Hongyan Wang

Soil salinization is a critical environmental challenge threatening plant survival. To adapt, certain plants have evolved tolerance to highly saline-alkali environments through long-term natural selection. Tamarix chinensis L., a typical halophyte with strong adaptability to salt and alkali stresses, serves as an essential germplasm resource and pioneer species for ecological conservation and remediation. However, the epigenetic mechanisms underlying its stress tolerance remain poorly understood. In this study, we systematically characterized the tolerance and genome-wide DNA methylation variations in T. chinensis under diverse salt and alkali stresses conditions. Phenotypic observations manifested severe leaf damage under 150 mM alkali stress over 10 days, whereas only slight injury occurred under 400 mM salt stress, indicating superior tolerance to salinity over alkalinity. MSAP analysis revealed that salt stress predominantly triggered genome-wide demethylation; conversely, alkali stress primarily induced hypermethylation, with both variations occurring mainly at CNG sites. Notably, DNA methylation alterations were more extensive under salt stress. Sequencing of methylation-variant bands yielded 17 stress-related sequences, eight of which are homologous to known stress-responsive genes. These findings provide a theoretical framework for dissecting differential epigenetic responses to salt and alkali stresses, facilitate the mining of resistance genes, and offer epigenetic references for the molecular breeding of T. chinensis to and ecological remediation of saline-alkaline lands.

Transposable elements (TEs) are major components of plant genomes and play crucial roles in adaptive genome evolution and stress tolerance. Under abiotic stress, activated TEs can generate abundant genetic variation and regulate the expression of stress-responsive genes. As a pioneer species in desert and saline–alkali environments, Tamarix chinensis L. has been little studied with respect to the abundance and evolutionary relationships of its LTR retrotransposons, particularly their activation patterns under salt and alkali stresses. This study aimed to investigate the characteristics of the reverse transcriptase (RT) domain of LTR retrotransposons in T. chinensis and to determine their patterns of activation in response to salt and alkali stresses. A total of 629 Ty1-copia and 607 Ty3-gypsy RT nucleotide sequences, which displayed high AT/GC ratios and evidence of stop codon insertions, were identified in T. chinensis by amplicon sequencing. Among these, 211 Ty1-copia and 117 Ty3-gypsy RT sequences with potential transpositional activity each contained distinct domains, suggesting a high degree of conservation. Phylogenetic analysis revealed that the RT sequences of T. chinensis are closely related to those of mangrove, wild potato, and Ipomoea, and may have undergone horizontal transfer. Expression analysis showed that 634 and 181 RT sequences were activated under salt and alkali stresses, respectively, with the majority belonging to salt-induced Ty1-copia families. Compared with the control group, under salt and alkali stresses, the cTy1-copia elements (Ty1-copia with amplificated from cDNA of T. chinensis, the same below) with dominant abundance were mainly concentrated in the Angela subfamily, while the cTy3-gypsy elements induced by alkali stress were primarily distributed in the Tekay and Reina subfamilies. Furthermore, four cTy1-copia and five cTy3-gypsy were identified as candidate key LTR retrotransposons responsive to salt and alkali stresses. Overall, this study provides new insights into the epigenetic mechanisms underlying the adaptation of T. chinensis to saline and alkali stresses and offers a theoretical basis for its potential applications in saline–alkali land reclamation.

