Article
Biochemistry & Molecular Biology
Du Jiao, Xiaorui Dong, Yingyan Yu, Chaochun Wei
Summary: The study revealed that the coronavirus family has 181 genes, with only 3 being highly conserved. The SARS-CoV-2 pan-genome consists of 13 core genes, showing a lower level of diversity compared to other RNA viruses. The three highly conserved genes in the coronavirus family and the core genes in the SARS-CoV-2 pan-genome could be potential targets for developing nucleic acid diagnostic reagents with reduced mutation potential.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Bruno Contreras-Moreira, Shradha Saraf, Guy Naamati, Ana M. Casas, Sandeep S. Amberkar, Paul Flicek, Andrew R. Jones, Sarah Dyer
Summary: This study proposes a crop pangenome approach using individual cultivar assemblies to access conserved genes more easily. However, the variability in genome content and inconsistent identifiers have hindered exploration. To overcome these challenges, the concept of pangenes is introduced to summarize a species coding potential and link back to original annotations. The protocol get_pangenes utilizes whole genome alignments to identify syntenic gene models based on coordinate overlaps. Benchmark tests with both small and large plant genomes demonstrate that pangenes accurately recapitulate phylogeny-based orthologies and generate complete soft-core gene sets.
Article
Biochemical Research Methods
Qihua Liang, Stefano Lonardi
Summary: PGV is a reference-agnostic representation of a species' pan-genome based on consensus ordering, enabling intuitive, effective, and interactive visualization of complex structural genomic variations. The PGV software can be easily installed via conda or downloaded from the website, with a companion browser available for testing using example bed tracks from the GitHub page.
BMC BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Hangling Bie, Yong Li, Yalin Zhao, Weichao Fang, Changwen Chen, Xinwei Wang, Jinlong Wu, Lirong Wang, Ke Cao
Summary: Gene presence/absence variation (PAV) plays an important role in genetic diversity, gene identification, and molecular marker development in plants. This study used genome resequencing of 100 peach accessions to identify PAVs and found 923 novel genes. The dispensable PAVs were enriched in resistance and selection sweeps related to peach domestication and improvement were identified. PAV identification was further validated through a genome-wide association study and a novel gene involved in chilling requirements was identified.
Article
Medicine, Research & Experimental
Laura M. Tsujikawa, Olesya A. Kharenko, Stephanie C. Stotz, Brooke D. Rakai, Christopher D. Sarsons, Dean Gilham, Sylwia Wasiak, Li Fu, Michael Sweeney, Jan O. Johansson, Norman C. W. Wong, Ewelina Kulikowski
Summary: The study reveals a new role for BET protein BRD4 in maintaining higher order chromatin structure at TADBs, highlighting the differential impact of BET inhibitors on TADB stability.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Biotechnology & Applied Microbiology
Rachel M. Colquhoun, Michael B. Hall, Leandro Lima, Leah W. Roberts, Kerri M. Malone, Martin Hunt, Brice Letcher, Jane Hawkey, Sophie George, Louise Pankhurst, Zamin Iqbal
Summary: Pandora is a novel pan-genome graph structure and algorithm that can identify variants across the full bacterial pan-genome, providing a stable framework for analyzing diverse samples without reference bias.
Article
Plant Sciences
Yang Sun, Jing Wang, Yan Li, Bin Jiang, Xu Wang, Wen-Hui Xu, Yu-Qing Wang, Pei-Tao Zhang, Yong-Jun Zhang, Xiang-Dong Kong
Summary: In this study, a melon pan-genome was constructed, revealing abundant genetic variations among different melon groups and identifying genes associated with fruit traits. In addition, novel gene sequences and genes were discovered.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Microbiology
Jiandong Bao, Zhe Wang, Meilian Chen, Shijie Chen, Xiaomin Chen, Jiahui Xie, Wei Tang, Huakun Zheng, Zonghua Wang
Summary: The study constructed a pan-genome database of Pyricularia oryzae based on genome data from NCBI, and revealed the population structure of the rice blast fungus. The pan-genome will provide a comprehensive reference for further research on Pyricularia oryzae.
Article
Cell Biology
Rachel A. Hoffman, Heather K. MacAlpine, David M. MacAlpine
Summary: This study provides insights into helicase activation within origin chromatin and its regulation in the absence of DNA replication. Activation of the helicase disrupts and disorganizes chromatin, extending up to 1 kb from early replication origins. The local sequence context plays a role in regulating helicase progression when uncoupled from replication.
