Journal of Genetics and Genomics

The teleost whole-genome duplication (TGD) contributed to functional diversification of opsins. Some TGD paralogs, including those of parapinopsin (PP), Vertebrate Ancient (VA) opsin, and long wavelength-sensitive (LWS) opsin, show different absorption spectra and/or expression patterns. However, our knowledge of detailed evolutionary processes and mechanisms by which TGD contributed to opsin diversification is still limited. Here, we report that TGD paralogs of parietopsin (PT1 and PT2) are retained in extant species. While most species, including the zebrafish, have only PT1, several characins, including the red piranha (Pygocentrus nattereri), retain both PT1 and PT2. The Mexican tetra (Astyanax mexicanus) and catfishes have only PT2. To assess the degree of functional diversification between PT1 and PT2, we characterized spectral properties and expression patterns. Maximum absorption spectra differ slightly among PTs. Those of red piranha PT1, PT2, Mexican tetra PT2, and Japanese catfish (Silurus asotus) PT2 were located at 517 nm, 528 nm, 517 nm, and ~535 nm, respectively. Fluorescence in situ hybridization showed that (1) piranha PT1 and PT2 are expressed in the same pineal cells, and (2) they are also co-expressed with PP1. Based on these findings, functional diversification of opsins after gene duplication is discussed.

Local ancestry inference (LAI) reveals population compositions of an individuals chromo-somes, which empowers population genetics and genetic association studies of diverse populations. The recent availability of large genomic datasets from biobanks offers unprecedented opportunities for LAI. However, such datasets are typically only accessible from cloud-based platforms, and the lack of efficient and cost-effective tooling makes LAI prohibitive for resource-constrained researchers. Here, we develop Recomb-Mix Cloud, a cloud-ready pipeline for LAI based on Recomb-Mix, a recently introduced efficient LAI method. Recomb-Mix focuses on individual variants while maintaining a lower computational burden than other LAI methods focusing on genomic windows. Recomb-Mix Cloud offers a cloud-friendly complete pipeline from panel sample selection, marker alignment, compact reference panel construction, Recomb-Mix threading, and generating LAI calls in common data formats. Recomb-Mix Cloud also offers a set of pre-computed compact population reference panels constructed based on data from the Human Genome Diversity Project and the 1000 Genomes Project. Our results showed Recomb-Mix is about one and two orders of magnitude cheaper and faster than FLARE and RFMix, two popular LAI methods, while offering largely consistent LAI calls on the All of Us Researcher Workbench. The estimated overall compute cost per All of Us sample for whole-genome LAI analysis using Recomb-Mix Cloud with a pre-computed reference panel is just $0.01, compared with $0.43 for FLARE and $4.58 for RFMix. Therefore, Recomb-Mix Cloud is well-positioned to democratize local ancestry-based genetics research on modern biobank-sized data. The Recomb-Mix Cloud pipeline and the compact reference panels are available at https://github.com/ucfcbb/Recomb-Mix.

Aldehyde dehydrogenase 1a3 (Aldh1a3) is an enzyme involved in retinoic acid synthesis with dynamic expression patterns during development, including in the urogenital system. Here, we generated a bicistronic Aldh1a3-P2A-TagBFP knock-in mouse using CRISPR/Cas9 genome editing, inserting TagBFP immediately upstream of the endogenous Aldh1a3 stop codon. Correct targeting was confirmed by Oxford Nanopore long-read sequencing, and heterozygous and homozygous mice were viable and fertile without overt morphological abnormalities. TagBFP fluorescence faithfully overlapped with endogenous Aldh1a3 immunoreactivity and reproduced established expression domains in the developing craniofacial region, intestine, kidney, and broader urogenital system. Extensive characterization of the urogenital system revealed dynamic, spatially restricted BFP reporter activity in Aldh1a3-expressing domains across several key structures, including the ureteric bud and collecting duct lineage, seminal vesicles, caput epididymis, and developing uterine horns. The Aldh1a3-P2A-TagBFP mouse provides a fluorescent resource for visualizing Aldh1a3 expression across development and in adult tissues, including for the characterization of Aldh1a3-expressing domains in the urogenital system. The relatively low fluorescence intensity of TagBFP should be considered when assessing low-level reporter expression.