Background: The BBR-BPC gene family is a relatively conservative group of transcription factors, playing a key role in plant morphogenesis, organ development, and responses to abiotic stress. Brassica napus L. (B. napus), commonly known as oilseed rape, is an allopolyploid plant formed by the hybridization and polyploidization of Brassica rapa L. (B. rapa) and Brassica oleracea L. (B. oleracea), and is one of the most important oil crops. However, little is known about the characteristics, conservation, and expression patterns of this gene family in B. napus, especially under abiotic stress. Methods: To explore the characteristics and potential biological roles of the BBR-BPC gene family members in B. napus, we conducted identification based on bioinformatics and comparative genomics methods. We further analyzed the expression patterns through RNA-seq and qRT-PCR. Results: We identified 25 BBR-BPC members, which were classified into three subfamilies based on phylogenetic analysis, and found them to be highly conserved in both monocots and dicots. The conserved motifs revealed that most members contained Motif 1, Motif 2, Motif 4, and Motif 8. After whole-genome duplication (WGD), collinearity analysis showed that BBR-BPC genes underwent significant purifying selection. The promoters of most BBR-BPC genes contained cis-acting elements related to light response, hormone induction, and stress response. RNA-seq and qRT-PCR further indicated that BnBBR-BPC7, BnBBR-BPC15, BnBBR-BPC20, and BnBBR-BPC25 might be key members of this family. Conclusions: This study provides a theoretical foundation for understanding the potential biological functions and roles of the BBR-BPC gene family, laying the groundwork for resistance breeding in B. napus.

Elevated near-surface ozone (O₃) concentrations have surpassed the tolerance limits of plants, significantly impacting crop growth and yield. To mitigate ozone pollution, plants must evolve a rapid and effective defense mechanism to alleviate ozone-induced damage. DNA methylation, as one of the most crucial epigenetic modifications, plays a pivotal role in maintaining gene stability, regulating gene expression, and enhancing plant resilience to environmental stressors. However, the epigenetic response of plants to O₃ stress, particularly DNA methylation variations and their intergenerational transmission, remains poorly understood. This study aims to explore the epigenetic mechanisms underlying plant responses to ozone stress across generations and to identify potential epigenetic modification sites or genes crucial in response to ozone stress. Using Open Top Chambers (OTCs), we simulated ozone conditions and subjected foxtail millet to continuous ozone stress at 200 nmol mol^-1 for two consecutive generations (S0 and S1). Results revealed that under high-concentration ozone stress, foxtail millet leaves exhibited symptoms ranging from yellowing and curling to desiccation, but the damage in the S1 generation was not more severe than that in the S0 generation. Methylation Sensitive Amplified Polymorphism (MSAP) analysis of the two generations indicated that ozone stress-induced methylation variations ranging from 10.82% to 13.59%, with demethylation events ranged from 0.52% to 5.58%, while hypermethylation occurred between 0.35% and 2.76%. Reproductive growth stages were more sensitive to ozone than vegetative stages. Notably, the S1 generation exhibited widespread demethylation variations, primarily at CNG sites, compared to S0 under similar stress conditions. The inheritance pattern between S0 and S1 generations was mainly of the A-A-B-A type. By recovering and sequencing methylation variant bands, we identified six stress-related differential amplification sequences, implicating these variants in various biological processes. These findings underscore the potential significance of DNA methylation variations as a critical mechanism in plants’ response to ozone stress, providing theoretical insights and references for a comprehensive understanding of plant adaptation mechanisms to ozone stress and the epigenetic role of DNA methylation in abiotic stress regulation.

The plant kingdom harbors the Plasmodesmata Callose Binding Protein (PDCB) gene family, which plays essential roles in plant growth, development, environmental adaptation, and yield. PDCB genes are closely involved in regulating cell-to-cell communication and controlling callose deposition at plasmodesmata (PD) throughout the whole plant. Remarkably, their functions remain largely unknown in many crops, including maize. This study sought to identify the members of the PDCB gene family within the maize genome and analyze their physicochemical properties and expression patterns. Utilizing bioinformatics methodologies, a comprehensive genome-wide analysis of the PDCB gene family was performed. The findings revealed that PDCB genes were highly abundant in maize, with a total of 56 PDCB genes identified and categorized into six distinct groups. Members of the PDCB family were dispersed across all chromosomes. The PDCBs within each group exhibited significant similarity in their conserved motifs and gene structures; all members contained the X8 domain, comprising one to five exons, while displaying a straightforward genomic structure. Numerous cis-acting elements associated with plant growth and development, light response, stress-associated responses, and plant hormones were identified in the promoter regions of PDCB genes. Moreover, the PDCBs exhibited diverse expression patterns across various tissues. This study improves the comprehension of the PDCB gene family and provides a robust foundation for further research on maize.

