Journal of Genetics and Genomics

Solving the puzzle of salicylic acid biosynthesis in plants

Pei Miao, Jian-Min Zhou

doi: 10.1016/j.jgg.2025.08.003

Abstract (0) PDF (0)

Abstract:

A telomere-to-telomere genome assembly of radish (Raphanus sativus L.) provides insights into QTL mapping of bolting traits

Feng Yang, Sihan Peng, et al.

doi: 10.1016/j.jgg.2025.07.014

Abstract (10) PDF (0)

Abstract:
Radish (Raphanus sativus L.) is an important cruciferous root vegetable, with bolting regulated by multiple genes; however, the genetic mechanisms underlying bolting regulation remain unclear. Here, the genome of the cultivar C60213 is assembled into a high-quality, gap-free telomere-to-telomere structure, spanning nine chromosomes and totaling 472.71 Mb, using a combination of Oxford Nanopore, PacBio, and Hi-C sequencing technologies. It identifies 49,768 protein-coding genes, 97.38% of which are functionally annotated. Repetitive sequences constitute 59.72% of the genome, primarily comprising long terminal repeats. A high-density genetic linkage map is constructed using an F₂ population derived from a cross between early- and late-bolting radishes, identifying seven major quantitative trait loci associated with bolting and flowering. RNA-seq and quantitative real-time PCR analysis reveal that the RsMIPS3 gene is found to be associated with bolting, with its expression decreasing during this process. Notably, RsMIPS3 overexpression in Arabidopsis delays bolting, confirming its role in regulating bolting time. These findings advance radish genome research and provide a valuable target for breeding late-bolting varieties.

Chromosome-level genome assembly of finger millet (Eleusine coracana) provides insights into drought resistance

Jiguang Li, Chaonan Guan, et al.

doi: 10.1016/j.jgg.2025.07.012

Abstract (10) PDF (0)

Abstract:
Finger millet (Eleusine coracana Gaertn.), a nutritionally rich and drought-resilient C4 cereal, possesses exceptional grain storage longevity (up to 50 years). Here, we report a high-quality genome assembly of the allotetraploid cultivar C142, revealing extensive structural rearrangements between its two subgenomes (subA and subB), which are associated with asymmetric gene expression and subgenome dominance favoring subA. SubB diverged from its presumed progenitor E. indica approximately 6.8 million years ago, and two whole-genome duplication events shaped the current genome architecture, contributing to gene redundancy and adaptive potential. Notably, expansion of stress-related gene families, such as aldo-keto reductases, suggests a role in oxidative stress response and drought adaptation. Using genome-wide association studies (GWAS), we identify several candidate genes associated with key agronomic traits. Among them, EcMDHAR, encoding monodehydroascorbate reductase, plays a critical role in enhancing drought tolerance. Different EcMDHAR haplotypes exhibit distinct expression profiles, supporting their functional relevance in drought adaptation. This genomic resource not only advances our understanding of polyploid genome evolution in millets but also provides a foundation for genome-assisted improvement of drought resistance and nutritional quality in finger millet.

Proximity labeling proteomics with cilia-TurboID transgenic mice identified regulators of motile cilia function

Pan Wang, Xiangnan Wu, et al.

doi: 10.1016/j.jgg.2025.07.013

Abstract (42) PDF (0)

Abstract:

Massively parallel characterization of non-coding de novo mutations in autism spectrum disorder

Congcong Chen, Songwei Guo, et al.

doi: 10.1016/j.jgg.2025.07.008

Abstract (24) PDF (0)

Abstract:
Autism spectrum disorder (ASD) is a neurodevelopmental disorder where de novo mutations play a significant role. Although coding mutations in ASD have been extensively characterized, the impact of non-coding de novo mutations (ncDNMs) remains less understood. Here, we integrate cortex cell-specific cis-regulatory element annotations, a deep learning-based variant prediction model, and massively parallel reporter assays to systematically evaluate the functional impact of 227,878 ncDNMs from Simons Simplex Collection (SSC) and Autism Speaks MSSNG resource (MSSNG) cohorts. Our analysis identifies 238 ncDNMs with confirmed functional regulatory effects, including 137 down-regulated regulatory mutations (DrMuts) and 101 up-regulated regulatory mutations (UrMuts). Subsequent association analyses reveal that only DrMuts regulating loss-of-function (LoF) intolerant genes rather than other ncDNMs are significantly associated with the risk of ASD (Odds ratio = 4.34; P = 0.001). A total of 42 potential ASD-risk DrMuts across 41 candidate ASD-susceptibility genes are identified, including 12 recognized and 29 unreported genes. Interestingly, these noncoding disruptive mutations tend to be observed in genes extremely intolerant to LoF mutations. Our study introduces an optimized approach for elucidating the functional roles of ncDNMs, thereby expanding the spectrum of pathogenic variants and deepening our understanding of the complex molecular mechanisms underlying ASD.

Universal single-copy ortholog benchmark gene set for bryophytes

Xuping Zhou, Tao Peng, et al.

doi: 10.1016/j.jgg.2025.07.009

Abstract (24) PDF (0)

Abstract: