Journal of Genetics and Genomics最新文献_第4页

Structural variation-based and gene-based pangenome construction reveals untapped diversity of hexaploid wheat. 基于结构变异和基因的全基因组构建揭示了六倍体小麦未开发的多样性。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-06-01 Epub Date: 2025-04-04 DOI: 10.1016/j.jgg.2025.03.015

Hong Cheng, Lingpeng Kong, Kun Zhu, Hang Zhao, Xiuli Li, Yanwen Zhang, Weidong Ning, Mei Jiang, Bo Song, Shifeng Cheng

{"title":"Structural variation-based and gene-based pangenome construction reveals untapped diversity of hexaploid wheat.","authors":"Hong Cheng, Lingpeng Kong, Kun Zhu, Hang Zhao, Xiuli Li, Yanwen Zhang, Weidong Ning, Mei Jiang, Bo Song, Shifeng Cheng","doi":"10.1016/j.jgg.2025.03.015","DOIUrl":"10.1016/j.jgg.2025.03.015","url":null,"abstract":"Increasing number of structural variations (SVs) have been identified as causative mutations for diverse agronomic traits. However, the systematic exploration of SVs quantity, distribution, and contribution in wheat was lacking. Here, we report high-quality gene-based and SV-based pangenomes comprising 22 hexaploid wheat assemblies showing a wide range of chromosome size, gene number, and TE component, which indicates their representativeness of wheat genetic diversity. Pan-gene analyses uncover 140,261 distinct gene families, of which only 23.2 % are shared in all accessions. Moreover, we build a ∼16.15 Gb graph pangenome containing 695,897 bubbles, intersecting 5132 genes and 230,307 cis-regulatory regions. Pairwise genome comparisons identify ∼1,978,221 non-redundant SVs and 497 SV hotspots. Notably, the density of bubbles as well as SVs show remarkable aggregation in centromeres, which probably play an important role in chromosome plasticity and stability. As for functional SVs exploration, we identify 2769 SVs with absolute relative frequency differences exceeding 0.7 between spring and winter growth habit groups. Additionally, several reported functional genes in wheat display complex structural graphs, for example, PPD-A1, VRT-A2, and TaNAAT2-A. These findings deepen our understanding of wheat genetic diversity, providing valuable graphical pangenome and variation resources to improve the efficiency of genome-wide association mapping in wheat.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"774-785"},"PeriodicalIF":6.6,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143797166","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

Unravelling sorghum functional genomics and molecular breeding: past achievements and future prospects. 揭示高粱功能基因组学和分子育种：过去的成就和未来的前景。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-06-01 Epub Date: 2024-07-23 DOI: 10.1016/j.jgg.2024.07.016

Fangyuan Liu, Baye Wodajo, Kangxu Zhao, Sanyuan Tang, Qi Xie, Peng Xie

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 : 2025-06-01 Epub 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 is found to have occurred independently and is unlikely to be 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":"761-773"},"PeriodicalIF":6.6,"publicationDate":"2025-06-01","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

Frequent polyploidization events in Hibiscus shaped its karyotype and species diversity. 木槿频繁的多倍体化事件塑造了其核型和物种多样性。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-06-01 Epub Date: 2024-05-25 DOI: 10.1016/j.jgg.2024.05.006

Cheng-Ao Yang, Shuai-Ya Hu, Jing Ge, Haibin Wang, Yue Wang, Chunsun Gu, Jia-Yu Xue

引用次数: 0

Multi-view BLUP: a promising solution for post-omics data integrative prediction. 多视图BLUP：一个有前途的后组学数据整合预测解决方案。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-06-01 Epub Date: 2024-12-05 DOI: 10.1016/j.jgg.2024.11.017

Bingjie Wu, Huijuan Xiong, Lin Zhuo, Yingjie Xiao, Jianbing Yan, Wenyu Yang

引用次数: 0

Genome-wide profiling of polymorphic short tandem repeats and their influence on gene expression and trait variation in diverse rice populations. 水稻多态短串联重复序列的全基因组分析及其对不同群体基因表达和性状变异的影响

