Journal of Genetics and Genomics最新文献_第7页

Enhancing crop yields to ensure food security by optimizing photosynthesis. 通过优化光合作用，提高作物产量，保障粮食安全。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-10 DOI: 10.1016/j.jgg.2025.01.002

Chunrong Li, Xuejia Du, Cuimin Liu

{"title":"Enhancing crop yields to ensure food security by optimizing photosynthesis.","authors":"Chunrong Li, Xuejia Du, Cuimin Liu","doi":"10.1016/j.jgg.2025.01.002","DOIUrl":"https://doi.org/10.1016/j.jgg.2025.01.002","url":null,"abstract":"The crop yields achieved through traditional plant breeding techniques appear to be nearing a plateau. Therefore, it is essential to accelerate advancements in photosynthesis, the fundamental process by which plants convert light energy into chemical energy, to further enhance crop yields. Research focused on improving photosynthesis holds significant promise for increasing sustainable agricultural productivity and addressing challenges related to global food security. This review examines the latest advancements and strategies aimed at boosting crop yields by enhancing photosynthetic efficiency. There has been a linear increase in yield over the years in historically released germplasm selected through traditional breeding methods, and this increase is accompanied by improved photosynthesis. We explore various aspects of the light reactions designed to enhance crop yield, including light harvest efficiency through smart canopy systems, expanding the absorbed light spectrum to include far-red light, optimizing non-photochemical quenching, and accelerating electron transport flux. At the same time, we investigate carbon reactions that can enhance crop yield, such as manipulating Rubisco activity, improving the Calvin-Benson-Bassham (CBB) cycle, introducing CO2 concentrating mechanisms (CCMs) in C3 plants, and optimizing carbon allocation. These strategies could significantly impact crop yield enhancement and help bridge the yield gap.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic characterization reveals distinct mutational landscape of acral melanoma in East Asian. 基因组特征揭示了东亚肢端黑色素瘤不同的突变景观。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-09 DOI: 10.1016/j.jgg.2024.12.018

Fenghao Zhang, Xiaowen Wu, Tao Jiao, Haizhen Dua, Qian Guo, Chuanliang Cui, Zhihong Chi, Xinan Sheng, Dezhi Jiang, Yuhong Zhang, Jiayan Wu, Yan Kong, Lu Si

{"title":"Genomic characterization reveals distinct mutational landscape of acral melanoma in East Asian.","authors":"Fenghao Zhang, Xiaowen Wu, Tao Jiao, Haizhen Dua, Qian Guo, Chuanliang Cui, Zhihong Chi, Xinan Sheng, Dezhi Jiang, Yuhong Zhang, Jiayan Wu, Yan Kong, Lu Si","doi":"10.1016/j.jgg.2024.12.018","DOIUrl":"10.1016/j.jgg.2024.12.018","url":null,"abstract":"Acral melanoma, the most common melanoma subtype in East Asia, is associated with a poor prognosis. This study aims to comprehensively analyze the genomic characteristics of acral melanoma in East Asians. We conduct whole-genome sequencing of 55 acral melanoma tumors and perform data mining with relevant clinical data. Our findings reveal a unique mutational profile in East Asian acral melanoma, characterized by fewer point mutations and structural variations, a higher prevalence of NRAS mutations, and a lower frequency of BRAF mutations compared to patients of European descent. Notably, we identify previously underestimated ultraviolet radiation signatures and their significant association with BRAF and NRAS mutations. Structural rearrangement signatures indicate distinct mutational processes in BRAF-driven versus NRAS-driven tumors. We also find that homologous recombination deficiency with MAPK pathway mutations correlated with poor prognosis. The structural variations and amplifications in EP300, TERT, RAC1, and LZTR1 point to potential novel therapeutic targets tailored to East Asian populations. The high prevalence of whole-genome duplication events in BRAF/NRAS-mutated tumors suggests a synergistic carcinogenic effect that warrants further investigation. In summary, our study provides important insights into the genetic underpinnings of acral melanoma in East Asians, creating opportunities for targeted therapies.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Deciphering the influence of gut and oral microbiomes on menopause for healthy aging. 解读肠道和口腔微生物群对更年期的影响，促进健康老龄化。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-09 DOI: 10.1016/j.jgg.2024.11.010

