INTRODUCTION: Molecular data is one of the most important bases for many biological studies, including phylogeny, ecology, and biogeography etc. Incomplete sampling may lead to biased results and inadequate conclusions. However, few studies have evaluated current state of sampling density for sequencing DNA data comprehensively. Plastid DNA sequences have been applied in scientific studies of plants extensively due to their easy accessibility, uniparental inheritance, and moderate rate of mutation. Therefore, it is essential to investigate the current state of sampling density for sequencing plastid DNA data in species and geographic area for researchers to better utilize it.

RATIONALE: The GenBank is the biggest and most commonly used database of sequencing DNA data. The data gap of plastid DNA in species and geographic area for vascular plants was investigated based on the GenBank database in this study. Firstly, the plastid DNA data of vascular plant species were downloaded from the GenBank database and cleaned. Secondly, species names were standardized according to the World Checklist of Vascular Plants (WCVP) database. Thirdly, to evaluate the current state of sampling density for plastid DNA data of vascular plants, we counted the number of species with plastid DNA sequenced and the proportion of missing data of lineages representing orders and families. We also mapped the proportion of missing data in each region to evaluate the current state of sampling density of plastid DNA data geographically. To further investigate the potential influencing factors of the plastid DNA data gap, Spearman’s correlations between the proportion of missing data and species diversity among major groups of vascular plants or regions were calculated.

RESULTS: Only 33.75% vascular plant species have at least one record of DNA in GenBank, covering 139 005 vascular plant species (angiosperms: 131 220 species, gymnosperms: 1 154 species, and pteridophytes: 6 631 species). For data gap in species, sequenced species were unevenly sampled among lineages, with the proportion of missing data generally correlated with species richness within the lineages. The top three orders of the highest proportion of missing data were Paracryphiales, Piperales, and Dilleniales, and the top three families were Triuridaceae, Pentaphragmataceae, and Xyridaceae. For data gap in geographic area, the proportion of missing data of plastid DNA of vascular plant species showed a trend of latitudinal gradient, with the degree of missing data decreasing from the equator to the poles. Regions with high proportion of missing data usually possess high biodiversity, including many biodiversity hotspots. In addition, endemic species were generally with the high proportion of missing data in the majority of regions.

CONCLUSION:Our research evaluated the current state of sampling density for plastid DNA data in species and geographic area comprehensively. Our results suggested that about 140 000 vascular plant species have been sequenced for the plastid DNAs. However, there are still large data gaps for the plastid DNA of vascular plants in the following three aspects: (1) Only 1/3 vascular plant species have been sequenced; (2) Ratios of species with plastid DNA sequenced are uneven among lineages; (3) The proportion of missing data decreases from the equator to the poles, with more deficiencies in biodiversity hotspots and endemic species. Based on the results of this study, we propose to give priority to collection and sequencing of vascular plants for groups with high proportion of missing data and regions with high biodiversity, particularly for the endemic species. Our research points out the direction of filling plastid DNA data gap and will be beneficial to biodiversity protection.

INTRODUCTION: The cell wall-associated kinase (WAK) family has annotated approximately 130 WAK genes in the genome of rice (Oryza sativa), which play an important role in rice growth and development and stress responses.

RATIONALE: Here, we investigated the regulation and physiological mechanism of OsWAK16, an encoding gene of the cell wall-associated kinase WAK16-RLK, on rice seed vigor and anti-aging ability.

 
RESULTS: The results showed that before and after artificial aging, the seed vigor of OsWAK16 knock out mutants and overexpression lines was significantly lower and higher than that of wild-type seeds, respectively, indicating that OsWAK16 positively regulates the anti-aging ability of seeds. Physiological and biochemical analyses indicated that compared with wild-type seeds before and after artificial aging treatment, malondialdehyde (MDA) content and electrical conductivity (EC) of seed soaking solution of OsWAK16 knock out mutant seeds were significantly increased, while antioxidant enzyme activity was significantly decreased. The reverse was true in overexpression seeds. In addition, the differential expression of OsWAK16 in three types of seeds, whether artificially aged or not, also caused synergistic changes in the expression of other seed vigor-related genes OsPER1A, OsbZIP23, OsPIMT1, OsSdr4, OsMSRB5 and OsHSP18.2.

 
CONCLUSION: Therefore, it is speculated that OsWAK16 may work synergistically with other seed vigor-related genes to clear reactive oxygen species in cells, thereby regulating seed vigor and anti-aging capacity.

