The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology.

Adaptation to unfavorable abiotic stresses is one of the key processes in the evolution of plants. Calcium (Ca²⁺) signaling is characterized by the spatiotemporal pattern of Ca²⁺ distribution and the activities of multi-domain proteins in integrating environmental stimuli and cellular responses, which are crucial early events in abiotic stress responses in plants. However, a comprehensive summary and explanation for evolutionary and functional synergies in Ca²⁺ signaling remains elusive in green plants. We review mechanisms of Ca²⁺ membrane transporters and intracellular Ca²⁺ sensors with evolutionary imprinting and structural clues. These may provide molecular and bioinformatics insights for the functional analysis of some non-model species in the evolutionarily important green plant lineages. We summarize the chronological order, spatial location, and characteristics of Ca²⁺ functional proteins. Furthermore, we highlight the integral functions of calcium-signaling components in various nodes of the Ca²⁺ signaling pathway through conserved or variant evolutionary processes. These ultimately bridge the Ca²⁺ cascade reactions into regulatory networks, particularly in the hormonal signaling pathways. In summary, this review provides new perspectives towards a better understanding of the evolution, interaction and integration of Ca²⁺ signaling components in green plants, which is likely to benefit future research in agriculture, evolutionary biology, ecology and the environment.

The projected increase in drought severity and duration worldwide poses a significant threat to crop growth and sustainable food production. Xyloglucan endotransglucosylase/hydrolases (XTHs) family is essential in cell wall modification through the construction and restructuring of xyloglucan cross-links, but their role in drought tolerance and stomatal regulation is still illusive. We cloned and functionally characterized HvXTH1 using genetic, physiological, biochemical, transcriptomic and metabolomic approaches in barley. Evolutionary bioinformatics showed that orthologues of XTH1 was originated from Streptophyte algae (e.g. some species in the Zygnematales) the closest clade to land plants based on OneKP database. HvXTH1 is highly expressed in leaves and HvXTH1 is localized to the plasma membrane. Under drought conditions, silencing HvXTH1 in drought-tolerant Tibetan wild barley XZ5 induced a significant reduction in water loss rate and increase in biomass, however overexpressing HvXTH1 exhibited drought sensitivity with significantly less drought-responsive stomata, lower lignin content and a thicker cell wall. Transcriptome profile of the wild type Golden Promise and HvXTH1-OX demonstrated that drought-induced differentially expressed genes in leaves are related to cell wall biosynthesis, abscisic acid and stomatal signaling, and stress response. Furthermore, overexpressing HvXTH1 suppressed both genes and metabolites in the phenylpropanoid pathway for lignin biosynthesis, leading to drought sensitivity of HvXTH1-OX. We provide new insight by deciphering the function of a novel protein HvXTH1 for drought tolerance in cell wall modification, stomatal regulation, and phenylpropanoid pathway for lignin biosynthesis in barley. The function of HvXTH1 in drought response will be beneficial to develop crop varieties adapted to drought.

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease (Cas) system allows precise and easy editing of genes in many plant species. However, this system has not yet been applied to any fern species through gametophytes due to the complex characteristics of fern genomes, genetics, and physiology. Here, we established a protocol for gametophyte-based screening of single-guide RNAs (sgRNAs) with high efficiency for CRISPR/Cas9-mediated gene knockout in a model fern species, Ceratopteris richardii. We utilized the C. richardii ACTIN promoter to drive sgRNA expression and the enhanced CaMV 35S promoter to drive the expression of Streptococcus pyogenes Cas9 in this CRISPR-mediated editing system, which was employed to successfully edit a few genes, such as Nucleotidase/phosphatase 1 (CrSAL1) and Phytoene Desaturase (CrPDS), which resulted in an albino phenotype in C. richardii. Knockout of CrSAL1 resulted in significantly (P<0.05) reduced stomatal conductance (g_s), leaf transpiration rate (E), guard cell length, and abscisic acid (ABA)-induced reactive oxygen species (ROS) accumulation in guard cells. Moreover, CrSAL1 overexpressing plants showed significantly increased net photosynthetic rate (A), g_s, and E as well as most of the stomatal traits and ABA-induced ROS production in guard cells compared to the wild-type (WT) plants. Taken together, our optimized CRISPR/Cas9 system provides a useful tool for functional genomics in a model fern species, allowing the exploration of fern gene functions for evolutionary biology, herbal medicine discovery, and agricultural applications.

As a major agricultural country, China is also one of the world’s most abundant sources of crop straw, with production expected to reach 900 million tons by 2025. As an agricultural by-product, straw has been widely regarded as a potential renewable resource. It is rich in organic matter and essential nutrients such as nitrogen (N), phosphorus (P), and potassium (K), playing a critical role in global carbon and nitrogen cycles, agricultural productivity, and green environmental development. The efficient and rational utilization of straw can not only meet the resource demands supporting economic growth but also contribute to environmental protection and sustainable social development in China. By closely integrating comprehensive straw utilization with the annual key tasks of agriculture, rural areas, and farmers, the focus remains on prioritizing agricultural applications while adopting diversified measures. The efforts aim to improve straw utilization methods, strengthen technological support, explore replicable and sustainable industrial development models, and establish efficient utilization mechanisms to enhance the quality of agricultural straw use. To fully leverage the agricultural potential of straw, numerous technologies and equipment for straw utilization in agriculture have been developed in recent years, including straw harvesting and collecting equipment, straw crushing and returning-to-field equipment, full-straw seeding anti-clogging technology, combined straw and green manure returning-to-field equipment, and specialized straw seedling-raising equipment. Nevertheless, many challenges remain to be addressed, including bridging the equipment gap in mechanized processing, overcoming technical bottlenecks in resource conversion, and filling the lack of agronomy-adapted technologies. Therefore, this paper aims to provide a comprehensive and critical analysis of present straw utilization technology and equipment in agriculture, discussing their potential benefits, limitations, and challenges, as well as future prospects and directions. This study provides insights from the perspective of key technologies and equipment to strengthen technological research, enhance straw’s agricultural potential, and explore green circular economy models in agriculture. By leveraging innovation in science and technology, it aims to ensure food security and improve grain production capacity.

Copper (Cu) is an essential micronutrient for plants, playing a crucial role in various physiological and molecular processes. Excess Cu induces oxidative stress and disrupts cellular functions, while Cu deficiency causes chlorosis and poor pollen development, thereby reducing crop yields. However, the molecular and evolutionary mechanisms of Cu tolerance and homeostasis remain unclear in the plant kingdom. In this review, we discuss the uptake, transport, and detoxification of Cu through high-affinity Cu transporters (COPTs). Additionally, we update recent studies on maintaining Cu balance by mediating the root exudation of organic acids (e.g., citrate and proline), xylem/phloem loading, cell wall binding, vacuolar sequestration, redistribution, and the activity of antioxidant enzymes (e.g., SOD, CAT, and APX). Furthermore, tissue-specific expression analyses reveal that COPT genes exhibit distinct spatial regulation in the roots and leaves, which are the primary sites of Cu transport and detoxification. Overall, our review highlights the critical roles of COPT gene families and detoxification pathways in maintaining Cu homeostasis in plants. Future research should focus on genetic engineering approaches to enhance Cu tolerance, optimize Cu distribution in grains, and mitigate soil contamination risks. By clarifying these mechanisms, we can develop strategies to sustain crop production under increasing Cu stress, thereby ensuring food security and human health.