Shuting Yu, Feiling Huang, Yixuan Huang, Fangxu Yan, Yi Li, Shenglong Xu, Yan Zhao, Xinlei Zhang, Rong Chen, Xingming Chen, Peng Zhang

{"title":"Deciphering the influence of gut and oral microbiomes on menopause for healthy aging.","authors":"Shuting Yu, Feiling Huang, Yixuan Huang, Fangxu Yan, Yi Li, Shenglong Xu, Yan Zhao, Xinlei Zhang, Rong Chen, Xingming Chen, Peng Zhang","doi":"10.1016/j.jgg.2024.11.010","DOIUrl":"10.1016/j.jgg.2024.11.010","url":null,"abstract":"Menopause is characterized by the cessation of menstruation and a decline in reproductive function, which is an intrinsic component of the aging process. However, it has been a frequently overlooked field of women's health. The oral and gut microbiota, constituting the largest ecosystem within the human body, are important for maintaining human health and notably contribute to the healthy aging of menopausal women. Therefore, a comprehensive review elucidating the impact of the gut and oral microbiota on menopause for healthy aging is of paramount importance. This paper presents the current understanding of the microbiome during menopause, with a particular focus on alterations in the oral and gut microbiota. Our study elucidates the complex interplay between the microbiome and sex hormone levels, explores microbial crosstalk dynamics, and investigates the associations between the microbiome and diseases linked to menopause. Additionally, this review explores the potential of microbiome-targeting therapies for managing menopause-related diseases. Given that menopause can last for approximately 30 years, gaining insights into how the microbiome and menopause interact could pave the way for innovative interventions, which may result in symptomatic relief from menopause and an increase in quality of life in women.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genetic interaction network of quantitative trait genes for heading date in rice. 水稻抽穗期数量性状基因的遗传互作网络。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-06 DOI: 10.1016/j.jgg.2024.12.019

Mengjiao Chen, Yifeng Hong, Jiongjiong Fan, Dengyi Cao, Chong Yin, Anjie Yu, Jie Qiu, Xuehui Huang, Xin Wei

{"title":"Genetic interaction network of quantitative trait genes for heading date in rice.","authors":"Mengjiao Chen, Yifeng Hong, Jiongjiong Fan, Dengyi Cao, Chong Yin, Anjie Yu, Jie Qiu, Xuehui Huang, Xin Wei","doi":"10.1016/j.jgg.2024.12.019","DOIUrl":"10.1016/j.jgg.2024.12.019","url":null,"abstract":"Several quantitative trait genes (QTGs) related to rice heading date, a key factor for crop development and yield, have been identified, along with complex interactions among genes. However, a comprehensive genetic interaction network for these QTGs has not yet been established. In this study, we use 18K-rice lines to identify QTGs and their epistatic interactions affecting rice heading date. We identify 264 pairs of interacting QTL and construct a comprehensive genetic network of these QTL. On average, the epistatic effects of QTL pairs are estimated to be approximately 12.5% of additive effects of identified QTL. Importantly, epistasis vary among different alleles of several heading date genes. Additionally, 57 pairs of interacting QTGs are also significant in their epistatic effects on 12 other agronomic traits. The identified QTL genetic interactions are further validated using near-isogenic lines, yeast two-hybrid, and split-luciferase complementation assays. Overall, this study provides a genetic network of rice heading date genes, which plays a crucial role in regulating rice heading date and influencing multiple related agronomic traits. This network serves as a foundation for understanding the genetic mechanisms of rice quantitative traits and for advancing rice molecular breeding.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142958986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Vitamin D receptor regulates methyltransferase like 14 to mitigate colitis-associated colorectal cancer. 维生素D受体调节甲基转移酶如14以减轻结肠炎相关结直肠癌。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-06 DOI: 10.1016/j.jgg.2024.12.020

Zheng Wang, Lingjuan Jiang, Xiaoyin Bai, Mingyue Guo, Runing Zhou, Qingyang Zhou, Hong Yang, Jiaming Qian