Tuber is a unique and extremely important organ of Cyperus esculentus, which is rich in oil and has the reproduction ability similar to seed. It is of great significance to study the specific expression genes in the tubers of C. esculentus for analyzing the regulation mechanism of tuber-specific growth and development (especially oil accumulation). Through transcriptome sequencing of the main organs (root, leaf, tillering node, stolon and tuber) of C. esculentus, the genes specifically expressed in tubers were comprehensively screened and the functions of related genes were analyzed. The results showed that a total of 155 tuber-specific expression genes were identified after multiple sets of comparative analysis by taking root, leaf, tillering node and stolon as reference, respectively. GO enrichment analysis showed that 7 GO terms including seed development, seed oilbody biogenesis, oil storage, abscisic acid response, response to abiotic stimulus and protein folding were significantly enriched, and some of the genes involved in these GO terms just reflected the unique development characteristics similar to seed of C. esculentus tubers. Among them, CESC_00080 and CESC_16572 encode caleosin, and meanwhile, CESC_08636, CESC_12549 and CESC_17828 encode oleosin, all of which are involved in the formation of plant oil bodies. Since oil body formation is a key step for plants to complete oil storage, it is indicated that the specific expression of these oil body formation-related genes in tubers may be the key to the storage of large amounts of oil in the tubers of C. esculentus. In addition, this study also screened eight tuber-specific expression transcription factor genes, such as CESC_00448 (abscisic acid insensitive 5-like protein ABI5) and CESC_03736 (heat stress transcription factor C), some of whose potential target genes were found in identified tuber-specific expression genes, indicating that these transcription factor genes may regulate the specific expression of their respective target genes. In summary, the results of this study can provide an important reference for the construction of gene regulatory networks related to tuber development of C. esculentus and the molecular mechanism analysis of tuber-specific gene expression.

ABF transcription factors are collectively referred to as basic leucine zipper proteins that can specifically recognize and bind to ABA-responsive elements (ABRE), participating in ABA signal transduction and serving as regulators of ABA signal transcriptional responses. This study analyzed the protein encoded by the BnaABF2 gene in Brassica napus. Subcellular localization results showed that the BnaABF2 protein is localized in the nucleus. Analysis of transcriptional activity in the yeast system indicated that BnaABF2 has no transcriptional activation activity; qRT-PCR detection revealed that the expression level of BnaABF2 is highest in leaves. We also found that ABA treatment, simulated drought, and salt stress can induce the expression of BnaABF2; BiFC results showed that BnaMPK1/2/6/7/9/12/13 can interact with BnaABF2. Dual-LUC results suggested that BnaMPK7 may enhance the transcriptional regulation of BnaABF2 on downstream target genes through phosphorylation. This study initially explored the basic characteristics and interacting proteins of the transcription factor BnaABF2, providing theoretical guidance for understanding its functions and mechanisms.

INTRODUCTION: The CPSF family (cleavage and polyadenylation specificity factor) is a crucial protein family that is responsible for polyadenylation signal recognition in mRNA precursors, cleavage and the addition of poly(A) tails to mRNAs in plants. This family plays crucial roles in the regulation of flowering time, the environmental response, and seed development. Currently, the function of the CPSF family genes in Brassica napus is unclear.

 
RATIONALE: To explore the function and expression patterns of the CPSF gene family, this study cloned BnaA02.CPSF6 from B. napus variety Zhongshuang No.11 and conducted bioinformatics analysis, subcellular localization, expression pattern, and functional characterization of the gene.

 
RESULTS: These results indicate that the coding region of the BnaA02.CPSF6 gene is 1 938 bp in length and encodes 646 amino acids without intron structures. Its promoter region contains multiple cis-acting elements involved in light responses and MYB binding sites. Additionally, there are six genes homologous to BnaA02.CPSF6 in B. napus. The BnaA02.CPSF6 gene expressed in the roots, stems, leaves, flowers and different developmental seeds of B. napus, especially significantly higher in 15-35 d developmental seeds, and its encoded protein was localized in the nucleus. The BnaA02.CPSF6 gene expression is upregulated under salt and drought stress. Under treatment with hormones such as ABA, IAA, GA₃, SA, and MeJA, the expression of BnaA02.CPSF6 gene is initially inhibited and then gradually recovers to normal levels. Under normal conditions, the overexpression of the BnaA02.CPSF6 gene in Arabidopsis thaliana results in an early bolting phenotype, along with a reduced number of rosette leaves.

CONCLUSION: In summary, the above results indicate that the BnaA02.CPSF6 is involved in abiotic stress responses, is regulated by phytohormones, and may also play a promoting role in flowering regulation.

A large number of software applications for plant identification based on plant images have been developed in recent years. However, those applications are mostly used for identifying the common species countrywide, and thus cannot meet the needs of identifying region-specific vegetation types. In this study, we developed an artificial intelligence model for identifying the dominant plants in Hulunbeier and Xilinhot grassland in Inner Mongolia, based on the image datasets in the Plant Photo Bank of China. The Top5 accuracy of this model reaches 94.6% in the actual field identification tests. Our model provides a new method for the intelligent identification of the major plant species in a specific area.