Chromosome was "self-assembled" into a complex three-dimensional topology in the nucleus, which provided the structural basis for important biological processes such as gene expression regulation and cell differentiation. The current understanding of the three-dimensional organization of the genome is based on high-throughput sequencing and imaging technologies to visualize the conformation of chromatin in its native environment. This study proposes a new research perspective and technical means to use fusion genes to determine the interaction information and three-dimensional structure of chromosomes. This three-dimensional information provided by the fusion gene spectrum not only shows the universality of the spatial layout of chromosomes, but also increases the interpretability of the occurrence of fusion genes. The chromatin conformation capture data of multiple tissues and periods is significantly correlated with the strength of fusion genes. For example, the frequency of trans-interaction between chromosomes 11 and 17 was the highest, and the frequency of fusion gene occurrence corresponding to KMT2A on chromosome 11 was the highest. Therefore, we infer that this structural universality is a common feature of the human genome, which provides a theoretical basis and data for predicting chromosome fusion events.

Mammalian cochlear hair cells (HC) are crucial for hearing, and histone modifications may play an important role in HC maturation and functions. However, whether and how NSD2, a histone H3 lysine 36 (H3K36) dimethyltransferase, affects cochlear HC maturation remains unclear. Here, we established an HC-specific Nsd2 knockout mouse model and discovered that the loss of NSD2 results in severe structural defects in stereociliary bundles and profound hearing impairment. Integrated multi-omics profiling revealed that NSD2 deficiency leads to a decreased expression of H3K36me2, which in turn alters genome-wide chromatin accessibility and gene expression. Mechanistically, NSD2 deficiency triggers the aberrant upregulation of extracellular matrix (ECM) genes at the transcriptional level, causing excessive collagen accumulation and compromising tissue structure. Crucially, ECM intervention can mitigate NSD2-deficiency mediated hearing damage. Our study reveals an epigenetic mechanism by which NSD2 regulates cochlear HC maturation through inhibition of chromatin remodeling-induced ECM accumulation, and provides a potential new therapeutic direction for hearing impairment.

A central question in developmental biology is how spatiotemporal embryo morphological events and cell differentiation are precisely coordinated to eventually develop into a mature organism. Previous research has shown cell positions and asymmetric division stages are related to cell lineage specification since morula stage. However, the detailed spatiotemporal dynamics and histories of embryonic cells and their relations with cell lineage specification remain incompletely understood from the onset of embryo development onward. My study on in-vitro embryos showed that continuous live cell tracking mapped community-like patterns in cell origin and differentiation. Cell positions, cell temporal factors (such as cell division order and cell cycle) and their histories intricately interacted over pre- and peri-implantation stages. These interactions of spatiotemporal cellular activities directed embryo morphological events and asymmetric cell lineage origin and differentiation throughout 2-cell to around 100-cell stage. In conclusion, this study provides comprehensive insights into the cellular spatiotemporal dynamics of cell inheritance and differentiation during pre- and peri-implantation morphological events and cell lineage specification. By longitudinally integrating spatial and temporal parameters relating to early embryogenesis, the findings not only bridge divergent explanations stemmed from different studies in the field but also offers a refined foundation for evaluating embryo potential and improving outcomes in assisted reproductive technologies, stem cell research, and regenerative medicine.

Ancestry-related genomic variation may contribute to phenotypic diversity. However, its cellular consequences remain difficult to evaluate. To address this, we developed a human induced pluripotent stem cell (hiPSC)-based framework for investigating such phenotypes. We used the Japanese population as a model of Jomon-related and continental East Asian ancestry admixture. Jomon ancestry, estimated using the Jomon allele score (JAS), was associated with clinical measures, including renal-related traits and serum triglycerides in 34,152 Tohoku Medical Megabank participants. Peripheral blood mononuclear cell transcriptomics of donors from the upper and lower extremes of the JAS distribution (n = 10) suggested group-level differences in immune-related gene expression. To test whether the serum triglyceride association coincided with hepatic cellular phenotypes, we differentiated hiPSCs from these donors into hepatocyte-like cells. Neither intracellular triglycerides nor lipid-related gene expression differed between groups. These findings highlight the value of a genetically characterized hiPSC-based framework for investigating ancestry-associated phenotypes across cellular contexts.

