The Allium genus is cultivated globally as vegetables, condiments, or medicinal plants and is characterized by large genomes and strong pungency. However, the genome evolution and genomic basis underlying their unique flavor formation remain poorly understood. Herein, we report an 11.27-Gb chromosome-scale genome assembly for bunching onion (A. fistulosum). The uneven bursts of long-terminal repeats contribute to diversity in genome constituents, and dispersed duplication events largely account for gene expansion in Allium genomes. The extensive duplication and differentiation of alliinase and lachrymatory factor synthase manifest as important evolutionary events during flavor formation in Allium crops. Furthermore, differential selective preference for flavor-related genes likely lead to the variations in isoalliin content in bunching onions. Moreover, we reveal that China is the origin and domestication center for bunching onions. Our findings provide insights into Allium genome evolution, flavor formation and domestication history and enable future genome-assisted breeding of important traits in these crops.

Plant evolution is driven by key innovations of functional traits that enables their survivals in diverse ecological environments. However, plant adaptive evolution from land to atmospheric niches remains poorly understood. In this study, we use the epiphytic Tillandsioideae subfamily of Bromeliaceae as model plants to explore their origin, evolution and diversification. We provide a comprehensive phylogenetic tree based on nuclear transcriptomic sequences, indicating that core tillandsioids originated approximately 11.3 million years ago in the Andes. The geological uplift of the Andes drives the divergence of tillandsioids into tank-forming and atmospheric types. Our genomic and transcriptomic analyses reveal gene variations and losses associated with adaptive traits such as impounding tanks and absorptive trichomes. Furthermore, we uncover specific nitrogen-fixing bacterial communities in the phyllosphere of tillandsioids as potential source of nitrogen acquisition. Collectively, our study provides integrative multi-omics insights into the adaptive evolution of tillandsioids in response to elevated aerial habitats.

Drought stress has detrimental effects on crop productivity worldwide. A strong root system is crucial for maintaining water and nutrients uptake under drought stress. Wild watermelons possess resilient roots with excellent drought adaptability. However, the genetic factors controlling this trait remain uninvestigated. In this study, we conducted a bulk segregant analysis (BSA) on an F₂ population consisting of two watermelon genotypes, wild and domesticated, which differ in their lateral root development under drought conditions. We identified two quantitative trait loci (qNLR_Dr. Chr01 and qNLR_Dr. Chr02) associated with the lateral root response to drought. Furthermore, we determined that a small region (0.93 Mb in qNLR_Dr. Chr01) is closely linked to drought adaptation through quantitative trait loci (QTL) validation and fine mapping. Transcriptome analysis of the parent roots under drought stress revealed unique effects on numerous genes in the sensitive genotype but not in the tolerant genotype. By integrating BSA, fine mapping, and the transcriptome, we identified six genes, namely L-Ascorbate Oxidase (AO), Cellulose Synthase-Interactive Protein 1 (CSI1), Late Embryogenesis Abundant Protein (LEA), Zinc-Finger Homeodomain Protein 2 (ZHD2), Pericycle Factor Type-A 5 (PFA5), and bZIP transcription factor 53-like (bZIP53-like), that might be involved in the drought adaptation. Our findings provide valuable QTLs and genes for marker-assisted selection in improving water-use efficiency and drought tolerance in watermelon. They also lay the groundwork for the genetic manipulation of drought-adapting genes in watermelon and other Cucurbitacea species.

Celery (Apium graveolens) is a globally cultivated vegetable renowned for its health-promoting and nutraceutical benefits. Exploring its genomic and metabolic diversity can help to facilitate breeding selection. Here, by integrating genomic and metabolomic analyses of 305 globally representative accessions, we reveal pronounced east–west population structure that parallels geographical distribution and varietal differentiation, with three major variety groups showing distinct domestication trajectories. We identify key loci associated with domestication-related traits, including petiole morphology and bolting time. Metabolite profiling uncovers divergence among populations: var. dulce, predominantly consumed raw in Western culinary traditions, exhibits marked reductions in bitter coumarins and alkaloids—a metabolic signature consistent with fresh-eating preferences. Metabolite GWAS map 335,692 loci for 1552 metabolites. We develop genomic prediction models for metabolite abundance to aid breeding. Collectively, our study reveals the genomic and metabolic landscape of celery domestication, and provides hypotheses regarding how cultural practices, alongside regional environmental factors, may have jointly shaped current diversity.