Journal of Genetics and Genomics最新文献_第10页

Paleolithic divergence and multiple Neolithic expansions of ancestral nomadic emperor-related paternal lineages. 古代游牧帝王父系的旧石器时代分化和新石器时代的多次扩张。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-11-27 DOI: 10.1016/j.jgg.2024.11.012

Mengge Wang, Qiuxia Sun, Yuhang Feng, Lan-Hai Wei, Kaijun Liu, Lintao Luo, Yuguo Huang, Kun Zhou, Haibing Yuan, Hongliang Lv, Yu Lu, Jing Cheng, Shaoqing Wen, Chuan-Chao Wang, Renkuan Tang, Fengxiao Bu, Chao Liu, Huijun Yuan, Zhiyong Wang, Guanglin He

{"title":"Paleolithic divergence and multiple Neolithic expansions of ancestral nomadic emperor-related paternal lineages.","authors":"Mengge Wang, Qiuxia Sun, Yuhang Feng, Lan-Hai Wei, Kaijun Liu, Lintao Luo, Yuguo Huang, Kun Zhou, Haibing Yuan, Hongliang Lv, Yu Lu, Jing Cheng, Shaoqing Wen, Chuan-Chao Wang, Renkuan Tang, Fengxiao Bu, Chao Liu, Huijun Yuan, Zhiyong Wang, Guanglin He","doi":"10.1016/j.jgg.2024.11.012","DOIUrl":"10.1016/j.jgg.2024.11.012","url":null,"abstract":"The reconstruction of demographic history using ancient and modern genomic resources reveals extensive interactions and admixture between ancient nomadic pastoralists and the social organizations of the Chinese Central Plain. However, the extent to which Y-chromosome genetic legacies from nomadic emperor-related ancestral lineages influence the Chinese paternal gene pool remains unclear. Here, we genotype 2717 ethnolinguistically diverse samples belonging to C2a lineages, perform whole-genome sequencing on 997 representative samples and integrate these data with ancient genomic sequences. We reconstruct the evolutionary histories of Northern Zhou-, Qing emperor-, and pastoralist-related lineages to assess their genetic impact on modern Chinese populations. This reassembled fine-scale Y-chromosome phylogeny identifies deep divergence and five Neolithic expansion events contributing differently to the formation of northern Chinese populations. Phylogeographic modeling indicates that the nomadic empires of the Northern Zhou and Qing dynasties genetically originated from the Mongolian Plateau. Phylogenetic topology and shared haplotype patterns show that three upstream ancestors of Northern Zhou (C2a1a1b1a2a1b-FGC28857), Donghu tribe (C2a1a1b1-F1756), and Qing (C2a1a3a2-F10283) emperor-related lineages expanded during the middle Neolithic, contributing significantly to genetic flow between ancient northeastern Asians and modern East Asians. Notably, this study reveals limited direct contributions of Emperor Wu of Northern Zhou's lineages to modern East Asians.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142752364","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

Znf706 regulates germ plasm assembly and primordial germ cell development in zebrafish. Znf706调控斑马鱼生殖质的组装和原始生殖细胞的发育。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-11-20 DOI: 10.1016/j.jgg.2024.11.007

Weiying Zhang, Yaqi Li, Han Li, Xin Liu, Tao Zheng, Guangyuan Li, Boqi Liu, Tong Lv, Zihang Wei, Cencan Xing, Shunji Jia, Anming Meng, Xiaotong Wu

{"title":"Znf706 regulates germ plasm assembly and primordial germ cell development in zebrafish.","authors":"Weiying Zhang, Yaqi Li, Han Li, Xin Liu, Tao Zheng, Guangyuan Li, Boqi Liu, Tong Lv, Zihang Wei, Cencan Xing, Shunji Jia, Anming Meng, Xiaotong Wu","doi":"10.1016/j.jgg.2024.11.007","DOIUrl":"10.1016/j.jgg.2024.11.007","url":null,"abstract":"The cell fate of primordial germ cells (PGCs) in zebrafish is pre-determined by maternally deposited germ plasm, which is packaged into ribonucleoprotein complex in oocytes and inherited into PGCs-fated cells in embryos. However, the maternal factors regulating the assembly of germ plasm and PGC development remain poorly understood. In this study, we report that the maternal transcription factor Znf706 regulates the assembly of germ plasm factors into a granule-like structure localized perinuclearly in PGCs during migration. Maternal and zygotic mutants of znf706 (MZznf706) exhibit deficient germ plasm scattering at the early embryonic stage, decreased PGC numbers with some mislocation during PGC migration, and a lower female ratio in adulthood. Notably, the implementation of Znf706 CUT&Tag and RNA-seq on immature oocytes uncovers that Znf706 in stage I oocytes may promote transcription of several mitochondrial genes in addition to other functions. Hence, we propose that Znf706 is implicated in germ plasm assembly and PGC development in zebrafish.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142689698","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 insights into the genetic diversity, lateral gaits and high-altitude adaptation of Chakouyi (CKY) horses. 从基因组学角度了解查古伊（CKY）马的遗传多样性、侧向步态和高海拔适应性。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-11-19 DOI: 10.1016/j.jgg.2024.11.008

Yang-Kai Liu, Wei-Wei Fu, Zhong-Yu Wang, Sheng-Wei Pei, Kai-Hui Li, Wei-Wei Wu, Meng-Zhen Le, Xiang-Peng Yue

{"title":"Genomic insights into the genetic diversity, lateral gaits and high-altitude adaptation of Chakouyi (CKY) horses.","authors":"Yang-Kai Liu, Wei-Wei Fu, Zhong-Yu Wang, Sheng-Wei Pei, Kai-Hui Li, Wei-Wei Wu, Meng-Zhen Le, Xiang-Peng Yue","doi":"10.1016/j.jgg.2024.11.008","DOIUrl":"10.1016/j.jgg.2024.11.008","url":null,"abstract":"Chakouyi (CKY) horses from the Qinghai‒Xizang Plateau are well known for their unique lateral gaits and high-altitude adaptation, but genetic mechanisms underlying these phenotypes remain unclear. This study presents a comparison of 60 newly resequenced genomes of gaited CKY horses with 139 public genomes from 19 horse breeds. Population structure analyses (admixture, PCA, and neighbor-joining tree) reveal a close genetic relationship between CKY and other highland breeds (Tibetan and Chaidamu horses). Compared with other Chinese breeds, CKY horses present reduced nucleotide diversity (θπ) and lower inbreeding (FROH coefficient), suggesting possible selective pressures. A key region on chromosome 23 (Chr23: 22.3 -22.6 Mb) is associated with the lateral gaits and harbors a highly prevalent nonsense mutation (Chr 23:22,391,254 C>A, Ser301STOP) in the DMRT3 gene, with an 88% homozygosity rate, which is strongly correlated with the distinctive gait of CKY horses. Furthermore, selection signals reveal that the EPAS1 gene is related to high-altitude adaptation, and the CAT gene contributes to altitude resilience in CKY horses. These findings suggest that preserving genetic diversity is essential for maintaining the unique gaits and high-altitude adaptations of CKY horses.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142689696","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

An LRR-RLK protein modulates drought- and salt-stress responses in maize. 一种 LRR-RLK 蛋白调节玉米的干旱和盐胁迫反应。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-11-13 DOI: 10.1016/j.jgg.2024.10.016

Zhirui Yang, Chen Wang, Tengfei Zhu, Jiafan He, Yijie Wang, Shiping Yang, Yu Liu, Bochen Zhao, Chaohui Zhu, Shuqing Ye, Limei Chen, Shengxue Liu, Feng Qin

{"title":"An LRR-RLK protein modulates drought- and salt-stress responses in maize.","authors":"Zhirui Yang, Chen Wang, Tengfei Zhu, Jiafan He, Yijie Wang, Shiping Yang, Yu Liu, Bochen Zhao, Chaohui Zhu, Shuqing Ye, Limei Chen, Shengxue Liu, Feng Qin","doi":"10.1016/j.jgg.2024.10.016","DOIUrl":"10.1016/j.jgg.2024.10.016","url":null,"abstract":"Maize (Zea mays), which is a vital source of food, feed, and energy feedstock globally, has significant potential for higher yields. However, environmental stress conditions, including drought and salt stress, severely restrict maize plant growth and development, leading to great yield losses. Leucine-rich repeat receptor-like kinases (LRR-RLKs) function in biotic and abiotic stress responses in the model plant Arabidopsis (Arabidopsis thaliana), but their roles in abiotic stress responses in maize are not entirely understood. In this study, we determine that the LRR-RLK ZmMIK2, a homolog of the Arabidopsis LRR-RK MALE DISCOVERER 1 (MDIS1)-INTERACTING RECEPTOR LIKE KINASE 2 (MIK2), functions in resistance to both drought and salt stress in maize. Zmmik2 plants exhibit enhanced resistance to both stresses, whereas overexpressing ZmMIK2 confers the opposite phenotypes. Furthermore, we identify C2-DOMAIN-CONTAINING PROTEIN 1 (ZmC2DP1), which interacts with the intracellular region of ZmMIK2. Notably, that region of ZmMIK2 mediates the phosphorylation of ZmC2DP1, likely by increasing its stability. Both ZmMIK2 and ZmC2DP1 are mainly expressed in roots. As with ZmMIK2, knockout of ZmC2DP1 enhanced resistance to both drought and salt stress. We conclude that ZmMIK2-ZmC2DP1 acts as a negative regulatory module in maize drought- and salt-stress responses.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640297","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

