge for the identification of biflavonoids in herbal samples and further insights into the chemopreventive function of this plant.

Main conclusion The evolutionary conservation of type III polyketide synthases (PKS) in Selaginella has been elucidated, and the critical amino acid residues of the anther-specific chalcone synthase-like enzyme (SmASCL) have been identified. Selaginella species are the oldest known vascular plants and a valuable resource for the study of metabolic evolution in land plants. Polyketides, especially flavonoids and sporopollenin precursors, are essential prerequisites for plant land colonization. Although type III polyketide synthases (PKS) are widely studied in seed plants, the related enzymes in Selaginella remain poorly characterized. Here, eight type III PKSs were identified in the Selaginella moellendorffii genome and classified into three clusters . Two PKSs were selected for further research based on their phylogenetic relationships and protein sequence similarity. Functional studies revealed that they were chalcone synthase (SmCHS) and anther-specific CHS-like enzyme (SmASCL). These enzymes are involved in the biosynthesis of flavonoids and sporopollenin, respectively. Their sequence information and enzymatic activity are similar to the orthologs in other plants. Phylogenetic analysis revealed that the ASCL and CHS enzymes were separated into two clades from the Bryophyta. These results suggest that CHS and ASCL emerged in the first land plants and then remained conserved during plant evolution. To study the structural basis of the enzymatic function of SmASCL, a series of mutants were constructed. The number of condensation reactions catalyzed by the P210L/Y211D and I200V/G201T double mutants exceeds that of the wild-type enzyme. Our study provides insight into the characteristics and functions of type III PKSs in S. moellendorffii . It also offers clues for a deeper understanding of the relationship between active sites and the enzymatic function of ASCLs.