GENES & DEVELOPMENT
(2021)
Article
Multidisciplinary Sciences
Lijin K. Gopi, Benjamin L. Kidder
Summary: An integrative analysis of 60 human cancer epigenomes identified activating and repressive histone modifications, chromatin state features, and correlations with genetic mutations, DNA methylation, and gene activity. These findings highlight the importance of integrating epigenomic maps with gene expression and genetic variation data to understand the molecular basis of human cancer.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Dan Wang, Liu Yang, Chao Ning, Jian-Feng Liu, Xingbo Zhao
Summary: This study compared the accuracy of mitogenome alignment and SNP calling using three different types of reference sequences for mitochondrial DNA analyses. The results showed that breed-specific reference sequences were optimal for mitogenome analyses, providing a refined processing perspective for NGS data.
Article
Biochemistry & Molecular Biology
Rong Zhou, Shang-Tong Li, Wen-Ye Yao, Chun-Di Xie, Zhiqiang Chen, Zhi-Jie Zeng, Di Wang, Kui Xu, Zhao-Ji Shen, Yulian Mu, Wenbin Bao, Wenkai Jiang, Ruiqiang Li, Qiqi Liang, Kui Li
Summary: This study assembled a high-quality genome for the Asian Meishan breed using a hybrid approach, revealing numerous structural variations between Asian and European pig breeds; Asian pig breeds share a common ancestor and possess a specific gene hotspot; Transcriptomics showed the transcriptional suppression roles of these variant genes in multiple tissues.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Genetics & Heredity
Eliza Thulson, Eric S. Davis, Susan D'Costa, Philip R. Coryell, Nicole E. Kramer, Karen L. Mohlke, Richard F. Loeser, Brian O. Diekman, Douglas H. Phanstiel
Summary: This study used a multiomic approach and genome editing to identify and characterize potential osteoarthritis risk genes. The researchers found that the SOCS2 gene plays a role in resolving inflammation in response to cartilage matrix damage, providing a possible mechanistic explanation for its influence on osteoarthritis risk. A total of 56 unique putative osteoarthritis risk genes were identified for further research and potential therapeutic development.
Review
Biochemistry & Molecular Biology
Yi Chi, Jenny Shi, Dong Xing, Longzhi Tan
Summary: The three-dimensional structure of chromosomes has significant effects on biological processes, and single-cell Hi-C has emerged as a new method to reveal the actual 3D structure of individual genomes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Genetics & Heredity
Zhenping Chen, Xuepeng Chen
Summary: The 3D chromatin structure plays a crucial role in gene expression regulation and embryonic development. Recent advancements in low-input chromatin conformation capture technologies have allowed for the study of 3D chromatin structures in gametes, zygotes, and early embryos in various species. The reorganization of 3D chromatin structure during embryogenesis shows both conserved and divergent patterns across different species, with distinct molecular mechanisms. These findings contribute to our understanding of the contribution of 3D chromatin structure reorganization to embryonic development and its role in acquiring totipotent developmental potential.
Article
Biochemistry & Molecular Biology
Anning Li, Qimeng Yang, Ran Li, Xuelei Dai, Keli Cai, Yinghu Lei, Kangsheng Jia, Yu Jiang, Linsen Zan
Summary: This study constructed the first reference genome of the takin and provided valuable information on its taxonomic status, genetic diversity, and evolution. The takin was found to be more closely related to muskox, showed low genetic diversity, and displayed severe inbreeding depression. The effective population size of takins has significantly declined over the past 100,000 years.
Article
Agriculture, Dairy & Animal Science
Xiaoshu Xue, Honghong Hu, Junxing Zhang, Yanfen Ma, Liyun Han, Feng Hao, Yu Jiang, Yun Ma
Summary: Genetic parameters are crucial for understanding the relationship between conformation traits and milk production traits in Chinese Holstein dairy cows. The study found positive genetic correlations between most conformation traits and milk production traits, indicating that selecting certain traits can improve the performance of dairy cows. The heritability of conformation traits ranged from medium to high, and the heritability of milk production traits varied as well.
Article
Zoology
Hojjat Asadollahpour Nanaei, Yudong Cai, Akil Alshawi, Jiayue Wen, Tanveer Hussain, Wei-Wei Fu, Nai-Yi Xu, Abdulameer Essa, Johannes A. Lenstra, Xihong Wang, Yu Jiang
Summary: Understanding the genetic background and history of goat populations in Southwest Asia, this study analyzed whole-genome sequencing data from native goat populations in Iraq and Pakistan, combined with data from modern, ancient, and wild Capra species worldwide. The results showed that gene flow from the eastern Mediterranean during the Chalcolithic period deeply influenced the genetic structure of Southwest Asian goats, reflecting adaptation to gradual warming and aridity in the region. Additionally, the study revealed adaptive introgression of a genetic locus from the Nubian ibex into African and Southwest Asian goats.