{"title":"Vitamin D receptor regulates methyltransferase like 14 to mitigate colitis-associated colorectal cancer.","authors":"Zheng Wang, Lingjuan Jiang, Xiaoyin Bai, Mingyue Guo, Runing Zhou, Qingyang Zhou, Hong Yang, Jiaming Qian","doi":"10.1016/j.jgg.2024.12.020","DOIUrl":"https://doi.org/10.1016/j.jgg.2024.12.020","url":null,"abstract":"Colitis-associated colorectal cancer (CAC), a serious complication of ulcerative colitis (UC), is associated with a poor prognosis. The vitamin D receptor (VDR) is recognized for its protective role in UC and CAC through the maintenance of intestinal barrier integrity and the regulation of inflammation. This study demonstrates a significant reduction in m6A-related genes, particularly methyltransferase like 14 (METTL14), in UC and CAC patients and identifies an association between METTL14 and VDR. In the azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced mouse model, vitamin D treatment increases METTL14 expression and reduces tumor burden, while Vdr-knockout mice exhibit lower METTL14 levels and increased tumorigenesis. In vitro, the VDR agonist calcipotriol upregulates METTL14 in NCM460 cells, with this effect attenuated by VDR knockdown. VDR knockdown in DLD-1 colon cancer cells decreases METTL14 expression and promotes proliferation, which is reversed by METTL14 overexpression. Mechanistic studies reveal that VDR regulates METTL14 expression via promoter binding, modulating key target genes such as SOX4, DROSH, and PHLPP2. This study highlights the role of the VDR-METTL14 axis as a protective mechanism in CAC and suggests its potential as a therapeutic target for preventing and treating CAC.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Improving precision base editing of the zebrafish genome by Rad51DBD-incorporated single-base editors. 通过 Rad51DBD 导入单碱基编辑器改进斑马鱼基因组的精确碱基编辑。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-01 Epub Date: 2024-10-18 DOI: 10.1016/j.jgg.2024.10.006

Zhilin Zhong, Xueli Hu, Renjie Zhang, Xu Liu, Wenqi Chen, Shubin Zhang, Jianjian Sun, Tao P Zhong

{"title":"Improving precision base editing of the zebrafish genome by Rad51DBD-incorporated single-base editors.","authors":"Zhilin Zhong, Xueli Hu, Renjie Zhang, Xu Liu, Wenqi Chen, Shubin Zhang, Jianjian Sun, Tao P Zhong","doi":"10.1016/j.jgg.2024.10.006","DOIUrl":"10.1016/j.jgg.2024.10.006","url":null,"abstract":"Single-base editors, including cytosine base editors (CBEs) and adenine base editors (ABEs), facilitate accurate C⋅G to T⋅A and A⋅T to G⋅C, respectively, holding promise for the precise modeling and treatment of human hereditary disorders. Efficient base editing and expanded base conversion range have been achieved in human cells through base editors fusing with Rad51 DNA binding domain (Rad51DBD), such as hyA3A-BE4max. Here, we show that hyA3A-BE4max catalyzes C-to-T substitution in the zebrafish genome and extends editing positions (C12-C16) proximal to the protospacer adjacent motif. We develop a codon-optimized counterpart zhyA3A-CBE5, which exhibits substantially high C-to-T conversion with 1.59- to 3.50-fold improvement compared with the original hyA3A-BE4max. With these tools, disease-relevant hereditary mutations can be more efficaciously generated in zebrafish. We introduce human genetic mutation rpl11Q42∗ and abcc6aR1463C by zhyA3A-CBE5 in zebrafish, mirroring Diamond-Blackfan anemia and Pseudoxanthoma Elasticum, respectively. Our study expands the base editing platform targeting the zebrafish genomic landscape and the application of single-base editors for disease modeling and gene function study.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"105-115"},"PeriodicalIF":6.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481280","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Pan-genome analyses add ∼1000 genes to the "complete" genome assembly of chicken. 泛基因组分析为鸡的 "完整 "基因组组装增加了 1000 个基因。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-01 Epub Date: 2024-11-05 DOI: 10.1016/j.jgg.2024.10.009

Jilong Ren, Wenyan Kou, Yuan Xu, Meixuan Lu, Mian Gong, Xinmiao Zhang, Zhenyu Liu, Hengkuan Li, Qimeng Yang, Ali Mujtaba Shah, Feng Zhu, Zhuocheng Hou, Naiyi Xu, Yu Jiang, Fei Wang

引用次数: 0

SpaGRA: Graph augmentation facilitates domain identification for spatially resolved transcriptomics. SpaGRA：图增强技术有助于空间解析转录组学的领域识别。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-01 Epub Date: 2024-10-02 DOI: 10.1016/j.jgg.2024.09.015