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-06-01 Epub Date: 2025-03-14 DOI: 10.1016/j.jgg.2025.03.005

Xiyu Tan, Wanyong Zeng, Yujian Yang, Zhansheng Lin, Fuquan Li, Jianhong Liu, Shaotong Chen, Yao-Guang Liu, Weibo Xie, Xianrong Xie

{"title":"Genome-wide profiling of polymorphic short tandem repeats and their influence on gene expression and trait variation in diverse rice populations.","authors":"Xiyu Tan, Wanyong Zeng, Yujian Yang, Zhansheng Lin, Fuquan Li, Jianhong Liu, Shaotong Chen, Yao-Guang Liu, Weibo Xie, Xianrong Xie","doi":"10.1016/j.jgg.2025.03.005","DOIUrl":"10.1016/j.jgg.2025.03.005","url":null,"abstract":"Short tandem repeats (STRs) modulate gene expression and contribute to trait variation. However, a systematic evaluation of the genomic characteristics of STRs has not been conducted, and their influence on gene expression in rice remains unclear. Here, we construct a map of 137,629 polymorphic STRs in the rice (Oryza sativa L.) genome using a population-scale resequencing dataset. A genome-wide survey encompassing 4726 accessions shows that the occurrence frequency, mutational patterns, chromosomal distribution, and functional properties of STRs are correlated with the sequences and lengths of repeat motifs. Leveraging a transcriptome dataset from 127 rice accessions, we identify 44,672 expression STRs (eSTRs) by modeling gene expression in response to the length variation of STRs. These eSTRs are notably enriched in the regulatory regions of genes with active transcriptional signatures. Population analysis identifies numerous STRs that have undergone genetic divergence among different rice groups and 1726 tagged STRs that may be associated with agronomic traits. By editing the (ACT)7 STR in OsFD1 promoter, we further experimentally validate its role in regulating gene expression and phenotype. Our study highlights the contribution of STRs to transcriptional regulation in plants and establishes the foundation for their potential use as alternative targets for genetic improvement.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"733-746"},"PeriodicalIF":6.6,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143634072","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

Gap-free genome assembly and metabolomics analysis of common bean provide insights into genomic characteristics and metabolic determinants of seed coat pigmentation. 普通豆无间隙基因组组装和代谢组学分析提供了对种皮色素沉着的基因组特征和代谢决定因素的见解。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-06-01 Epub Date: 2025-03-08 DOI: 10.1016/j.jgg.2025.03.002

Bo Zhao, Hui Zhang, Qin Zhao, Rina Wu, Qian You, Bihui Wang, Yiming Wang, Zhilan Yan, Peng Wang, Chunguo Huang, Wei Zhang, Youmei Wang, Xiaopeng Hao, Jing Wu, Lixiang Wang, Zhaosheng Kong

引用次数: 0

Deep learning on chromatin profiles reveals the cis-regulatory sequence code of the rice genome. 深度学习染色质谱揭示了水稻基因组的顺式调控序列代码。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-06-01 Epub Date: 2024-12-18 DOI: 10.1016/j.jgg.2024.12.007

Xinkai Zhou, Zhonghao Ruan, Chenlu Zhang, Kerstin Kaufmann, Dijun Chen

引用次数: 0

Phenotypic advantages and improved genomic stability following selection in advanced selfing-generations of Brassica allohexaploids. 等位六倍体高级自交代选择后的表型优势和改进的基因组稳定性。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-06-01 Epub Date: 2025-03-14 DOI: 10.1016/j.jgg.2025.03.004

Yan Niu, Rui Yang, Zelong Li, Zhengxuan Huo, Shihao Chang, Entang Tian, Han Qin, Wallace A Cowling, Kadambot H M Siddique, Annaliese S Mason, Sheng Chen, Jun Zou

