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Genes, Volume 17, Issue 6 (June 2026) – 3 articles

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14 pages, 2788 KB  
Article
Overexpression of PeBBM2 and PeWUS Genes via Carbon Nanotube-Based DNA Delivery Enhances the Callus and Shoot Formation in Phyllostachys edulis
by Yiqian Ding, Ruotong Xu, Chao Xu, Xiaohong Zhou and Mingbing Zhou
Genes 2026, 17(6), 598; https://doi.org/10.3390/genes17060598 (registering DOI) - 22 May 2026
Abstract
Background/Objectives: Phyllostachys edulis is the most widely distributed and economically important bamboo species in China. However, the genetic transformation in P. edulis is still limited by a long regeneration cycle and low regeneration and transformation efficiency. Carbon nanotube-based delivery systems in plants [...] Read more.
Background/Objectives: Phyllostachys edulis is the most widely distributed and economically important bamboo species in China. However, the genetic transformation in P. edulis is still limited by a long regeneration cycle and low regeneration and transformation efficiency. Carbon nanotube-based delivery systems in plants have the advantages of simplicity, rapidity and low cost. Moreover, morphogenetic regulators BBM (BABY BOOM) and WUS (WUSCHEL) play significant roles in plant regeneration. Methods: Here, immature zygotic embryos were used to induce P. edulis callus, and using single-walled carbon nanotubes (SWNTs)-based delivery technology, PeBBM2, PeWUS-DNA (with introns) and PeWUS-cDNA (without introns) were introduced to P. edulis callus either individually or in combination. Conclusions: The results showed that the 0.9–1.0 mm (long axis) embryos exhibited the lowest contamination rate and the highest induction efficiency. Moreover, the results indicated that the co-transformation of PeBBM2-PeWUS more effectively boosted the growth area of the callus. However, only the PeBBM2-overexpression callus could form shoots. Compared with the wild type, the PeBBM2-overexpression lines showed reduced expression of AGL15 and increased expression of IAA30 and YUC. In conclusion, these findings suggested that SWNTs-mediated DNA delivery is a potential strategy for the genetic transformation of P. edulis callus. Additionally, the findings indicate‌ that the PeBBM2 and PeWUS genes can accelerate callus enlargement in P. edulis, whereas PeBBM2 might play a more important role in shoot formation. This study provides a basis for developing a genetic transformation system for plants based on SWNTs-mediated DNA delivery and morphogenetic regulators. Full article
(This article belongs to the Section Plant Genetics and Genomics)
19 pages, 8178 KB  
Article
PANA-Surv: A Pathway-Guided Adaptive Neighborhood Augmentation Framework Using KEGG Pathways for Multi-Omics Cancer Prognosis
by Xiaowen Cao, Yijin Zhou, Yao Dong, Xuekui Zhang, Jia-peng Mei, Jianwei Li, Yixiao Wang, Jiaming Zhuo, Hua He and Junhua Gu
Genes 2026, 17(6), 597; https://doi.org/10.3390/genes17060597 - 22 May 2026
Abstract
Background/Objectives: Integrating multi-omics data for cancer prognosis remains a challenging problem in bioinformatics because molecular profiles are high-dimensional, heterogeneous, and structured by incomplete biological relationships. Pathway databases provide biologically meaningful prior knowledge for modeling gene-level associations, but the sparsity and local incompleteness [...] Read more.
Background/Objectives: Integrating multi-omics data for cancer prognosis remains a challenging problem in bioinformatics because molecular profiles are high-dimensional, heterogeneous, and structured by incomplete biological relationships. Pathway databases provide biologically meaningful prior knowledge for modeling gene-level associations, but the sparsity and local incompleteness of pathway-derived networks often limit the performance of graph-based survival models. This study aimed to develop a pathway-guided framework for improving multi-omics survival prediction and identifying biologically relevant prognostic signals. Methods: We proposed PANA-Surv, a pathway-guided adaptive neighborhood augmentation framework for multi-omics cancer survival analysis. In this framework, KEGG pathways were used to construct gene graphs, and gene-level multi-omics profiles were encoded as node features. A conditional variational autoencoder module (PANA-VAE) was designed to enhance local representations through neighborhood reconstruction and adaptive weighting. The augmented features were then integrated into a graph convolutional survival model optimized with the Cox partial likelihood. Results: PANA-Surv was evaluated on 10 cancer cohorts from The Cancer Genome Atlas (TCGA). The proposed method achieved the highest mean concordance index (C-index) among all compared models and significantly outperformed Cox-EN, DeepSurv, GraphSurv, and LAGProg (all p < 0.01). Ablation analyses showed that both neighborhood reconstruction and adaptive weighting contributed to the observed performance gains, and KEGG-guided graph construction was more effective than alternative graph construction strategies. In a breast cancer (BRCA) case study, PANA-Surv identified 18 prognostic genes, including 12 genes supported by previous studies and 6 potentially novel candidates. Conclusions: These findings indicate that the integration of pathway prior knowledge with adaptive local feature enhancement can improve multi-omics survival modeling and support the identification of biologically relevant prognostic signals associated with cancer outcomes. Full article
(This article belongs to the Topic Multi-Omics in Precision Medicine)
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19 pages, 2073 KB  
Article
A Chromosome-Level Genome Assembly and Annotation of the Chinese Porcupine (Hystrix hodgsoni) Reveals the Expansion of Olfactory-Related Gene Families
by Nannan Chen, Jianxuan Zhou, Xinjie Liu, Meidong Jing, Libo Jiang and Fengtang Yang
Genes 2026, 17(6), 596; https://doi.org/10.3390/genes17060596 - 22 May 2026
Abstract
Background/Objectives: The Chinese porcupine (Hystrix hodgsoni) is a distinctive rodent species characterized by specialized ecological adaptations and sensory traits; however, genomic resources for this species have remained limited. This study aims to provide a reliable reference for comparative and evolutionary analyses [...] Read more.
Background/Objectives: The Chinese porcupine (Hystrix hodgsoni) is a distinctive rodent species characterized by specialized ecological adaptations and sensory traits; however, genomic resources for this species have remained limited. This study aims to provide a reliable reference for comparative and evolutionary analyses by constructing a high-quality genome. Methods: We generated a chromosome-level genome assembly of the Chinese porcupine using long-read sequencing combined with chromatin conformation-based scaffolding, followed by comprehensive structural and functional annotation. Comparative genomic analyses across representative mammals and functional enrichment analyses were conducted to investigate lineage-specific gene family dynamics. Results: The assembled genome shows high contiguity and completeness. Comparative analyses revealed a substantial number of gene families significantly expanded along the porcupine lineage. Functional enrichment demonstrated strong overrepresentation of olfactory-related processes, including olfactory receptor activity, odorant binding, and detection of chemical stimuli. Additionally, several expanded families were associated with epidermal differentiation, keratinization, and skin development. Conclusions: Gene family expansions in the Chinese porcupine are biased toward sensory perception and epidermal functions, suggesting potential genetic bases for its enhanced environmental sensing and integumentary specialization. This assembly provides an important genomic resource for porcupine research and new insights into the molecular mechanisms underlying sensory and skin-related adaptations in rodents. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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