Journal of Genetics and Genomics

The application and prospects of spatial omics technologies in clinical medical research and molecular diagnostics

Xiaofeng Wu, Weize Xu, et al.

doi: 10.1016/j.jgg.2025.09.003

Abstract (0) PDF (0)

Abstract:
While conventional FISH and IHC methods struggle to decode complex tissue heterogeneity and comprehensive molecular diagnosis due to low-throughput spatial information, spatial omics technologies enable high-throughput molecular mapping across tissue microenvironments. These technologies are emerging as transformative tools in molecular diagnostics and medical research. By integrating histopathological morphology with spatial multi-omics profiling (genome, transcriptome, epigenome, and proteome), spatial omics technologies open an avenue for understanding disease progression, therapeutic resistance mechanisms, and precise diagnosis. It particularly enhances tumor microenvironment analysis by mapping immune cell distributions and functional states, which may greatly facilitate tumor molecular subtyping, prognostic assessment, and predicting the efficacy of radiotherapy and chemotherapy. Despite the substantial advancements in spatial omics, the translation of spatial omics into clinical applications remains challenging due to robustness, efficacy, clinical validation, and cost constraints. In this review, we will summarize the current progress and prospects of spatial omics technologies, particularly in medical research and diagnostic applications.

Genome of aerial alga Trentepohlia odorata reveals insights into the evolution of terrestrial lifestyle in green algae

Yuanhao Li, Jiao Fang, et al.

doi: 10.1016/j.jgg.2025.09.004

Abstract (0) PDF (0)

Abstract:
Trentepohliales is a completely terrestrial order within Ulvophyceae (the core Chlorophyta), and its closely related lineages are mainly marine macroalgae (green seaweeds). Despite the considerable interest in their biotechnological potential, little is known about their adaptations to challenging terrestrial habitats. Here, we assemble the high-quality reference genome of Trentepohlia odorata. This alga shows duplications of key genes associated with lipid metabolism and carotenoid synthesis, potentially facilitating intracellular accumulation of lipid droplets and carotenoids. We further reveal positive selection and expansion of gene families involved in vesicle trafficking and cell division regulation in T. odorata compared to other algae (cleavage furrow-mediated cell division) in Ulvophyceae, providing a genetic foundation for the evolution of phragmoplast-mediated cell division. The combined C₄-like and biophysical carbon-concentrating mechanisms (CCMs) of T. odorata enable adaptation to fluctuating CO₂ environments, and support efficient photosynthesis under CO₂-limited conditions. Adaptive strategies of T. odorata to terrestrial stressors, such as drought, intense light, and UV-B radiation, include horizontally acquired genes involved in cell wall synthesis and remodeling, homeostasis of aldehydes, and expanded genes associated with reactive oxygen species (ROS), DNA repair, and photoprotection. Our study provides a valuable genomic resource for studying aerial algae and improves understanding of plant terrestrialization.

Genomic sequencing as a key primary recommendation for neonatal hyperbilirubinemia: a population-based multicenter study

Dabin Huang, Xia Gu, et al.

doi: 10.1016/j.jgg.2025.09.002

Abstract (12) PDF (0)

Abstract:
Genetic variations are risk factors for neonatal hyperbilirubinemia (NHB), a common cause of infant hospitalization in the first postnatal week, but their contribution and long-term impacts remain unclear. This population-based multicenter study enrolls 1,780 hospitalized NHB newborns and 38,158 genetically screened newborns across 20 hospitals (2019–2022). Excluding cases with clear clinical causes, 977 NHB cases are categorized into genetic variation-positive and -negative groups. Results show significantly higher NHB-related gene variants (81.63% vs. 65.62%) and positive variation rates (36.29% vs. 9.4%) in NHB cases than in the general newborn population (all P < 0.001). Among the 977 NHB cases, 325 (33.3%) have positive variants, with higher rates of severe hyperbilirubinemia (16.9% vs. 9.7%, P = 0.001), prolonged jaundice (36.3% vs. 27.6%, P = 0.005), and cholestasis/hypercholanaemia (23.7% vs. 14.7%, P < 0.001) in the positive group. Cumulative genetic variants in bilirubin metabolism pathways exhibit dose-dependent associations with increased risks of complications. Long-term follow-up reveals that UGT1A1 variants prolong jaundice up to 1 month, while severe SLC10A1 variants cause persistent cholestasis/hypercholanaemia beyond 9 months. This large-scale evidence highlights genetic factors as key NHB determinants, with implications for neonatal care protocols to integrate genetic testing and establish long-term surveillance for variant carriers.

