Ginkgo biloba L. is a relic tree species that integrates medicinal, edible, ornamental, and scientific research value, offering substantial economic and social benefits. However, market demand for new cultivars with superior ornamental characteristics, high bioactive compound content, and enhanced stress tolerance is becoming increasingly urgent, and conventional breeding approaches can no longer adequately meet these needs. The rapid advancement of omics technologies has provided novel perspectives and a rich data foundation for deciphering the molecular mechanisms underlying key traits in G. biloba from multiple dimensions. This review systematically summarizes the progress and application of omics technologies in studies on G. biloba morphogenesis, sex determination and differentiation, biosynthesis of pharmacologically active compounds (flavonoids and terpene lactones), and stress resistance. To address the limitations of current omics-based research on G. biloba traits, this paper proposes a multidisciplinary framework integrating systems biology, precision phenomics, and machine learning modeling, aiming to propel molecular design breeding in G. biloba and provide strategic reference for its precision genetic improvement as well as the quality and efficiency enhancement of the entire industrial chain.

As an important spice species in Rutaceae, the Sichuan pepper (Zanthoxylum armatum) can provide pungent and numbing taste, as well as aroma in its mature fruit. Here we assembled a chromosome-level genome of green prickly ash which was widely cultivated in a major production area including Chongqing and Sichuan province, China. We generated 712 Gb (~112 ×) PacBio long reads and 511 Gb (~82 ×) Hi-C data, and yielded an assembly of 99 pseudochromosomes with total size of 5.32 Gb and contig N50 of 796 kb. The genomic analyses and cytogenetic experiments both indicated that the cultivar ‘Zhuye Huajiao’ was a triploid. We identified a Zanthoxylum-specific whole genome duplication event emerging about 24.8 million years ago (Mya). We also detected a transposition burst event (0.3–0.4 Mya) responsible for the large genome size of Z. armatum. Metabolomic analysis of the Zanthoxylum fruits during development stages revealed profiles of 39 volatile aroma compounds and 528 secondary metabolites, from which six types of sanshools were identified. Based on metabolomic and transcriptomic network analysis, we screened candidate genes encoding long chain acyl-CoA synthetase, fatty acid desaturase, branched-chain amino acid aminotransferase involved in sanshool biosynthesis and three genes encoding terpene synthase during fruit development. The multi-omics data provide insights into the evolution of Zanthoxylum and molecular basis of numbing and aroma flavor of Sichuan pepper.