Xue Sun, Wei Zhang, Wenrui Li, Na Yu, Daoliang Zhang, Qi Zou, Qiongye Dong, Xianglin Zhang, Zhiping Liu, Zhiyuan Yuan, Rui Gao

{"title":"SpaGRA: Graph augmentation facilitates domain identification for spatially resolved transcriptomics.","authors":"Xue Sun, Wei Zhang, Wenrui Li, Na Yu, Daoliang Zhang, Qi Zou, Qiongye Dong, Xianglin Zhang, Zhiping Liu, Zhiyuan Yuan, Rui Gao","doi":"10.1016/j.jgg.2024.09.015","DOIUrl":"10.1016/j.jgg.2024.09.015","url":null,"abstract":"Recent advances in spatially resolved transcriptomics (SRT) have provided new opportunities for characterizing spatial structures of various tissues. Graph-based geometric deep learning has gained widespread adoption for spatial domain identification tasks. Currently, most methods define adjacency relation between cells or spots by their spatial distance in SRT data, which overlooks key biological interactions like gene expression similarities, and leads to inaccuracies in spatial domain identification. To tackle this challenge, we propose a novel method, SpaGRA (https://github.com/sunxue-yy/SpaGRA), for automatic multi-relationship construction based on graph augmentation. SpaGRA uses spatial distance as prior knowledge and dynamically adjusts edge weights with multi-head graph attention networks (GATs). This helps SpaGRA to uncover diverse node relationships and enhance message passing in geometric contrastive learning. Additionally, SpaGRA uses these multi-view relationships to construct negative samples, addressing sampling bias posed by random selection. Experimental results show that SpaGRA presents superior domain identification performance on multiple datasets generated from different protocols. Using SpaGRA, we analyze the functional regions in the mouse hypothalamus, identify key genes related to heart development in mouse embryos, and observe cancer-associated fibroblasts enveloping cancer cells in the latest Visium HD data. Overall, SpaGRA can effectively characterize spatial structures across diverse SRT datasets.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"93-104"},"PeriodicalIF":6.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The interplay between extracellular and intracellular auxin signaling in plants. 植物中细胞外和细胞间叶绿素信号的相互作用

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-01 Epub Date: 2024-07-03 DOI: 10.1016/j.jgg.2024.06.019

Wenxin Tang, Yongqiang Yu, Tongda Xu

引用次数: 0

Ancestral genome reconstruction and the evolution of chromosomal rearrangements in Triticeae. 麦属植物祖先基因组重建与染色体重排进化。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-01 DOI: 10.1016/j.jgg.2024.12.017

Xueqing Yan, Runxian Yu, Jinpeng Wang, Yuannian Jiao

{"title":"Ancestral genome reconstruction and the evolution of chromosomal rearrangements in Triticeae.","authors":"Xueqing Yan, Runxian Yu, Jinpeng Wang, Yuannian Jiao","doi":"10.1016/j.jgg.2024.12.017","DOIUrl":"10.1016/j.jgg.2024.12.017","url":null,"abstract":"Chromosomal rearrangements (CRs) often cause phenotypic variations. Although several major rearrangements have been identified in Triticeae, a comprehensive study of the order, timing, and breakpoints of CRs has not been conducted. Here, we reconstruct high-quality ancestral genomes for the most recent common ancestor (MRCA) of the Triticeae, and the MRCA of the wheat lineage (Triticum and Aegilops). The protogenes of MRCA of the Triticeae and the wheat lineage are 22,894 and 29,060, respectively, which were arranged in their ancestral order. By partitioning modern Triticeae chromosomes into sets of syntenic regions and linking each to the corresponding protochromosomes, we revisit the rye chromosome structural evolution and propose alternative evolutionary routes. The previously identified 4L/5L reciprocal translocation in rye and Triticum urartu are found to have occurred independently and are unlikely the result of chromosomal introgression following distant hybridization. We also clarify that the 4AL/7BS translocation in tetraploid wheat was a bidirectional rather than unidirectional translocation event. Lastly, we identify several breakpoints in protochromosomes that independently reoccur following Triticeae evolution, representing potential CR hotspots. This study demonstrates that these reconstructed ancestral genomes can serve as special comparative references and facilitate a better understanding of the evolution of structural rearrangements in Triticeae.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142924040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0