Genome engineering via CRISPR/Cas9 has been widely applied in biological research and developing gene therapies. However, genome editing flexibility is strongly constrained by the position and quality of guide RNAs relative to the intended edit: desired edit sites are frequently positioned far from efficient protospacer adjacent motifs (PAM). SMART (Silently Mutate And Repair Template) technique relaxes this constraint by silently mutating the gap between the Cas9 cut and the edit in the repair donor, preserving the encoded protein while expanding the usable guide-RNA design space. Designing such donors manually requires coordinated reasoning over transcript structure, reading frame, candidate protospacers, codon usage, homology arms and the expected edited allele. Auto-SMART is a web platform that automates this process for CRISPR/Cas9-mediated insertion, deletion, point mutation and sequence replacement in coding exons and in introns. Users choose a genome assembly, search a gene symbol or transcript, select a modification site and select an editing operation. Auto-SMART finds nearby Streptococcus pyogenes Cas9 (SpCas9) guides, ranks them by predicted on-target activity and cut-to-edit geometry, builds repair templates with synonymous substitutions, automatically recodes residual on-target sites to prevent re-cutting and renders interpretable panels for the target locus, donor template and locus after HDR, together with a downloadable report and a Primer3 genotyping handoff. The web application for Auto-SMART is freely available at https://auto-smart.chuanping.org/.

Although Cinnamomum includes globally important spice and medicinal plants, genome-scale knowledge of Cinnamomum species native to Japan remains limited. The Nansei Islands are an approximately 1,200-km-long archipelago located between the Pacific Ocean and the East China Sea and represent a key biogeographic region shaped by deep-sea barriers such as the Tokara and Kerama Gaps. Here, we integrated chloroplast and nuclear genome data generated in this study with public datasets to examine the phylogenetic relationships of four Cinnamomum species native to the Nansei Islands and ten related species. Chloroplast genomes showed no major structural differences among the four island species, whereas nuclear genome data resolved two distinct evolutionary lineages in the Nansei Islands: C. yabunikkei, C. x durifruticeticola, and C. daphnoides formed a distinct Nansei Islands lineage separate from Sri Lankan, Indonesian, and Taiwanese lineages, whereas C. sieboldii was placed in a Taiwanese lineage. Ancestry estimation indicated that C. x durifruticeticola and C. daphnoides share a common ancestral component, while C. sieboldii exhibited a single homogeneous ancestral component, suggesting reduced ancestral diversity after divergence from a Taiwanese lineage. These findings reveal previously unrecognized genomic differentiation among Japanese Cinnamomum species and suggest that deep-sea barriers, dispersal, and long-term isolation shaped their diversification.

Tectonic uplift and mountain building are major drivers of species diversification and adaptation, yet how they reshape genome architecture and promote evolutionary innovation remains poorly understood. Here, we generated multiple chromosome-level genomes for Asian torrent catfishes (Sisoridae) and performed phylogenomic and comparative genomic analyses. Our results support an Asian origin of Sisoridae and provide a refined phylogenetic topology for catfishes. Comparative analyses revealed extensive chromosomal rearrangements during sisorid evolution, indicating highly dynamic genome architectures. The timing of sisorid diversification overlaps with major phases of regional tectonic change, and analyses of phylogenetic discordance indicate heterogeneous contributions from incomplete lineage sorting and introgression. Elevational distribution was associated with variation in estimated molecular evolutionary rates, while exploratory scans identified lineage-specific candidates for selection and convergent evolution. Candidate coding and non-coding changes occur near genes with known roles in fin development, body patterning, and liver biology, but their effects on sisorid traits remain to be tested. Together, our results demonstrate how tectonic uplift reshaped genome architecture and diversification in Asian torrent catfishes and provide new insights into the genomic basis of adaptation in mountainous freshwater ecosystems.

