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PREMISE OF THE STUDY: This paper investigates the occurrence and evolution of aluminum (Al) accumulation within ferns and lycophytes, which is characterized by Al concentrations above 1000 mg·kg−1 in aboveground plant tissues. We hypothesize that this feature is more common in ferns than in angiosperms, and potentially correlated with growth form and other chemical elements. METHODS: Aluminum concentrations were obtained from novel analyses and literature for a total of 354 specimens and 307 species. Moreover, a semiquantitative aluminon test was applied for a subset of 105 species and validated against exact Al measurements. KEY RESULTS: Molecular phylogenetic analyses showed that the major Al‐accumulating groups were primarily found in the Gleicheniales and Cyatheales, and largely absent in the Polypodiales. At the species and generic level, Al accumulation was typically either absent or present, and mixed results within a single species and genus were limited to less than 30% of the species and genera tested. Epiphytic ferns had significantly lower Al levels than terrestrial ferns, although this finding was not significant after phylogenetic correction. In addition, a significant, positive correlation was found between Al and iron, while Al was negatively correlated with phosphorus and potassium concentrations. CONCLUSIONS: Aluminum accumulation is most common outside of the Polypodiales and occurs in 38% of the species studied, indicating that this trait is indeed common within subtropical and tropical ferns, a finding that could be in line with their role as pioneer species on landslides and soils with high levels of soluble Al.

Selaginellaceae is a family of nonseed plants with special evolutionary significance. Plants of the family Selaginellaceae are similarly shaped and easily confused, complicating identification via traditional methods. This study explored, for the first time, the use of the DNA barcode ITS2 to identify medicinal plants of the Selaginellaceae family. In our study, 103 samples were collected from the main distribution areas in China; these samples represented 34 species and contained almost all of the medicinal plants of Selaginellaceae. The ITS2 region of the genome was amplified from these samples and sequenced using universal primers and reaction conditions. The success rates of the PCR amplification and sequencing were 100%. There was significant divergence between the interspecific and intraspecific genetic distances of the ITS2 regions, while the presence of a barcoding gap was obvious. Using the BLAST1 and nearest distance methods, our results proved that the ITS2 regions could successfully identify the species of all Selaginellaceae samples examined. In addition, the secondary structures of ITS2 in the helical regions displayed clear differences in stem loop number, size, position, and screw angle among the medicinal plants of Selaginellaceae. Furthermore, cluster analysis using the ITS2 barcode supported the relationship between the species of Selaginellaceae established by traditional morphological methods. The ITS2 barcode can effectively identify medicinal plants of Selaginellaceae. The results provide a scientific basis for the precise identification of plants of the family Selaginellaceae and the reasonable development of these resources. This study may broaden the application of DNA barcoding in the medicinal plant field and benefit phylogenetic investigations.

The doubling of genomes does not cause increased plant speciation unless the progenitor lineages are highly fit. Polyploidy, the doubling of genomic content, is a widespread feature, especially among plants, yet its macroevolutionary impacts are contentious. Traditionally, polyploidy has been considered an evolutionary dead end, whereas recent genomic studies suggest that polyploidy has been a key driver of macroevolutionary success. We examined the consequences of polyploidy on the time scale of genera across a diverse set of vascular plants, encompassing hundreds of inferred polyploidization events. Likelihood-based analyses indicate that polyploids generally exhibit lower speciation rates and higher extinction rates than diploids, providing the first quantitative corroboration of the dead-end hypothesis. The increased speciation rates of diploids can, in part, be ascribed to their capacity to speciate via polyploidy. Only particularly fit lineages of polyploids may persist to enjoy longer-term evolutionary success.

Bin Han and colleagues performed low-coverage sequencing of 517 rice landraces and constructed a high-density haplotype map of the rice genome. They have used this resource to carry out genome-wide association studies for 14 agronomic traits and identify 80 loci with strong association signals. Uncovering the genetic basis of agronomic traits in crop landraces that have adapted to various agro-climatic conditions is important to world food security. Here we have identified ∼3.6 million SNPs by sequencing 517 rice landraces and constructed a high-density haplotype map of the rice genome using a novel data-imputation method. We performed genome-wide association studies (GWAS) for 14 agronomic traits in the population of Oryza sativa indica subspecies. The loci identified through GWAS explained ∼36% of the phenotypic variance, on average. The peak signals at six loci were tied closely to previously identified genes. This study provides a fundamental resource for rice genetics research and breeding, and demonstrates that an approach integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical biparental cross-mapping for dissecting complex traits in rice.

