Conifers dominate the world's forest ecosystems and are the most widely planted tree species. Their giant and complex genomes present great challenges for assembling a complete reference genome for evolutionary and genomic studies. We present a 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) and revealed that its genome size is mostly attributable to huge intergenic regions and long introns with high transposable element (TE) content. Large genes with long introns exhibited higher expressions levels. Despite a lack of recent whole-genome duplication, 91.2% of genes were duplicated through dispersed duplication, and expanded gene families are mainly related to stress responses, which may underpin conifers' adaptation, particularly in cold and/or arid conditions. The reproductive regulation network is distinct compared with angiosperms. Slow removal of TEs with high-level methylation may have contributed to genomic expansion. This study provides insights into conifer evolution and resources for advancing research on conifer adaptation and development.

Summary: Phytoplasmas are specialized phloem‐limited bacteria that cause diseases on various crops, resulting in significant agricultural losses. This research focuses on the jujube witches' broom (JWB) phytoplasma and investigates the host‐manipulating activity of the effector SJP39. We found that SJP39 directly interacts with the plant transcription factor bHLH87 in the nuclei. SJP39 stabilizes the bHLH87 homologs in Arabidopsis thaliana and jujube, leading to growth defects in the plants. Transcriptomic analysis indicates that SJP39 affects the gibberellin (GA) pathway in jujube. We further demonstrate that ZjbHLH87 regulates GA signaling as a negative regulator, and SJP39 enhances this regulation. The research offers important insights into the pathogenesis of JWB disease and identified SJP39 as a virulence factor that can contribute to the growth defects caused by JWB phytoplasma infection. These findings open new opportunities to manage JWB and other phytoplasma diseases.

Current research does not fully elucidate the key compounds and their mechanisms that define the aroma profile of fresh jujube fruits. Therefore, this study conducted a comprehensive analysis of both free and glycosidically bound aroma compounds in fresh jujube fruits of ten cultivars. Utilizing gas chromatography–mass spectrometry (GC-MS), we identified 76 volatile free aroma compounds and 19 glycosidically bound volatile compounds, with esters, aldehydes, and ketones emerging as the predominant volatile compounds in the jujube fruits. Odor activity value (OAV) analysis revealed that the primary aroma profile of the jujubes is characterized by fruity and fatty odors, with β-damascenone being a key contributor to the fruity aroma, and (E)-2-oct-en-1-al and nonanal significantly influencing the fatty aroma. Moreover, the integration of sensory evaluation and partial least squares regression (PLSR) analysis pinpointed octanal, (E)-2-oct-en-1-al, nonanal, β-damascenone, and pentanal as significant contributors to the jujube’s characteristic aroma, while isoamyl acetate was identified as significantly influencing the fatty acid taste. This study not only underscores the complexity of the jujube aroma composition but also highlights the impact of environmental factors on aroma profiles, offering valuable insights into the sensory characteristics of jujube fruits.

The texture of fresh jujube fruit is related to its popularity and commercial value. The metabolic networks and essential genes that regulate the texture of jujube (Ziziphus jujuba) fruit are still unknown. In this study, two jujube cultivars with significantly different textures were selected by a texture analyzer. The four developmental stages of the exocarp and mesocarp of jujube fruit were studied separately using metabolomic and transcriptomic analyses. Differentially accumulated metabolites were enriched in several critical pathways related to cell wall substance synthesis and metabolism. Transcriptome analysis confirmed this by finding enriched differential expression genes in these pathways. Combined analysis showed that ‘Galactose metabolism’ was the most overlapping pathway in two omics. Genes such as β-Gal, MYB and DOF may affect fruit texture by regulating cell wall substances. Overall, this study provides an essential reference for the establishment of texture-related metabolic and gene networks of jujube fruit.

Roots are essential for nutrient uptake and structural stability in trees. Despite their critical role, the genetic determinants underlying root system architecture (RSA) remain poorly understood. In this study, we employed an integrated approach combining automated three-dimensional (3D) spatial imaging, multi-omics analyses, genetic transformation, and molecular experiments to investigate the genetic architecture and regulatory networks governing RSA in Simon poplar (Populus simonii). Here, using a panel of 303 P. simonii accessions collected from different geographical regions in China, we performed a genome-wide association study (GWAS) on 96 RSA traits and identified S-phase kinase-associated protein 2B (PsiSKP2B) as a candidate gene co-localized by six traits. By integrating the findings from GWAS, transcriptome, and single-cell RNA-seq (scRNA-seq) analyses, we identified PsiSKP2B as a key regulator of meristematic tissue cells involved in lateral root (LR) development. Overexpression of PsiSKP2B in 84k (Populus alba × Populus glandulosa) had a substantial effect on RSA traits, increasing the number and density of LRs by 65.9% and 98.6%, respectively, compared with wild-type plants. Our in vitro and in vivo assays revealed that PsiSKP2B modulates LR development by interacting with WUSCHEL RELATED HOMEOBOX 4 (PsiWOX4) or ZINC FINGER HOMEODOMAIN 9 (PsiZHD9), both of which are specifically expressed in atrichoblast cells, thereby activating a regulatory feedback loop. These findings highlight an atrichoblast-dependent regulatory mechanism through which PsiSKP2B governs LR development. Our study not only introduces an advanced image recognition methodology for quantifying RSA traits in P. simonii but also provides a comprehensive multi-omics framework for elucidating the genetic and molecular basis of RSA.