Tensor decomposition reveals trans-regulated gene modules in maize drought response. 张量分解揭示玉米干旱响应中的跨调控基因模块

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-11-08 DOI: 10.1016/j.jgg.2024.10.011

Jiawen Lu, Yuxin Xie, Chunhui Li, Jinliang Yang, Junjie Fu

{"title":"Tensor decomposition reveals trans-regulated gene modules in maize drought response.","authors":"Jiawen Lu, Yuxin Xie, Chunhui Li, Jinliang Yang, Junjie Fu","doi":"10.1016/j.jgg.2024.10.011","DOIUrl":"10.1016/j.jgg.2024.10.011","url":null,"abstract":"When plants respond to drought stress, dynamic cellular changes occur, accompanied by alterations in gene expression, which often act through trans-regulation. However, the detection of trans-acting genetic variants and networks of genes is challenged by the large number of genes and markers. Using a tensor decomposition method, we identify trans-acting expression quantitative trait loci (trans-eQTLs) linked to gene modules, rather than individual genes, which were associated with maize drought response. Module-to-trait association analysis demonstrates that half of the modules are relevant to drought-related traits. Genome-wide association studies of the expression patterns of each module identify 286 trans-eQTLs linked to drought-responsive modules, the majority of which cannot be detected based on individual gene expression. Notably, the trans-eQTLs located in the regions selected during maize improvement tend towards relatively strong selection. We further prioritize the genes that affect the transcriptional regulation of multiple genes in trans, as exemplified by two transcription factor genes. Our analyses highlight that multidimensional reduction could facilitate the identification of trans-acting variations in gene expression in response to dynamic environments and serve as a promising technique for high-order data processing in future crop breeding.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632883","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 dynamics of fungal genome organization and its impact on host adaptation and antifungal resistance. 真菌基因组组织的动态及其对宿主适应性和抗真菌性的影响。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-11-08 DOI: 10.1016/j.jgg.2024.10.010

Alex Z Zaccaron, Ioannis Stergiopoulos

{"title":"The dynamics of fungal genome organization and its impact on host adaptation and antifungal resistance.","authors":"Alex Z Zaccaron, Ioannis Stergiopoulos","doi":"10.1016/j.jgg.2024.10.010","DOIUrl":"10.1016/j.jgg.2024.10.010","url":null,"abstract":"Fungi are a diverse kingdom characterized by remarkable genomic plasticity that facilitates pathogenicity and adaptation to adverse environmental conditions. In this review, we delve into the dynamic organization of fungal genomes and its implications for host adaptation and antifungal resistance. We examine key features and the heterogeneity of genomes across different fungal species, including but not limited to their chromosome content, DNA composition, distribution and arrangement of their content across chromosomes, and other major traits. We further highlight how this variability in genomic traits influences their virulence and adaptation to adverse conditions. Fungal genomes exhibit large variations in size, gene content, and structural features, such as abundance of transposable elements (TEs), compartmentalization into gene-rich and TE-rich regions, and the presence or absence of dispensable chromosomes. Genomic structural variations are equally diverse in fungi, ranging from whole-chromosome duplications that may enhance tolerance to antifungal compounds, to targeted deletion of effector encoding genes that may promote virulence. Finally, the often-overlooked fungal mitochondrial genomes can also affect virulence and resistance to fungicides. Such and other features of fungal genome organization are reviewed and discussed in the context of host-microbe interactions and antifungal resistance.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632885","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 and molecular mechanisms underlying nitrogen use efficiency in maize. 玉米氮利用效率的遗传和分子机制。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-11-06 DOI: 10.1016/j.jgg.2024.10.007

Jianfang Li, Huairong Cao, Shuxin Li, Xiaonan Dong, Zheng Zhao, Zhongtao Jia, Lixing Yuan