Whirly transcription factors are unique to plants, playing pivotal roles in managing leaf senescence and DNA repair. While present in various species, their identification in Brassica napus L. (B. napus) and their differences during hybridization and polyploidy has been elusive. Addressing this, our study delves into the functional and evolutionary aspects of the Whirly gene family during the emergence of B. napus, applying bioinformatics and comparative genomics. We identified six Whirly genes in B. napus. In Brassica rapa L. (B. rapa), three Whirly genes were identified, while four were found in Brassica oleracea L. (B. oleracea). The results show that the identified Whirly genes not only have homology but also share the same chromosomal positions. Phylogenetic analysis indicates that Whirly genes in monocots and dicots exhibit high conservation. In the evolutionary process, the Whirly gene family in B. napus experienced events of intron/exon loss. Collinearity insights point to intense purifying selection post-duplication. Promoter regions housed diverse cis-acting elements linked to photoresponse, anaerobic initiation, and methyl jasmonate responsiveness. Notably, elements tied to abscisic acid signaling and meristem expression were prominent in diploid ancestors but subdued in tetraploid B. napus. Tissue-specific expression unveiled analogous patterns within subfamily genes. Subsequent qRT-PCR analysis spotlighted BnAWHY1b’s potential significance in abiotic stress response, particularly drought. These findings can be used as theoretical foundations to understand the functions and effects of the Whirly gene family in B. napus, providing references for the molecular mechanism of gene evolution between this species and its diploid ancestors.

The EIN3/EIL gene family holds a pivotal role as it encodes a crucial transcription factor in plants. During the process of polyploidization in broomcorn millet (Panicum miliaceum L.), there is an intriguing above-average amplification observed within the EIN3/EIL gene family. Nonetheless, our current knowledge of this gene family in broomcorn millet remains limited. Hence, in this study, we conducted a comprehensive analysis of the EIN3/EIL gene family in broomcorn millet, aiming to provide a deeper understanding of the potential evolutionary changes. Additionally, we analyzed the EIN3/EIL gene family of Panicum hallii L., a close relative of broomcorn millet, to enhance our characterization efforts. Within this study, we identified a total of 15 EIN3/EIL genes specific to broomcorn millet. Through covariance analysis, it was revealed that all PmEIL genes, except PmEIL1 and PmEIL15, had duplicate copies generated through genome-wide duplication events. Importantly, the Ka/Ks values of all duplicated genes were found to be less than 1, indicating strong purifying selection. Phylogenetic analysis showed that these genes could be categorized into four distinct evolutionary branches, showcasing similar characteristics among members within the same branch. However, there appeared to be an uneven distribution of cis-acting elements amid the EIN3/EIL genes. Further examination of transcriptomic data shed light on the diverse spatiotemporal and stress-related expression patterns exhibited by the EIN3/EIL genes in broomcorn millet. Notably, under cold stress, the expression of PmEIL3/4/8/14 was significantly up-regulated, while under drought stress, PmEIL4/5/6 displayed significant up-regulation. Intriguingly, the expression pattern of PmEIL15 showed an opposite pattern in resistant and sensitive cultivars. The findings of this study augment our understanding of the EIN3/EIL gene family in broomcorn millet and offer a valuable reference for future investigations into polyploid studies. Moreover, this study establishes a theoretical foundation for further exploration of the ethylene signaling pathway in broomcorn millet.