Transposable elements (TEs) are a major source of genomic diversity in mammals, yet their regulatory roles in the bovine genome remain poorly understood. Through characterizing bovine TE landscape, despite the substantial proportion (25.6%) of ruminant-specific TEs, we observe age- and class-dependent genomic distribution patterns similar to those observed in other mammals. Next, we profile TE and gene expression dynamics in pre-implantation embryos generated in vivo (IVV), by in vitro fertilization (IVT), and through somatic cell nuclear transfer (SCNT). The zygotic genome activation (ZGA) is shifted from the 4-cell stage to the 8-cell stage in IVT and SCNT embryos compared to IVV embryos. SCNT embryos exhibit impaired initiation of early transcription programs at the 4-cell stage and disrupted developmental trajectories, including abnormal activation of pluripotency-associated genes. A subset of retroviral LTR elements are strongly activated at ZGA in IVV and IVT embryos, whereas their activation is markedly muted in SCNT embryos, suggesting that impaired gene and TE reprogramming may contribute to the developmental defects commonly observed in SCNT embryos. By epigenomic profiling, the MLT1D elements from the ERVL-MaLR LTR family lose repressive marks and gain H3K27ac at ZGA, together with DUXA-binding motif enrichment. Knockdown of DUXA in bovine embryos significantly reduced MLT1D expression and ZGA marker genes. We propose that a subset of DUXA-enriched MLT1D functions as enhancers that promote ZGA. Overall, our study provides new insights into the regulatory roles of TEs during bovine embryogenesis and establishes a framework for comparative studies of TE-mediated gene regulation in early mammalian development.

Neurodevelopmental disorders (NDDs) are clinically and genetically heterogeneous, and evidence linking additional genes to disease evolves rapidly. We developed SysNDD, an open-access, expert-curated resource that represents distinct gene-inheritance-disease associations as entities with standardized confidence, phenotype, and variant annotations. Each entity retains its curation history, so its evidence category can change as evidence accumulates. Currently, SysNDD contains 4,275 entities curated from 4,932 publications. Of these, 3,758 entities involving 3,271 genes describe NDDs; the remainder record non-NDD disorders, nearly all linked to NDD-associated genes, included for completeness. Regarding NDD evidence categories, 1,838 genes are Definitive, 179 Moderate, 1,248 Limited, and 6 Refuted. The entity model captures inheritance-specific disorders, including 220 genes with both autosomal dominant and autosomal recessive NDD associations. Comparison with seven other NDD gene resources showed complementary coverage, and evidence categories largely agreed with those of ClinGen, Gene2Phenotype, and PanelApp for shared gene-disease pairs. NDD genes formed distinct molecular modules, whereas associated disorders formed broad, overlapping phenotype groups that corresponded to those modules only selectively. SysNDD provides a continuously maintained, programmatically accessible framework for gene-disease evidence assessment, inheritance-aware interpretation, and systematic NDD research.

Two rounds of whole-genome duplication (2R-WGD) in the vertebrate lineage are thought to have driven gene diversification. Mammals have four genes encoding five nebulin superfamily proteins (LASP1, LASP2/NEBL, NEB, and NRAP) hypothesised to have arisen from invertebrate LASP via WGD. Here, we examined the evolutionary fate of the nebulin superfamily after an additional WGD, teleost-specific genome duplication (TGD). Genome and transcriptome analysis of zebrafish (Danio rerio) and medaka (Oryzias latipes), of which the complete genomes were recently determined, showed only lasp family genes retained duplicate copies. Zebrafish retained two LASP2/NEBL-derived ohnologs; one (LASP2L) had been misidentified as a nebulette gene in the Zebrafish Information Network (ZFIN) despite lacking nebulette-specific exons. Another (LASP2/NEBL) is newly identified in this study because it lies in a newly determined region of the latest genome assembly. Contrastingly, medaka retained two LASP1 ohnologs and one LASP2/NEBL. The duplicated lasp family proteins showed overlapping and specific tissue expression patterns. We confirmed all three zebrafish lasp proteins bound actin and co-localized with actin-rich structures when ectopically expressed in cultured fibroblasts. This supports that TGD-derived lasp duplicates underwent lineage-specific retention and expression divergence in teleosts whilst conserving core actin-binding properties.