{"title":"Phenotypic advantages and improved genomic stability following selection in advanced selfing-generations of Brassica allohexaploids.","authors":"Yan Niu, Rui Yang, Zelong Li, Zhengxuan Huo, Shihao Chang, Entang Tian, Han Qin, Wallace A Cowling, Kadambot H M Siddique, Annaliese S Mason, Sheng Chen, Jun Zou","doi":"10.1016/j.jgg.2025.03.004","DOIUrl":"10.1016/j.jgg.2025.03.004","url":null,"abstract":"Allopolyploids often exhibit advantages in vigor and adaptability compared to diploids. A long-term goal in the economically important Brassica genus has been to develop a new allohexaploid crop type (AABBCC) by combining different diploid and allotetraploid crop species. However, early-generation allohexaploids often face challenges like unstable meiosis and low fertility, and the phenotypic performance of these synthetic lines has rarely been assessed. This study analyzes agronomic traits, fertility, and genome stability in ArArBcBcCcCc lines derived from four crosses between B. carinata and B. rapa after 9-11 selfing generations. Our results demonstrate polyploid advantage in vigor and seed traits, considerable phenotypic variation, and high fertility and genome stability. Meanwhile, parental genotypes significantly influence outcomes in advanced allohexaploids. Structural variants, largely resulting from A-C homoeologous exchanges, contribute to genomic variation and influence hexaploid genome stability, with the A sub-genome showing the highest variability. Both positive and negative impacts of SVs on fertility and seed weight are observed. Pseudo-euploids, frequently appearing, do not significantly affect fertility or other agronomic traits compared to euploids, indicating a potential pathway toward a stable allohexaploid species. These findings provide insights into the challenge and potential for developing an adaptable and stable Brassica hexaploid through selection.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"799-811"},"PeriodicalIF":6.6,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143639896","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

Single-cell transcriptome analysis revealed critical causative candidates for down syndrome-related lung diseases. 单细胞转录组分析揭示了唐氏综合征相关肺部疾病的关键致病候选者。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-05-30 DOI: 10.1016/j.jgg.2025.05.009

Chunchun Zhi, Xucong Shi, Siqi Chen, Zhaowei Cai, Xiaoling Jiang

{"title":"Single-cell transcriptome analysis revealed critical causative candidates for down syndrome-related lung diseases.","authors":"Chunchun Zhi, Xucong Shi, Siqi Chen, Zhaowei Cai, Xiaoling Jiang","doi":"10.1016/j.jgg.2025.05.009","DOIUrl":"10.1016/j.jgg.2025.05.009","url":null,"abstract":"Down syndrome (DS) is caused by an extra copy of chromosome 21 (Hsa21). Children with DS have an increased frequency of respiratory tract infections, impaired alveolar and vascular development, and pulmonary hypertension. How trisomy 21 causes lung diseases remains poorly understood. In this study, we use the Dp16 mouse model, which contains a segmental chromosomal duplication of the entire Hsa21 syntenic region on mouse chromosome 16, to explore the gene dosage effects on DS-related lung diseases. The Dp16 mice present impaired alveolar development and inflammatory-like pathological changes. Single-cell transcriptome (scRNA-seq) analysis highlights increased APP-related interactions among male Dp16 lung cells. Specifically, altered antigen processing and presentation with increased MHC-II signaling are found in Dp16 immune cells. Reduced angiogenesis and altered inflammatory responses of Dp16 endothelial cells are also suggested. Moreover, scRNA-seq indicates hyperplasia of Dp16 vascular smooth muscle cells, which is validated by tissue immunofluorescence assessment. Transthoracic echocardiography further shows the existence of pulmonary hypertension in young Dp16 mice. Independent scRNA-seq analysis of the female lung cells recapitulates the majority of key findings identified in male mice, confirming the reproducibility of the results. Collectively, our results provide important clues for the further development of therapeutic approaches for DS-related lung diseases.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144200832","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