AbstractBanana fruits ripening at or above 30 °C soften but retain a green peel. Elucidating the mechanism underlying this high temperature-induced repression of chlorophyll catabolism would help to improve the marketability of bananas. Toward this end, we compared banana fruits ripened at 20 °C and 30 °C using transcriptome analysis, revealing several E3 ubiquitin ligases repressed in green fruits ripened at 30 °C. Among them, only the U-box type E3 ligase MaPUB23 promoted chlorophyll degradation when transiently overexpressed in tobacco leaves. MaPUB23 interacted with and targeted MaHSFB1 and MaHDA2 for ubiquitination and proteasomal degradation. MaHSFB1 specifically interacted with and recruited MaHDA2 to the promoters of chlorophyll catabolic genes (CCGs), transcriptionally repressed these genes via decreased histone acetylation, and inhibited chlorophyll degradation. However, high temperature attenuated the MaPUB23-mediated degradation of MaHSFB1 and MaHDA2, which enhanced the MaHSFB1–MaHDA2-mediated repression of CCGs. These results suggest that high temperature attenuates the MaPUB23-mediated proteasomal degradation of MaHSFB1–MaHDA2, leading to green ripening in banana fruit. This study thus illustrates a novel, dynamic regulatory module controlling the high temperature-induced repression of chlorophyll catabolism in banana fruits. Elucidating this mechanism provides a theoretical basis for strategies to manage temperature-induced fruit quality deterioration.Read more

AbstractBiomolecular condensates formed by transcription factors (TFs) via liquid-liquid phase separation enable precise spatiotemporal control of eukaryotic gene expression. Although phosphorylation is a well-established regulator of TF activity, its capacity to remodel condensate organization and transcriptional function in plant immunity remains largely undefined. Here, we report that pathogen-induced phosphorylation converts a pre-existing TF condensate into a dynamic transcriptional hub to enhance the immune response in potato. Upon infection by the oomycete pathogen Phytophthora infestans, the mitogen-activated protein kinase StMPK9 phosphorylates the TF StbZIP18 at the conserved residue threonine 337. This modification triggers rapid changes in the nuclear StbZIP18 condensates, transforming pre-existing condensates into numerous smaller assemblies. The phospho-null StbZIP18T337A mutant maintains its presence in low-activity condensates and compromises immunity, whereas the phospho-mimetic variant StbZIP18T337E constitutively forms active condensates and enhances resistance. The gene encoding the TF StMYB44 was identified as the direct downstream gene target of StbZIP18. TurboID-based proximity labeling revealed that both wild-type StbZIP18 and StbZIP18T337E, but not the phospho-null variant StbZIP18T337A, selectively interact with the transcriptional cofactor StMBF1c to form transcriptional activation hubs that drive defense gene expression, including StMYB44. Together, our findings establish that phosphorylation-directed condensate reprogramming operates as a tunable phase-separation switch, converting a low-activity assembly into a transcriptional amplifier. This study unveils a biophysical mechanism for signal amplification in plant immunity and provides insight into how post-translational modifications modulate transcriptional condensate function.Read more

AbstractAchieving complete, gap-free genome assemblies remains a central challenge in genomics, particularly for repeat-rich plant genomes. Although several telomere-to-telomere (T2T) assemblies have been reported for soybean, highly repetitive genomic regions and the mitochondrial genome remain insufficiently resolved. Here, we assembled gap-free T2T nuclear genomes together with complete mitochondrial and chloroplast genomes for the wild soybean (Glycine soja) SoyW02 and the cultivated soybean (Glycine max) Zhonghuang 13. These assemblies substantially improved the resolution of repetitive genomic regions and enabled biological insights that were previously inaccessible. Comparative analyses uncovered a conserved subtelomeric exchange hub and refined the landscape of soybean satellite repeats, including pericentromere-enriched and chromosome-specific satellites. We further developed a de novo pipeline for identifying tandem duplication gene clusters, enabling systematic analyses of transcriptional and protein sequence divergence, and experimentally demonstrating expression and functional diversification between two duplicated oxidosqualene cyclases. Together, these assemblies establish a foundation for investigating the evolution and functional organization of repetitive genomic regions and will facilitate future soybean functional genomics and molecular breeding.Read more

AbstractGenetic alleles derived from wild resources are of great importance for crop breeding and improvement; however, connecting the dots between the functional variants and genetic traits is a significant challenge due to the need for precise, diverse, and large-scale phenotyping. Differential transcripts, which carry genetic variants or alternative splicing (AS) sites, may exhibit altered gene expression and protein coding, therefore influence phenotypes, showing their potential for high-throughput identification of functional genes. In this study, full-length transcripts were assembled and analyzed from eight developmental stage tissues of wild and cultivated cucumbers, utilizing PacBio Iso-seq and Illumina RNA-seq. We identified 6,980 genes underwent AS in cucumber. Approximately 66% of AS events were cultivar-specific, and genetic variants significantly increased around these divergent AS events. Based on the transcript structure of genes and variant annotation, we focused on cis-acting genetic variants that may affect gene function, in which a 21-bp insertion in the 5' untranslated region (UTR) of SnRK-Activating Kinase1 (CsSnAK1), an energy signaling regulator, was demonstrated to inhibit lateral branch development in cultivated cucumber by promoting CsSnAK1 mRNA abundance. Our work provides a straightforward yet reliable approach for integrating transcript structure and variant annotation to identify novel functional alleles in domestication traits.Read more

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AbstractBiofortification offers a sustainable solution to "hidden hunger, " yet the trade-off between grain yield and nutritional quality remains a persistent breeding bottleneck. Modern crop breeding emphasises the balance between high yield and nutritional values. Use of novel genes/alleles for grain quality lost during domestication and genetic improvement has been proven an efficient way to help achieve the dual goals. In sorghum, we report here the discovery of SbSTP20, encoding a sorghum monosaccharide transporter, as an essential component for biofortification by mediating the endosperm hexose influx and sub-aleurone (SA) thickness. SbSTP20 was ectopically expressed in sorghum developing grains and its expression levels were negatively associated with SA thickness. CRISPR edited Sbstp20 lines decreased the influx of hexoses, and exhibited thicker sub-aleurone layers and 6.6-7.5% higher grain protein and enriched micronutrients (Fe, Zn). SbSTP20thick natural variant increased sub-aleurone layer thickness and improved grain nutritional quality without altering grain size or thousand-grain weight. The SbSTP20thick allele was absent in 93% of modern improved lines, implying that the genomic region containing SbSTP20 showed a moderate selection signature. The metabolizable energy of SbSTP20thick containing sorghum lines was up to 6% higher than that of commercial corn standards in swine digestion and metabolism experiments. Reintroducing this haplotype via marker-assisted selection could provide a molecular strategy for nutritional enhancement.Read more