East Asia has an abundant resource of fragrant japonica rice that is gaining increasing interest among both consumers and producers. However, genomic resources and in particular complete genome sequences currently available for the breeding of fragrant japonica rice are still scarce. Here, integrating Nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C methods, we presented a high-quality chromosome-level genome assembly (~378.78 Mb) for a new fragrant japonica cultivar ‘Changxianggeng 1813’, with 31,671 predicated protein-coding genes. Based on the annotated genome sequence, we demonstrated that it was the badh2-E2 type of deletion (a 7-bp deletion in the second exon) that caused fragrance in ‘Changxianggeng 1813’. Comparative genomic analyses revealed that multiple gene families involved in the abiotic stress response were expanded in the ‘Changxianggeng 1813’ genome, which further supported the previous finding that no generalized loss of abiotic stress tolerance associated with the fragrance phenotype. Although the ‘Changxianggeng 1813’ genome showed high genomic synteny with the genome of the non-fragrant japonica rice cultivar Nipponbare, a total of 289,970 single nucleotide polymorphisms (SNPs), 96,093 small insertion-deletion polymorphisms (InDels), and 8690 large structure variants (SVs, >1000 bp) were identified between them. Together, these genomic resources will be valuable for elucidating the mechanisms underlying economically important traits and have wide-ranging implications for genomics-assisted breeding in fragrant japonica rice.

Zelkova schneideriana (Ulmaceae), an endemic relict species of the Tertiary in China, has experienced a sharp decline in population due to habitat fragmentation, poor natural regeneration, and anthropogenic disturbances. It is currently listed as a category II national key protected wild plant and categorized as Vulnerable by the International Union for Conservation of Nature (IUCN). To explore its response mechanisms to climate change, this study integrates 11 species distribution models (SDMs) to comprehensively predict its suitable habitat distribution patterns. Key environmental variables were identified as Bio06 (minimum temperature of the coldest month, 21.57%), Bio02 (mean diurnal range, 19.81%), Bio17 (precipitation of the driest quarter, 13.52%), Bio15 (precipitation seasonality, 8.32%), Bio07 (temperature annual range, 8.15%), Bio12 (annual precipitation, 6.58%), and elevation (6.57%), collectively contributing approximately 85%. Spatiotemporal analysis revealed that during historical glacial periods, suitable habitats were significantly restricted, and highly suitable zones were absent under extreme climatic conditions, suggesting the presence of potential glacial refugia. Under current climatic conditions, highly suitable habitats have expanded notably. However, under the high-emission scenario (SSP585) in the future, the suitable range is projected to shrink considerably, with a drastic reduction in highly suitable areas. Moreover, the suitability centroid is expected to shift markedly toward higher elevations in the northeast, indicating a potential adaptation strategy of Z. schneideriana toward mountainous regions in Hunan, Hubei, and Chongqing. These findings provide quantitative guidance for the formulation of targeted conservation strategies for Z. schneideriana and offer methodological insights for predicting suitable habitats and managing related relict plant species under the threat of climate change.

Elaeagnus 'viridis', an artificial hybrid of E. macrophylla (male ) Thunb. (1784) x E. pungens (female ) Thunb. (1784), is known for its economic and ecological value. In this study, we sequenced and assembled the whole chloroplast (cp) genome of E. 'viridis'. The results showed that its cp genome was 152,284 bp long, showing a typical quadripartite structure and containing a large single-copy region (LSC, 82,299 bp), a small single-copy region (SSC, 18,239 bp), and a pair of inverted repeats (IRs, 51,746 bp). The cp genome contains 132 genes, including 86 protein-coding genes (PCGs), 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 66 common PCGs revealed that E. 'viridis' is most closely related to its maternal parent E. pungens. The chloroplast genomic information reported in this study will shed some useful light for further genetic studies in the genus Elaeagnus.

Catalpa bungei, a fast-growing timber tree, is threatened by the lepidopteran pest Omphisa plagialis. Previous studies in our laboratory successfully generated transgenic C. bungei lines overexpressing Cry genes (Cry1Ab, Cry2A, and Cry9-2) that exhibited resistance to O. plagialis, but their potential impact on soil bacterial communities remains unclear. In this study, we analyzed nine transgenic C. bungei lines (three independent lines for each Cry gene) to characterize their rhizosphere bacterial communities using high-throughput sequencing of the 16S ribosomal DNA (rDNA) V4–V5 regions. A total of 628 amplicon sequence variants (ASVs) were shared among all transgenic and wild-type (WT) lines, forming a stable core microbiome dominated by Proteobacteria, Bacteroidota, Acidobacteriota, and Actinobacteriota. Alpha diversity showed no significant differences, while beta diversity revealed minor but distinct compositional shifts. Cry1Ab lines exhibited higher abundances of fast-growing taxa, particularly Proteobacteria and Bacteroidota; Cry2A lines displayed intermediate profiles, whereas Cry9-2 lines were nearly indistinguishable from WT communities. Linear discriminant analysis of the effect size revealed significant enrichment of taxa such as Burkholderiaceae and Ralstonia in the Cry1Ab rhizosphere, in contrast to the higher abundance of Chloroflexi in the WT. Functional predictions indicated consistent metabolic pathways across all treatments, suggesting strong ecological redundancy. This study demonstrates minimal impact on rhizosphere microbial communities in transgenic C. bungei plants. The Cry9-2 construct exhibited superior environmental stability, whereas the Cry1Ab construct caused only slight but ecologically acceptable shifts. These findings support the ecological safety of Bt-transgenic C. bungei and identify Cry9-2 as a particularly favorable candidate for forestry applications. This comparative evaluation of three Cry genes in a tree species provides a framework for future gene-specific biosafety assessments in woody plants.