Integrative multi-omics and genomic prediction reveal genetic basis of early salt tolerance in alfalfa

Fei He, Ming Xu, et al.

doi: 10.1016/j.jgg.2025.09.001

Abstract (10) PDF (0)

Abstract:

The genetic basis of early-stage salt tolerance in alfalfa (Medicago sativa L.), a key factor limiting its productivity, remains poorly understand. To dissect this complex trait, we integrate genome-wide association study (GWAS) and transcriptomics (RNA-seq) from 176 accessions within a machine learning based genomic prediction framework. Analysis reveals weak genetic correlations among four salt-tolerance traits and a gradual decline in performance under increasing salt stress. GWAS identify 60 significant associated SNPs, with the highest number detected under 100 mM salt stress. Salt tolerance exhibits an additive effect from favorable haplotypes, which are most abundant in Chinese accessions. GWAS-associated genes are related to key regulators of hormone signaling and osmotic adjustment, while transcriptome analysis indicates a global repression of stress-responsive transcription factors. Integrating these multi-omics datasets allow us to identify 14 candidate genes, including MsHSD1 (seed dormancy) and MsMTATP6 (energy metabolism). Crucially, incorporating these markers into genomic prediction models improve cross-population predictive accuracy to an average of 54.4%. This study provides insights into the genetic architecture of salt tolerance in alfalfa and offers valuable markers to facilitate molecular breeding.

ATPase-deficient CHD7 disease variant disrupts neural development via chromatin dysregulation

Guangfu Wang, Zhuxi Huang, et al.

doi: 10.1016/j.jgg.2025.08.012

Abstract (15) PDF (0)

Abstract:
Chromodomain helicase DNA binding protein 7 (CHD7), an ATP-dependent chromatin remodeler, plays versatile roles in neurodevelopment. However, the functional significance of its ATPase/nucleosome remodeling activity remains incompletely understood. Here, we generate genetically engineered mouse embryonic stem cell lines harboring either an inducible Chd7 knockout or an ATPase-deficient missense variant identified in individuals with CHD7-related disorders. Through in vitro neural induction and differentiation assays combined with mouse brain analyses, we demonstrate that CHD7 enzymatic activity is indispensable for gene regulation and neurite development. Mechanistic studies integrating transcriptomic and epigenomic profiling reveal that CHD7 enzymatic activity is essential for establishing a permissive chromatin landscape at target genes, marked by the open chromatin architecture and active histone modifications. Collectively, our findings underscore the pivotal role of CHD7 enzymatic activity in neurodevelopment and provide critical insights into the pathogenic mechanisms of CHD7 missense variants in human disease.

Deciphering the genetic regulation of flowering time in rapeseed for early-maturation breeding

Minghao Zhang, Wei Chang, et al.

doi: 10.1016/j.jgg.2025.08.011

Abstract (12) PDF (0)

Abstract:
Flowering time is a critical agronomic trait with a profound effect on the productivity and adaptability of rapeseed (Brassica napus L.). Strategically advancing flowering time can reduce the risk of yield losses due to extreme climatic conditions and facilitate the cultivation of subsequent crops on the same land, thereby enhancing overall agricultural efficiency. In this review, we synthesize current information on flowering time regulation in rapeseed through an integrated analysis of its genetic, hormonal, and environmental dimensions, emphasizing their crosstalk and implications for yield. We consolidate multi-omics evidence from population genetics, functional genomics, and systems biology to create a haplotype-based framework that overcomes the trade-off between flowering time and yield, providing support for the precision breeding of early-maturing cultivars. The insights presented here could inform future research on flowering time regulation and guide strategies for increasing rapeseed productivity.