In silico perturbation (ISP) enables virtual genetic screens, prioritizing candidate regulators before costly wet-lab experiments. However, applying foundation models requires programming expertise. Here, we present the ISP Platform, that automates ISP powered by Geneformer without code execution. The platform enables cross-species analyses by independently selecting input species and human or mouse Geneformer models. The platform also implements sequential multi-gene ISP, in which each perturbation chains from the cell state produced by the preceding step. Using induced pluripotent stem cell (iPSC) datasets, the platform successfully performed cross-species analysis of human and mouse single cell-RNA (scRNA)-seq data. Screening all 24 permutations of the Yamanaka factors identified an optimal overexpression sequence that produced the highest shift toward the pluripotent state. Genome-wide knockdown screens prioritized key pluripotency regulators but revealed an asymmetric cross-species concordance. The human model effectively captured mouse pluripotency programs, whereas applying the mouse model to human cells yielded predominantly translation-related terms. Furthermore, a targeted pairwise overexpression screen nominated candidate modulators of the primed-to-naive transition beyond the conventional NANOG and KLF2 benchmark. Together, the ISP Platform provides a unified, accessible framework for three dimensions of in silico perturbation (cross-species, sequential, and multi-gene) to guide focused experimental validation and reduce exploratory animal use.

Targeted gene panels (TGPs) dominate clinical sequencing, yet most copy-number (CN) signature studies rely on genome-wide assays. Whether signatures can be recovered from TGPs and retain clinical relevance remains unclear. We analyzed two real-world TGP cohorts comprising 1,726 patients across 62 tumor types, including 825 with clinical annotations, and made the underlying data publicly available. TGP-derived signatures recapitulated established biological associations, including links to homologous recombination deficiency and TP53 alterations, concordant with published genome-wide assay-derived CN signatures. Using our detailed clinical data, we found TGP-derived CN signatures associated with overall survival under standard therapies in ovarian, pancreatic, and colorectal cancer. In ovarian cancer, CN2 was associated with CCNE1 amplification and shorter survival under paclitaxel/carboplatin, with the survival association validated in an independent SNP-array cohort. These findings demonstrate that routine TGPs yield biologically and clinically relevant CN signatures with potential as biomarkers for therapy stratification.

Transcriptomic classification is often hindered by the small number of samples relative to the high dimensionality of gene expression data. We introduce General Gene Expression (GGE), a deep meta-learning framework designed to support robust classification in this limited-sample setting. By training across 5,220 distinct biomedical prediction objectives drawn from 1,779 different human datasets, GGE learns a model initialization that captures biological patterns shared across heterogeneous classification tasks. This learned initialization has two key advantages. First, it enables improved performance to new datasets using only a small number of labeled samples. Second, because it is learned across diverse prediction objectives, it can be applied to a broad range of biomedical problems. We show that GGE outperforms established classifiers in data-limited settings across a wide range of applications, including datasets generated using different RNA-seq platforms and preprocessing pipelines. In addition, attention-based analysis identifies recurrent genes that contribute to performance across multiple biological objectives, providing insight into shared determinants of human biological states. Together, these results establish GGE is a general-purpose framework for human transcriptome-based classification in biomedical settings where labeled data are scarce.

Predicting molecular receptor status, including estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2), directly from routine hematoxylin and eosin (H&E)-stained whole-slide images (WSIs) could reduce reliance on costly immunohistochemistry, but image-only models have no access to the transcriptomic programs that define these subtypes. Here we show that coupling a whole-slide vision transformer (GigaPath) with bulk RNA-sequencing profiles through a training-time-only contrastive objective improves receptor-status classification from WSIs alone, without requiring any RNA-seq data at inference. Rather than training a dedicated bulk-transcriptomics encoder, we purpose the gene-sentence encoding and pretrained text encoder from BioBERT1 and apply them to bulk RNA-seq profiles from The Cancer Genome Atlas breast cancer cohort (TCGA-BRCA). Under five-fold cross-validation, this RNA-guided pre-training consistently improved AUROC for ER, PR, and HER2 relative to a contrastive-pre-training-free baseline and reproducibly introduced receptor-relevant structure into the learned slide representation. However, evaluation on independent external cohorts revealed a striking, receptor-dependent divergence: gains for ER and PR, both governed by broad, multi-gene luminal transcriptional programs, generalized robustly, whereas the apparent AUROC improvement for HER2, driven by focal ERBB2 amplification rather than a coordinated transcriptional signature, masked a severe loss of classification sensitivity at the operating threshold. These findings establish training-time transcriptomic supervision as a practical route to enhancing histology-only molecular subtyping, while showing that gene-selection strategy, and not model architecture alone, determines which molecular alterations such supervision can teach a vision model to recognize.