We report a high-quality draft genome sequence of the domesticated apple (Malus x domestica). We show that a relatively recent (> 50 million years ago) genome-wide duplication (GWD) has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae. Traces of older GWDs partly support the monophyly of the ancestral paleohexaploidy of eudicots. Phylogenetic reconstruction of Pyreae and the genus Malus, relative to major Rosaceae taxa, identified the progenitor of the cultivated apple as M. sieversii. Expansion of gene families reported to be involved in fruit development may explain formation of the pome, a Pyreae-specific false fruit that develops by proliferation of the basal part of the sepals, the receptacle. In apple, a subclade of MADS-box genes, normally involved in flower and fruit development, is expanded to include 15 members, as are other gene families involved in Rosaceae-specific metabolism, such as transport and assimilation of sorbitol.

Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

Pteridophytes have been studied and preserved in botanical gardens. However, only a few have discovered and documented the medicinal properties of Pteridophyta species. This study aims to promote the utilization of Pteridophyta species in Taman Cyathea, Bali, as traditional medicine agents by conducting a comprehensive literature review with a novelty of 15 years (2008-2022) on the ethnopharmacology and species diversity of the plant division. This research was conducted by directly exploring Pteridophyta species collected in Taman Cyathea, Bali, and a meta-synthesis was carried out related to the potential use of these species as traditional medicinal agents. The STARLITE principle was used for the article search, and ENTREQ was used for transparency in reporting meta-synthetic results. The study was conducted by searching the databases with keywords set according to the inclusion criteria. Findings in the field showed that there were as many as nine species of Pteridophyta identified as having benefits as traditional medicine agents, including Cyathea contaminans (Wall ex Hook) Copel., Asplenium nidus L., Asplenium sp., Selaginella sp., Diplazium esculentum, Angiopteris evecta (G.Forst.) Hoffm, Cyathea sp., Nephrolepis hirsutula (Forst) C. Presl and Dicksonia blumei (Kunze) Moore. The results of the meta-synthesis obtained 49 articles that met the study criteria; leaves, shoots, roots, stems, and hairs were used for various purposes, including restorative materials, planting media, crafts, game materials, and food ingredients. Pteridophyta species treat fever, cough, anticonvulsant, antibacterial, anti-inflammatory, antipyretic, antidiuretic, immunomodulatory, antioxidant, insecticide, larvicide, diabetes, and antiretroviral diseases, among others, so their potential use as traditional medicine agents and candidates for standardized herbs or phytopharmaceuticals have promising prospects in the future. However, its pharmacological, phytochemical, and toxicity properties must be investigated further.

Key Points Circadian rhythms in mammals are regulated by a master circadian pacemaker located in the hypothalamic suprachiasmatic nucleus (SCN), which coordinates rhythmic processes throughout the organism. Circadian clocks are cell autonomous and these cellular clocks are located in SCN neurons as well as in almost every cell in the body. The molecular mechanism of circadian clocks in mammals involves an autoregulatory transcriptional feedback loop involving the positive elements CLOCK and BMAL1, which transcriptionally activate the negative feedback elements period (PER) and cryptochrome (CRY), which inhibit their own transcription by repressing the CLOCK–BMAL1 complex. Post-translational regulation (for example, phosphorylation, acetylation and ubiquitylation) of clock proteins have important roles in regulating the stability, localization and turnover of clock components. The sleep disorder familial advanced sleep phase syndrome (FASPS) has been found to be caused by mutations in two core clock genes, period homologue 2 (PER2) and casein kinase 1 delta (CSNK1D), in humans. There is weak but emerging evidence for allelic variants in clock genes to be associated with diurnal preference, mood disorders, sleep and metabolic disorders. Peripheral circadian oscillators are controlled by signals arising from the SCN and from proximal signals related to feeding behaviour, hormonal signals and body-temperature fluctuations. In addition to their primary role in the generation of circadian rhythms, recent work has shown that circadian clock genes can affect a wide variety of other physiological processes. Emerging examples of circadian regulation of physiological pathways include diverse aspects of cellular metabolism, cell growth and DNA-damage control, xenobiotic responses, and the modulation of behavioural responses to drugs and alcohol. The knowledge that circadian clocks are cell autonomous and distributed throughout the body provide a new perspective to target central as well as peripheral circadian oscillators for therapeutic intervention. Many biological processes are regulated by circadian rhythms, which keep them in time with the Earth's 24-hour light–dark cycle. Elucidating the genetic control of circadian rhythms will help to understand the many diseases that can result when the clock goes wrong. Circadian cycles affect a variety of physiological processes, and disruptions of normal circadian biology therefore have the potential to influence a range of disease-related pathways. The genetic basis of circadian rhythms is well studied in model organisms and, more recently, studies of the genetic basis of circadian disorders has confirmed the conservation of key players in circadian biology from invertebrates to humans. In addition, important advances have been made in understanding how these molecules influence physiological functions in tissues throughout the body. Together, these studies set the scene for applying our knowledge of circadian biology to the understanding and treatment of a range of human diseases, including cancer and metabolic and behavioural disorders.