Cereal starch endosperm is the main source of human staple food, but the methods for observing its mature cell structure are not well developed. Micro CT technology, a non-destructive three-dimensional imaging technique, is a powerful tool for studying plant morphology. However, due to the uniform density of cereal starch endosperm, whose cell structures cannot be distinguished clearly by conventional micro CT techniques. In this study, we used phosphotungstic acid to treat ten different kinds of cereal seeds of seven crops, and then dried them by CO₂ critical point dryer. We found that the cell structure of the treated endosperms can be clearly displayed by micro CT. Our method provides a new way for studying the structures and functions of cereal starch endosperm cells.

Membrane microdomains, which are highly dynamic structures rich in sterols and sphingolipids on the plasma membrane, play crucial roles in various biological processes such as signal transduction, vesicle transport, endocytosis, and exocytosis. Consequently, the investigation of membrane microdomain dynamics is an important area of research in plant cell biology. Fluorescence probes combined with fluorescence microscopy are widely used to monitor the status of living plant cells. The PA probe (push-pull pyrene) is a novel, highly efficient and stable fluorescence probe based on pyrene: however, its application in imaging studies of living plant cells is limited. In this study, we used PA probes and laser scanning confocal microscopy, combined with image processing and the polar normalized value mapping method, to quantitatively analyze the order of the plasma membrane in Arabidopsis root cells. The results revealed that the emission spectrum of the liquid-ordered phase in the plasma membrane of Arabidopsis root cells labeled with the PA probe ranged from 500-550 nm, whereas the emission spectrum of the liquid-disordered phase ranged from 580-700 nm. Treatment of wild-type plants with the sterol extraction agent MβCD resulted in a decrease in plasma membrane order. In the smt2/smt3 double mutant lacking the key methyltransferase in sterol synthesis, the plasma membrane order was consistent with that of the wild-type plants after treatment with MβCD. In the smt2/smt3 mutant, the plasma membrane order of the root hair cells was lower than the plasma membrane order of the wild-type root hair cells, indicating that sterols, as key components of membrane microdomains, play an important role in regulating the order of the plasma membrane. This study provides a straightforward and rapid detection method for monitoring the dynamic characteristics of living plant cell membranes and changes in membrane microdomains.

Single-cell transcriptomics has improved the spatiotemporal resolution from multi-cell to single-cell levels, and notable progress in this technique has facilitated the identification of new rare cell types, exploration of intercellular heterogeneity, and mapping of cell developmental trajectories. Single-cell transcriptomics is currently being widely used in various research fields such as plant growth and development, stress response, and environmental adaptability, which helps to more thoroughly and precisely uncover the molecular regulatory mechanisms underlying plant life processes. However, there are numerous challenges associated with the study and analysis of different plant species. In this review, we compare and evaluate various single-cell transcription techniques and processes, summarize plant single-cell studies in recent years, and explore new single-cell analysis tools to support researchers studying plant biology with high precision and dynamics. In addition, we propose future directions in using single-cell transcriptomics technologies to address some of the key challenges in plant research and breeding. Furthermore, some important methods for addressing plant research and breeding with single-cell transcriptomics are discussed, along with their difficulties and potential applications.

Nicotinamide adenine dinucleotide (NAD⁺) and nicotinamide adenine dinucleotide phosphate (NADP⁺) act as an integral regulator of plant core energy metabolism, growth and development, and stress response, which can directly and indirectly influence many key cellular functions. As the cornerstone of cell metabolism, NAD(P)⁺ homeostasis is crucial for normal plant growth and development, and stress response. Impaired synthesis of NAD(P)⁺ or deficiency can trigger metabolic disorders and a series of defective phenotypes, and may even lead to plant death in severe cases. Currently, NAD(P)⁺ biosynthesis pathway and its key enzymes have been well studied in plants, but its homeostatic regulation in plants and the mechanism of coordinating plant growth and stress response are still unclear. Therefore, isolating NAD(P)⁺ deficiency-related mutants is crucial for exploring the regulatory mechanisms of NAD(P)⁺ homeostasis and its balancing in plant growth and stress response. This review summarizes the biosynthetic metabolic pathways of plant NAD(P)⁺, focuses on the participation of NAD(P)⁺ in plant growth and stress response processes, and looks into the future on the research prospects of NAD(P)⁺ in plants.

Rice (Oryza sativa) is a globally important cereal crop, and the rational application of fertilizers is necessary agricultural practice to ensure its sustainable and stable yield. Phosphorus is one of the essential nutrients for rice, primarily absorbed through the rice roots. Since rice is mostly grown in flooded conditions, the root surface of rice generally forms iron plaques rich in iron oxides, which play a crucial role in the migration of inorganic phosphorus in the rhizosphere of rice. This paper reviews the impact of biotic and abiotic factors on the formation of iron plaques in rice and discusses the effect of iron plaques on the absorption and transport of phosphorus in plant nutrition. Furthermore, we discuss the prospects of future research on iron plaques, aiming to provide clues for our further understanding of the interactions between iron and phosphorus in the rhizosphere of rice.