Journal of Genetics and Genomics

MitoQ alleviates m.3243A>G-induced mitochondrial dysfunction by stabilizing PINK1 and enhancing mitophagy

Baige Cao, Lei Fang, et al.

doi: 10.1016/j.jgg.2025.08.007

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Abstract:
The mitochondrial 3243A>G mutation (m.3243A>G) is associated with diverse clinical phenotypes. To elucidate the underlying mechanisms and explore intervention strategies in m.3243A>G patients, urine-derived stem cells (USCs) and a mitochondrial leucyl-tRNA synthetase (lars-2) deficient Caenorhabditis elegans (C. elegans) model are used to assess mitochondrial homeostasis and neuromuscular dysfunction. Patient-derived USCs with high levels of m.3243A>G heteroplasmy exhibit impaired mitochondrial function, disrupted mitochondrial dynamics, and inhibited mitophagy, which are reversed by MitoQ through suppression of OMA1 zinc metallopeptidase (OMA1)-induced mitochondrial phosphatase and tensin (PTEN) induced kinase 1 (PINK1) degradation. Furthermore, lars-2 knockdown in C. elegans induces mitochondrial stress and mimics the loss of neural and muscle functions observed in patients with the m.3243A>G mutation. MitoQ treatment partially improves neurobehavioral function by promoting the PINK1 pathway. These findings suggest that MitoQ has therapeutic potential in the context of the m.3243A>G mutation.

Assembly of a high-quality reference genome and characterization of a chemical-mutagenized library of an elite soybean cultivar Tianlong 1

Yinghua Sheng, Yicheng Huang, et al.

doi: 10.1016/j.jgg.2025.08.006

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Abstract:
Soybean (Glycine max L.) is a globally vital crop for oil production and food security. High-quality genomic resources are instrumental for both functional genomics and breeding. Here, we report a near-complete, high-quality genome assembly of the elite cultivar Tianlong 1 (TL1), featuring fully resolved telomeres and centromeres, as well as a gap-free assembly of 14 of its 20 chromosomes. On the basis of the genome assembly, we generate an ethyl methanesulfonate (EMS)-mutagenized population comprising 2,555 M₇ plants. Whole-genome re-sequencing of 288 EMS mutants uncovers 1,163,869 high-confidence single-nucleotide polymorphisms (SNPs) and 542,709 insertions/deletions (InDels), achieving 91.89% coverage of predicted protein-coding genes. Phenotypic screening demonstrates robust genotype–phenotype associations, with two nonsynonymous mutants displaying pronounced defects in seed and leaf development. Collectively, the chromosome-scale TL1 genome assembly and the extensively characterized mutant population establish valuable resources for functional genomics and precision breeding in soybean and related legume species.

The interplay between phosphorus nutrition and abiotic stresses in plants

Houqing Zeng, Feiyu Chen, et al.

doi: 10.1016/j.jgg.2025.08.008

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Abstract:
Phosphorus (P) is an essential macronutrient required for plant growth, development, and resilience to environmental stresses. Its availability in soil and homeostasis within plants are strongly influenced by environmental conditions, with unfavorable environments and soil factors disrupting phosphate availability, absorption, transport, and utilization. Optimizing phosphate supply can alleviate the detrimental impacts of abiotic stresses, thereby supporting growth and improving stress tolerance. Recent studies reveal that abiotic stresses modulate phosphate signalling pathways and alter the expression of phosphate-responsive genes, often affecting key regulators of P homeostasis. Strategic manipulation of phosphate transporters and their regulatory pathways offers a promising approach to enhance plant adaptation to challenging environments. This review highlights current advances in understanding the molecular mechanisms that coordinate P-responsive gene expression and homeostasis pathways under fluctuating P availability and stress conditions. It emphasizes the critical role of P nutrition in enhancing plant stress tolerance through antioxidant activation, osmolyte accumulation, membrane stabilization, and metal-phosphate complex formation. An in-depth mechanistic understanding of P-stress interactions will inform the development of P-efficient, and stress-resistant crop varieties and guide more sustainable P fertilizer management in agriculture.

Recapitulation of key phenotypes and pathological features of primary familial brain calcification (PFBC) in a mouse Slc20a2^S602W/S602W model

Junyu Luo, Man Jiang, et al.

doi: 10.1016/j.jgg.2025.08.005

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Gene traffic mediated by transposable elements shaped the dynamic evolution of ancient sex chromosomes of varanid lizard

Zexian Zhu, Jason Dobry, et al.

doi: 10.1016/j.jgg.2025.08.002

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Abstract:
Lizards usually exhibit frequent turnovers and a much greater diversity of sex determination mechanisms compared to birds and mammals, with the conserved ZW sex chromosomes of anguimorph lizards originating over 115 million years ago a seeming exception. We previously discovered in an anguimorph lizard Varanus acanthurus (Vac) whose entire chrW, but not chrZ is homologous to part of the chr2 by cytogenetic mapping, suggesting its complex history of sex chromosome evolution yet to be elucidated. To address this, we assemble a chromosome-level genome, and provide evidence that the Vac sex chromosome pair has undergone at least two times of recombination loss, producing a pattern of evolutionary strata like that of birds and mammals. Comparison to other lizard genomes date the stepwise propagation of specific retrotransposon subfamilies enriched near the duplicated gene pairs on the chrW and chr2 to the varanid ancestor. These retrotransposons probably have mediated the recruitment and amplification of autosomal genes on the chrW, including members of a large vomeronasal chemosensory receptor gene family V2R. Our results suggest that the W or Y chromosome as a refugium of repetitive elements, may recurrently recruit short-lived functional genes responsible for sexual dimorphisms during its long-term course of degeneration.

Spatiotemporal dynamics of neuron differentiation and migration in the developing human spinal cord

Yuan Yu, Mengjie Pan, et al.

doi: 10.1016/j.jgg.2025.08.004

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Abstract:
Precise formation of complex neural circuits in the spinal cord, achieved through the integration of diverse neuronal populations, is essential for central nervous system function. However, the specialization and migration of human spinal cord neurons remain poorly understood. In this study, we perform single-cell transcriptome sequencing of human spinal cord from Carnegie Stage (CS) 16-21 and mouse spinal cord from embryonic day (E) 8.0-11.5, complemented by in situ sequencing of human spinal cord (CS 16-20). Our results reveal the critical role of the precursor state in neuronal differentiation and migration, identifying key transcription factors that regulate these processes across species. Notably, each neuronal lineage expresses unique markers as early as the progenitor stage at the spinal cord midline, and subsequently undergoes a shared transcriptional program during precursor commitment that guides migration. This synchronized migration, validated by spatial transcriptomics, occurs in both dorsal and ventral regions. Our findings offer important insights into the migration patterns and regulatory factors that guide spinal cord neuron subtype specification during embryogenesis.