{"title":"Genetic and molecular mechanisms underlying nitrogen use efficiency in maize.","authors":"Jianfang Li, Huairong Cao, Shuxin Li, Xiaonan Dong, Zheng Zhao, Zhongtao Jia, Lixing Yuan","doi":"10.1016/j.jgg.2024.10.007","DOIUrl":"10.1016/j.jgg.2024.10.007","url":null,"abstract":"Nitrogen (N) is vital for crop growth and yield, impacting food quality. However, excessive use of N fertilizers leads to high agricultural costs and environmental challenges. This review offers a thorough synthesis of the genetic and molecular regulation of N uptake, assimilation, and remobilization in maize, emphasizing the role of key genes and metabolic pathways in enhancing N use efficiency (NUE). We summarize the genetic regulators of N transports for nitrate (NO3-) and ammonium (NH4+) that contribute to efficient N uptake and transportation. We further discuss the molecular mechanisms by which root system development adapts to N distribution and how N influences root system development and growth. Given the advancements in high-throughput microbiome studies, we delve into the impact of rhizosphere microorganisms on NUE and the complex plant-microbe interactions that regulate maize NUE. Additionally, we conclude with intricate regulatory mechanisms of N assimilation and remobilization in maize, involving key enzymes, transcription factors, and amino acid transporters. We also scrutinize the known N signaling perception and transduction mechanisms in maize. This review underscores the challenges in improving maize NUE and advocates for an integrative research approach that leverages genetic diversity and synthetic biology, paving the way for sustainable agriculture.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632867","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

CCDC181 is required for proper spermiogenesis in mice. 小鼠精子正常生成需要 CCDC181。

IF 5.3 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-11-01 Epub Date: 2024-07-15 DOI: 10.1016/j.jgg.2024.07.010

Xirui Zi, Qingchao Li, Yue Lu, Qian Lyu, Heng Guo, Xiaoqian Meng, Jun Zhou, Huijie Zhao

引用次数: 0

A human-specific cytotoxic neopeptide generated by the deafness gene Cingulin. 由耳聋基因 Cingulin 生成的人类特异性细胞毒性新肽。

IF 5.3 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-11-01 Epub Date: 2024-08-05 DOI: 10.1016/j.jgg.2024.07.017

Yuhang Huang, Linqing Zhang, Yuecen Sun, Qing Liu, Jie Chen, Xiaoyun Qian, Xia Gao, Guang-Jie Zhu, Guoqiang Wan

{"title":"A human-specific cytotoxic neopeptide generated by the deafness gene Cingulin.","authors":"Yuhang Huang, Linqing Zhang, Yuecen Sun, Qing Liu, Jie Chen, Xiaoyun Qian, Xia Gao, Guang-Jie Zhu, Guoqiang Wan","doi":"10.1016/j.jgg.2024.07.017","DOIUrl":"10.1016/j.jgg.2024.07.017","url":null,"abstract":"Accumulation of mutant proteins in cells can induce proteinopathies and cause functional damage to organs. Recently, the Cingulin (CGN) protein has been shown to maintain the morphology of cuticular plates of inner ear hair cells and a frameshift mutation in CGN causes autosomal dominant non-syndromic hearing loss. Here, we find that the mutant CGN proteins form insoluble aggregates which accumulate intracellularly and lead to cell death. Expression of the mutant CGN in the inner ear results in severe hair cell death and hearing loss in mice, resembling the auditory phenotype in human patients. Interestingly, a human-specific residue (V1112) in the neopeptide generated by the frameshift mutation is critical for the aggregation and cytotoxicity of the mutant human CGN. Moreover, the expression of heat shock factor 1 (HSF1) decreases the accumulation of insoluble mutant CGN aggregates and rescues cell death. In summary, these findings identify mutant-specific toxic polypeptides as a disease-causing mechanism of the deafness mutation in CGN, which can be targeted by the expression of the cell chaperone response regulator HSF1.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"1215-1227"},"PeriodicalIF":5.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141891031","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

Overexpression of CRYPTOCHROME 2 enhances shoot growth and wood formation in poplar under growth-restrictive short days. 在生长受限的短日照条件下，过量表达 CRYPTOCHROME 2 可促进杨树的嫩枝生长和木材形成。

IF 5.3 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-11-01 Epub Date: 2024-08-20 DOI: 10.1016/j.jgg.2024.08.003

Hongbin Wei, Fan Sun, Jianghai Mo, Bingrui Hu, Keming Luo

引用次数: 0