ZOOLOGICAL RESEARCH
(2023)
Article
Agriculture, Dairy & Animal Science
Huanhuan Zhang, Yilin Liang, Shaomei Chen, Zeyi Xuan, Yu Jiang, Ran Li, Yanhong Cao
Summary: Despite progress in generating high-quality reference genome assemblies, gene annotation for most livestock species, including goats, is still inadequate. Full-length transcriptome data obtained through single-molecule long-read sequencing greatly improves gene annotation. In this study, full-length transcriptome data from the abomasum and testicle were generated using PacBio Iso-Seq technology, and the goat genome annotation was evaluated and improved. Novel genes were identified, and their low expression levels were found to contribute to missed annotations in the current genome annotation. This study highlights the importance of full-length transcriptome data in improving gene annotation for the goat genome and other species.
Article
Biochemistry & Molecular Biology
Xiaokai Li, Zhining Zhong, Ruowei Zhang, Jiaman Zhang, Yu Zhang, Sha Zeng, Qinjiao Du, Haoming Wang, Songling Zhang, Lu Lu, Mingzhou Li, Keren Long
Summary: In this study, a muscular dystrophy mouse model was created by Ptrf knockout, and single-nucleus RNA sequencing was used to investigate the transcriptional changes in skeletal muscle. The study revealed significant alterations in the transcriptome of different types of muscle fibers and mononuclear cells in response to muscular dystrophy, providing valuable insights into the molecular mechanisms of muscular dystrophy.
Article
Multidisciplinary Sciences
Long Jin, Danyang Wang, Jiaman Zhang, Pengliang Liu, Yujie Wang, Yu Lin, Can Liu, Ziyin Han, Keren Long, Diyan Li, Yu Jiang, Guisen Li, Yu Zhang, Jingyi Bai, Xiaokai Li, Jing Li, Lu Lu, Fanli Kong, Xun Wang, Hua Li, Zhiqing Huang, Jideng Ma, Xiaolan Fan, Linyuan Shen, Li Zhu, Yanzhi Jiang, Guoqing Tang, Bin Feng, Bo Zeng, Liangpeng Ge, Xuewei Li, Qianzi Tang, Zhihua Zhang, Mingzhou Li
Summary: Using a pig model, the study investigates how chromatin architecture in adipose tissue is regulated in relation to obesity. Analysis of the data reveals similarities and differences in chromatin architecture between humans and pigs, providing valuable insights into the regulation of obesity-related genes.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Yujie Wang, Xun Wang, Yi Luo, Jiaman Zhang, Yu Lin, Jie Wu, Bo Zeng, Lei Liu, Peiqi Yan, Jiyuan Liang, Hongrui Guo, Long Jin, Qianzi Tang, Keren Long, Mingzhou Li
Summary: This study generated a de novo pigeon genome assembly and conducted a high resolution spatio-temporal transcriptomic analysis of the crop epithelium in pigeons. The study identified "lactation"-related genes involved in lipid and protein metabolism and revealed extensive reorganization of promoter-enhancer interactions linked to the expression of these genes. The spatial localization of gene expression in specific epithelial layers was correlated with phenotypic changes in the crop.
Article
Biology
Qin Zou, Rong Yuan, Yu Zhang, Yifei Wang, Ting Zheng, Rui Shi, Mei Zhang, Yujing Li, Kaixin Fei, Ran Feng, Binyun Pan, Xinyue Zhang, Zhengyin Gong, Li Zhu, Guoqing Tang, Mingzhou Li, Xuewei Li, Yanzhi Jiang
Summary: Studying cellular specialization in different anatomical regions of pig skin can enhance our understanding of skin information and provide insights for human skin research.
Article
Geriatrics & Gerontology
Linyuan Shen, Tianci Liao, Qiuyang Chen, Yuhang Lei, Linghui Wang, Hao Gu, Yanhao Qiu, Ting Zheng, Yiting Yang, Chenggang Wei, Lei Chen, Ye Zhao, Lili Niu, Shunhua Zhang, Yan Zhu, Mingzhou Li, Jinyong Wang, Xuewei Li, Mailin Gan, Li Zhu
Summary: This study explores the role of tRNA-derived small RNAs (tsRNAs), specifically 5'tiRNA-Gly, in skeletal muscle regeneration. It is found that 5'tiRNA-Gly is significantly up-regulated after muscle injury and promotes inflammation through the TGF-beta signaling pathway. These findings provide a new potential target for skeletal muscle regeneration treatment.
JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE
(2023)
Article
Multidisciplinary Sciences
Mingle Dou, Ming Li, Zhuqing Zheng, Qiuming Chen, Yongji Wu, Jinxin Wang, Huiquan Shan, Fei Wang, Xuelei Dai, Yunjia Li, Zhirui Yang, Guanghui Tan, Funong Luo, Lei Chen, Yun Stone Shi, Jiang Wei Wu, Xiong-Jian Luo, Hojjat Asadollahpour Nanaei, Zhannur Niyazbekova, Guojie Zhang, Wen Wang, Shanting Zhao, Wenxin Zheng, Xihong Wang, Yu Jiang
Summary: The study suggests that reducing avoidance of humans in wild animals is a key step in domestication, which is primarily determined by genetic factors. However, the specific genetic mutations and their influence on animal behavior are still unclear. Behavioral tests on a wild-domestic hybrid goat population indicate that the region under strongest artificial selection during domestication may have a significant effect on flight distance. Within this region, only one missense mutation RRM1(I241V) was found in early domesticated goats approximately 6500 years ago. Genome editing of RRM1(I241V) in mice showed increased tameness, sociability, and reduced anxiety. These behavioral changes induced by RRM1(I241V) were modulated by alterations in glutamatergic synapse activity and other synapse-related pathways. This study establishes a link between RRM1(I241V) and tameness, demonstrating that complex behavioral changes can be achieved through mutations under strong selection during animal domestication.
Article
Biochemistry & Molecular Biology
Jingyi Bai, Yu Lin, Jiaman Zhang, Ziyu Chen, Yujie Wang, Mingzhou Li, Jing Li
Summary: The study used ATAC-seq and rRNA-depleted RNA-seq to analyze the chromatin accessibility and transcriptional features in multiple tissues of newborn pigs and during porcine liver development. The researchers obtained a comprehensive annotation of consensus ATAC-seq peaks for each tissue and developmental stage, and found that tissue-specific accessible promoters were associated with active transcription and tissue-specific functions. Additionally, they observed a close association between dynamic chromatin accessibility and hepatic function transition during liver postnatal development. This study expands our understanding of epigenetic regulation in mammalian tissues and organ development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jing Yang, Xingxing Zhu, Rui Wang, Mingzhou Li, Qianzi Tang
Summary: In this study, we comprehensively evaluated the performance of 24 popular state-of-the-art methods for complete end-to-end Hi-C data analysis using manually curated or experimentally validated benchmark datasets. Our results indicate that HiC-Pro, DomainCaller, and Fit-Hi-C2 showed relatively balanced performances in different aspects, providing a reference for researchers to choose suitable Hi-C analysis tools.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Simeng Yu, Zihua Liu, Ming Li, Dongke Zhou, Ping Hua, Hong Cheng, Wenlei Fan, Yaxi Xu, Dapeng Liu, Suyun Liang, Yunsheng Zhang, Ming Xie, Jing Tang, Yu Jiang, Shuisheng Hou, Zhengkui Zhou
Summary: Through artificial selection on Beijing ducks, we identified 53 selected regions associated with muscle weight improvement. Two genes, UTP25 and FBRSL1, were found to be most likely contributing to the increase in muscle weight. We also identified a copy number variation region involving the EXOC4 gene, which explains 1.9% of the variance in muscle weight. This study provides insights into the genomic dynamics under artificial selection and resources for genomics-enabled improvements in duck breeding.
Letter
Biotechnology & Applied Microbiology
Timothy P. L. Smith, Derek M. Bickhart, Didier Boichard, Amanda J. Chamberlain, Appolinaire Djikeng, Yu Jiang, Wai Y. Low, Hubert Pausch, Sebastian Demyda-Peyras, James Prendergast, Robert D. Schnabel, Benjamin D. Rosen
Summary: The Bovine Pangenome Consortium (BPC) aims to assemble cattle genomes to create a comprehensive representation of cattle genomic diversity. Their goal is to provide genome assemblies and a community-approved pangenome reference as a public resource to replace breed-specific reference genomes. The BPC invites partners to participate in this collaborative effort and contribute to the development of this community-driven resource. It will serve as a foundation for cattle genomic selection and enable comparison across studies.
Article
Agriculture, Dairy & Animal Science
Chunna Cao, Yuxin Kang, Qian Zhou, Hojjat Asadollahpour Nanaei, Didi Bo, Peiyao Liu, Yangyang Bai, Ran Li, Yu Jiang, Xianyong Lan, Chuanying Pan
Summary: This study identified candidate genes associated with the unique grey color and environmental adaptation in Romanov sheep through whole-genome sequencing. Understanding the genetic background and signatures of Romanov sheep is of great value for its conservation and utilization.
JOURNAL OF ANIMAL SCIENCE
(2023)