Mapping the methylome A newly developed method of characterizing an organism's 'methylome', that is the pattern of DNA methylation in the genome, has been used to generate a map of methylated cytosines in Arabidopsis to single base-pair resolution. The procedure, termed BS-Seq, combines bisulphite treatment of genomic DNA with ultra-high-throughput DNA sequencing to achieve a more precise and comprehensive result than previously possible. DNA methylation is an important factor in regulating gene expression, and this method, which can be applied to larger genomes like the mouse as well as to Arabidopsis , could prove a significant advance in the study of this form of gene regulation. In Arabidopsis , a map of methylated cytosines is generated at single base pair resolution by combining bisulphite treatment of genomic DNA with ultra-high-throughput sequencing. Cytosine DNA methylation is important in regulating gene expression and in silencing transposons and other repetitive sequences 1 , 2 . Recent genomic studies in Arabidopsis thaliana have revealed that many endogenous genes are methylated either within their promoters or within their transcribed regions, and that gene methylation is highly correlated with transcription levels 3 , 4 , 5 . However, plants have different types of methylation controlled by different genetic pathways, and detailed information on the methylation status of each cytosine in any given genome is lacking. To this end, we generated a map at single-base-pair resolution of methylated cytosines for Arabidopsis , by combining bisulphite treatment of genomic DNA with ultra-high-throughput sequencing using the Illumina 1G Genome Analyser and Solexa sequencing technology 6 . This approach, termed BS-Seq, unlike previous microarray-based methods, allows one to sensitively measure cytosine methylation on a genome-wide scale within specific sequence contexts. Here we describe methylation on previously inaccessible components of the genome and analyse the DNA methylation sequence composition and distribution. We also describe the effect of various DNA methylation mutants on genome-wide methylation patterns, and demonstrate that our newly developed library construction and computational methods can be applied to large genomes such as that of mouse.

The stomata of Equisetum - the sole extant representative of an ancient group of land plants - are unique with respect to both structure and development, yet little is known about details of ultrastructure and patterning, and existing accounts of key developmental stages are conflicting. We used light and electron microscopy to examine mature stomata and stomatal development in Equisetum myriochaetum, and compared them with other land plants, including another putative fern relative, Psilotum We reviewed published reports of stomatal development to provide a comprehensive discussion of stomata in more distantly related taxa. Stomatal development in Equisetum is basipetal and sequential in strict linear cell files, in contrast with Psilotum, in which stomatal development occurs acropetally. In Equisetum, cell asymmetry occurs in the axial stomatal cell file, resulting in a meristemoidal mother cell that subsequently undergoes two successive asymmetric mitoses. Each stomatal cell complex is formed from a single precursor meristemoid, and consists of four cells: two guard cells and two mesogene subsidiary cells. Late periclinal divisions occur in the developing intervening cells. In addition to the unique mature structure, several highly unusual developmental features include a well-defined series of asymmetric and symmetric mitoses in Equisetum, which differs markedly from Psilotum and other land plants. The results contribute to our understanding of the diverse patterns of stomatal development in land plants, including contrasting pathways to paracytic stomata. They add to a considerable catalogue of highly unusual traits of horsetails - one of the most evolutionarily isolated land-plant taxa.