The complete assembly of vast and complex plant genomes, like the hexaploid wheat genome, remains challenging. Here we present CS-IAAS, a comprehensive telomere-to-telomere (T2T) gap-free Triticum aestivum L. genome, encompassing 14.51 billion base pairs and featuring all 21 centromeres and 42 telomeres. Annotation revealed 90.8 Mb additional centromeric satellite arrays and 5,611 rDNA units. Genome-wide rearrangements, centromeric elements, transposable element expansion and segmental duplications were deciphered during tetraploidization and hexaploidization, providing a comprehensive understanding of wheat subgenome evolution. Among them, transposable element insertions during hexaploidization greatly influenced gene expression balances, thus increasing the genome plasticity of transcriptional levels. Additionally, we generated 163,329 full-length cDNA sequences and proteomic data that helped annotate 141,035 high-confidence protein-coding genes. The complete T2T reference genome (CS-IAAS), along with its transcriptome and proteome, represents a significant step in our understanding of wheat genome complexity and provides insights for future wheat research and breeding.

To decipher the genetic diversity within the cucurbit genus Citrullus, we generated telomere-to-telomere (T2T) assemblies of 27 distinct genotypes, encompassing all seven Citrullus species. This T2T super-pangenome has expanded the previously published reference genome, T2T-G42, by adding 399.2 Mb and 11,225 genes. Comparative analysis has unveiled gene variants and structural variations (SVs), shedding light on watermelon evolution and domestication processes that enhanced attributes such as bitterness and sugar content while compromising disease resistance. Multidisease-resistant loci from Citrullus amarus and Citrullus mucosospermus were successfully introduced into cultivated Citrullus lanatus. The SVs identified in C. lanatus have not only been inherited from cordophanus but also from C. mucosospermus, suggesting additional ancestors beyond cordophanus in the lineage of cultivated watermelon. Our investigation substantially improves the comprehension of watermelon genome diversity, furnishing comprehensive reference genomes for all Citrullus species. This advancement aids in the exploration and genetic enhancement of watermelon using its wild relatives.

Intron retention (IR) is the most common alternative splicing event in Arabidopsis. An increasing number of studies have demonstrated the major role of IR in gene expression regulation. The impacts of IR on plant growth and development and response to environments remain underexplored. Here, we found that IR functions directly in gene expression regulation on a genome-wide scale through the detainment of intron-retained transcripts (IRTs) in the nucleus. Nuclear-retained IRTs can be kept away from translation through this mechanism. COP1-dependent light modulation of the IRTs of light signaling genes, such as PIF4, RVE1, and ABA3, contribute to seedling morphological development in response to changing light conditions. Furthermore, light-induced IR changes are under the control of the spliceosome, and in part through COP1-dependent ubiquitination and degradation of DCS1, a plant-specific spliceosomal component. Our data suggest that light regulates the activity of the spliceosome and the consequent IRT nucleus detainment to modulate photomorphogenesis through COP1.

Soil salinization and alkalization disrupt redox homeostasis, impairing plant survival and crop production. Disruption of redox homeostasis can cause accumulation of reactive nitrogen species, such as nitric oxide (NO), which causes nitrosative damage in which the properties of biomacromolecules are altered. It is unclear whether melatonin regulates NO homeostasis, thereby affecting plant saline-alkali tolerance. In tomato (Solanum lycopersicum), excess NO caused by saline-alkali stress resulted in nitrosative damage, which was alleviated by S-nitrosoglutathione reductase (GSNOR). Moreover, saline-alkali stress-triggered NO stimulated caffeic acid O-methyltransferase (COMT) transcription and melatonin biosynthesis to scavenge excess NO and alleviate nitrosative damage at the proteome level. Under saline-alkali stress, plasma membrane-localized H+-ATPase 2 (HA2) was S-nitrosylated at Cys206, impairing its interaction with 14-3-3 protein 1 (TFT1). HA2 S-nitrosylation resulted in reduced HA activity, H+ efflux, and saline-alkali tolerance. Conversely, COMT-generated melatonin alleviated HA2 S-nitrosylation, recovering its function and tomato saline-alkali tolerance. Therefore, we propose that melatonin and NO are redox switches of HA2 S-nitrosylation for saline-alkali tolerance. Under natural saline-alkali conditions, tomato productivity was improved by grafting with COMT-, GSNOR-, or HA2-overexpression rootstocks, or by generating nonnitrosylated HA2C206S mutants. By establishing the melatonin–NO–HA2 module, this study illuminates a molecular function of melatonin and suggests possible genetic engineering strategies to improve agriculture.

Differential concentrations of phytohormone trigger distinct outputs, which provides a mechanism for the plasticity of plant development and an adaptation strategy among plants to changing environments. However, the underlying mechanisms of the differential responses remain unclear. Here we report that a high concentration of auxin, distinct from the effect of low auxin concentration, enhances abscisic acid (ABA) responses in Arabidopsis thaliana, which partially relies on TRANS-MEMBERANE KINASE 1 (TMK1), a key regulator in auxin signaling. We show that high auxin and TMK1 play essential and positive roles in ABA signaling through regulating ABA INSENSITIVE 1 and 2 (ABI1/2), two negative regulators of the ABA pathway. TMK1 inhibits the phosphatase activity of ABI2 by direct phosphorylation of threonine 321 (T321), a conserved phosphorylation site in ABI2 proteins, whose phosphorylation status is important for both auxin and ABA responses. This TMK1-dependent auxin signaling in the regulation of ABA responses provides a possible mechanism underlying the high auxin responses in plants and an alternative mechanism involved in the coordination between auxin and ABA signaling. Significance The complex and diverse functions of the phytohormone auxin rely on its concentration. A high concentration of auxin has distinct effects on plant development and environmental adaptation in comparison with a low level of auxin. In this study, we show that a high concentration of auxin is capable of stimulating ABA responses partially through a TMK1-based mechanism. This involves the phosphorylation of ABI1/2, two negative regulators of ABA signaling, and following the activation of downstream ABA responses. Our work reveals the interplay between the phytohormone auxin and ABA, and provides a basis for interpreting differential phytohormone responses during plant development.