Whether the homologous parallel triplex (HP-triplex, formed by dsDNA and a homologous ssDNA) acts as an intermediate prior to DNA recombination remains controversy, owing to the intrinsic instability and lake of experimental data. Here, we report a HP-triplex that is stable at least at 35 oC under protein-free conditions. Two complementary circular ssDNAs were first hybridized at a 1:1 ratio to form an LR-chimera containing both Z-DNA and B-DNA. Then the circular homologous ssDNA (T-rich) was found to easily hybridize with this LR-chimera to form the HP-triplex (strand ratio of 2:1), involving both left- and right-handed triplex parts under the topological constraint. The third strand locates in the major groove and forms hydrogen bonds with both bases in each base pair of dsDNA without obvious strand exchange. Our data indicate that the third-strand ssDNA may first bind to the B-DNA region, followed by association with the Z-DNA region to assemble the full triplex structure. Structural simulations and analyses reveal that topological constraint imposed by the circular architecture raises the energy barrier for strand displacement, thereby stabilizing this triplex. In summary, the dynamic HP triplex can be stabilized via a Z B junction structure that mimics the in vivo one formed by negative supercoiling. These findings demonstrate that HP-triplex may act as an intermediate for DNA recombination, anti-gene strategy, and other interactions between dsDNA and homologous ssDNA or RNA.

While single-cell RNA sequencing (scRNA-seq) is indispensable, existing analytical tools impose high computational barriers, requiring complex environment configurations and programming proficiency. To democratize single-cell analysis, we developed OmicsResonance, a code-free, web-based platform that eliminates local installations and empowers researchers to execute end-to-end analyses directly within a browser. The platform integrates standard processing pipelines and Large Language Model (LLM)-assisted cell annotation with a suite of advanced modules, including pseudo-time inference, CNV profiling, and virtual knockout simulations. Built on a scalable architecture, OmicsResonance champions "justified analysis" by avoiding black-box defaults. Its interactive interface allows users to dynamically adjust parameters and instantly visualize biological impacts, ensuring transparent and biologically sound analytical decisions. Validation across three public datasets successfully reproduced established findings and facilitated further interpretation of the data. Ultimately, OmicsResonance bridges the gap between complex computational pipelines and bench research, providing an accessible yet powerful environment for scRNA-seq data exploration. The platform is available at https://cloud.rnastar.com/.

Inverse design has advanced the discovery of molecules and materials. Yet it remains largely unexplored for steering cell fate, where inputs are continuous, combinatorial culture conditions and outputs are distributions of cell states. Human hematopoiesis, in which combinations and doses of growth factors steer stem cells toward each blood lineage, is a demanding test case. While forward models can evaluate discrete conditions, the vast combinatorial space renders searching for a specific, target-producing design an intractable inverse problem. Here, we introduce LabCompass, an inverse-modeling framework that optimizes experimental designs toward candidates expected to produce specified target cell states, using a flow-matching generative model guided by cellular phenotypes predicted by a forward surrogate. We applied LabCompass to primary human CD34+ in vitro cultures, where continuous cytokine and small-molecule parameters govern hematopoietic cell fate. In a lab-in-the-loop setting, we experimentally validated model-driven designs and used these measurements to update the model across four successive loops. LabCompass recovered established lineage-inducing designs, improved predictions with new data, and enriched target populations across lineages. Incorporating new parameters expanded the design space and enriched rare populations beyond initial reach. Across loops, we generated a 78-million-cell spectral flow cytometry dataset and identified distinct culture conditions converging on the same target cell states. Our results establish generative inverse modeling as a compelling paradigm for navigating high-dimensional, continuous experimental spaces, and demonstrate that virtual cell models should be judged not only by how accurately they predict cellular responses, but also by how effectively they guide experiments toward desired biological outcomes.