Low temperature significantly inhibits the plant growth in wheat (Triticum aestivum L.), prompting the exploration of effective strategies to mitigate low temperature stress. Several priming methods enhance low temperature stress tolerant, however, the role of ozone priming remains unclear in wheat. Here we found ozone priming alleviated low temperature stress in wheat. Transcriptome analysis showed that ozone priming positively modulated ‘photosynthesis-antenna proteins’ pathway in wheat under low temperature. Which was confirmed by the results of the ozone-primed plants had higher trapped energy flux and electron transport flux per reaction, and less damage to chloroplasts than non-primed plants under low temperature. Ozone priming also mitigated the overstimulation of glutathione metabolism and induced the accumulation of total ascorbic acid and glutathione, maintained redox homeostasis in wheat under low temperature. Moreover, gene expressions and enzyme activities in glycolysis pathways were upregulated in ozone priming comparing with non-priming after the low temperature stress. Furthermore, exogenous antibiotics significantly increased low temperature tolerance, which further proved that the inhibition of ribosome biogenesis by ozone priming was involved in low temperature tolerance in wheat. In conclusion, ozone priming enhanced wheat low temperature tolerance through promoting light-harvesting capacity, redox homeostasis, and carbohydrate metabolism, as well as inhibiting ribosome biogenesis.

The NDPK gene family is an important group of genes in plants, playing a crucial role in regulating energy metabolism, growth, and differentiation, cell signal transduction, and response to abiotic stress. However, our understanding of the NDPK gene family in Brassica napus L. remains limited. This paper systematically analyzes the NDPK gene family in B. napus, particularly focusing on the evolutionary differences within the species. In this study, sixteen, nine, and eight NDPK genes were identified in B. napus and its diploid ancestors, respectively. These genes are not only homologous but also highly similar in their chromosomal locations. Phylogenetic analysis showed that the identified NDPK proteins were divided into four clades, each containing unique motif sequences, with most NDPKs experiencing a loss of introns/exons during evolution. Collinearity analysis revealed that the NDPK genes underwent whole-genome duplication (WGD) events, resulting in duplicate copies, and most of these duplicate genes were subjected to purifying selection. Cis-acting element analysis identified in the promoters of most NDPK genes elements related to a light response, methyl jasmonate response, and abscisic acid response, especially with an increased number of abscisic acid response elements in B. napus. RNA-Seq results indicated that NDPK genes in B. napus exhibited different expression patterns across various tissues. Further analysis through qRT-PCR revealed that BnNDPK genes responded significantly to stress conditions such as salt, drought, and methyl jasmonate. This study enhances our understanding of the NDPK gene family in B. napus, providing a preliminary theoretical basis for the functional study of NDPK genes and offering some references for further revealing the phenomenon of polyploidization in plants.

Organelle-derived nuclear DNAs, nuclear plastid DNAs (NUPTs), and nuclear mitochondrial DNAs (NUMTs) have been identified in plants. Most, if not all, genes residing in NUPTs/NUMTs (NUPGs/NUMGs) are known to be inactivated and pseudogenized. However, the role of epigenetic control in silencing NUPGs/NUMGs and the dynamic evolution of NUPTs/NUMTs with respect to organismal phylogeny remain barely explored. Based on the available nuclear and organellar genomic resources of wheat (genus Triticum) and goat grass (genus Aegilops) within Triticum/Aegilops complex species, we investigated the evolutionary fates of NUPTs/NUMTs in terms of their epigenetic silencing and their dynamic occurrence rates in the nuclear diploid genomes and allopolyploid subgenomes. NUPTs and NUMTs possessed similar genomic atlas, including (i) predominantly located in intergenic regions and preferential integration to gene regulation regions and (ii) generating sequence variations in the nuclear genome. Unlike nuclear indigenous genes, the alien NUPGs/NUMGs were associated with repressive epigenetic signals, namely high levels of DNA methylation and low levels of active histone modifications. Phylogenomic analyses suggested that the species-specific and gradual accumulation of NUPTs/NUMTs accompanied the speciation processes. Moreover, based on further pan-genomic analyses, we found significant subgenomic asymmetry in the NUPT/NUMT occurrence, which accumulated during allopolyploid wheat evolution. Our findings provide insight into the dynamic evolutionary fates of organelle-derived nuclear DNA in plants.