iMeta最新文献

{"title":"Gut <i>Bifidobacterium pseudocatenulatum</i> protects against fat deposition by enhancing secondary bile acid biosynthesis.","authors":"Andong Zha, Ming Qi, Yuankun Deng, Hao Li, Nan Wang, Chengming Wang, Simeng Liao, Dan Wan, Xia Xiong, Peng Liao, Jing Wang, Yulong Yin, Bi'e Tan","doi":"10.1002/imt2.261","DOIUrl":"10.1002/imt2.261","url":null,"abstract":"<p><p>Gut microbiome is crucial for lipid metabolism in humans and animals. However, how specific gut microbiota and their associated metabolites impact fat deposition remains unclear. In this study, we demonstrated that the colonic microbiome of lean and obese pigs differentially contributes to fat deposition, as evidenced by colonic microbiota transplantation experiments. Notably, the higher abundance of <i>Bifidobacterium pseudocatenulatum</i> was significantly associated with lower backfat thickness in lean pigs. Microbial-derived lithocholic acid (LCA) species were also significantly enriched in lean pigs and positively correlated with the abundance of <i>B. pseudocatenulatum</i>. In a high-fat diet (HFD)-fed mice model, administration of live <i>B. pseudocatenulatum</i> decreased fat deposition and enhances colonic secondary bile acid biosynthesis. Importantly, pharmacological inhibition of the bile salt hydrolase (BSH), which mediates secondary bile acid biosynthesis, impaired the anti-fat deposition effect of <i>B. pseudocatenulatum</i> in antibiotic-pretreated, HFD-fed mice. Furthermore, dietary LCA also decreased fat deposition in HFD-fed rats and obese pig models. These findings provide mechanistic insights into the anti-fat deposition role of <i>B. pseudocatenulatum</i> and identify BSH as a potential target for preventing excessive fat deposition in humans and animals.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":"e261"},"PeriodicalIF":23.7,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683477/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pangenome and genome variation analyses of pigs unveil genomic facets for their adaptation and agronomic characteristics.","authors":"Dong Li, Yulong Wang, Tiantian Yuan, Minghao Cao, Yulin He, Lin Zhang, Xiang Li, Yifan Jiang, Ke Li, Jingchun Sun, Guangquan Lv, Guosheng Su, Qishan Wang, Yuchun Pan, Xinjian Li, Yu Jiang, Gongshe Yang, Martien A M Groenen, Martijn F L Derks, Rongrong Ding, Xiangdong Ding, Taiyong Yu","doi":"10.1002/imt2.257","DOIUrl":"10.1002/imt2.257","url":null,"abstract":"<p><p>The development of a comprehensive pig graph pangenome assembly encompassing 27 genomes represents the most extensive collection of pig genomic data to date. Analysis of this pangenome reveals the critical role of structural variations in driving adaptation and defining breed-specific traits. Notably, the study identifies <i>BTF3</i> as a key candidate gene governing intramuscular fat deposition and meat quality in pigs. These findings underscore the power of pangenome approaches in uncovering novel genomic features underlying economically important agricultural traits. Collectively, these results demonstrate the value of leveraging large-scale, multi-genome analyses for advancing our understanding of livestock genomes and accelerating genetic improvement.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":"e257"},"PeriodicalIF":23.7,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive lung microbial gene and genome catalogs assist the mechanism survey of <i>Mesomycoplasma hyopneumoniae</i> strains causing pig lung lesions.","authors":"Jingquan Li, Fei Huang, Yunyan Zhou, Tao Huang, Xinkai Tong, Mingpeng Zhang, Jiaqi Chen, Zhou Zhang, Huipeng Du, Zifeng Liu, Meng Zhou, Yiwen Xiahou, Huashui Ai, Congying Chen, Lusheng Huang","doi":"10.1002/imt2.258","DOIUrl":"10.1002/imt2.258","url":null,"abstract":"<p><p>Understanding the community structure of the lower respiratory tract microbiome is crucial for elucidating its roles in respiratory tract diseases. However, there are few studies about this topic due to the difficulty in obtaining microbial samples from both healthy and disease individuals. Here, using 744 high-depth metagenomic sequencing data of lower respiratory tract microbial samples from 675 well-phenotyped pigs, we constructed a lung microbial gene catalog containing the largest scale of 10,031,593 nonredundant genes to date, 44.8% of which are novel. We obtained 356 metagenome-assembled genomes (MAGs) which were further clustered into 256 species-level genome bins with 41.8% being first reported in the current databases. Based on these data sets and through integrated analysis of the isolation of the related bacterial strains, in vitro infection, and RNA sequencing, we identified and confirmed that <i>Mesomycoplasma hyopneumoniae</i> (<i>M. hyopneumoniae</i>) MAG_47 and its adhesion-related virulence factors (VFs) were associated with lung lesions in pigs. Differential expression levels of adhesion- and immunomodulation-related VFs likely determined the heterogenicity of adhesion and pathogenicity among <i>M. hyopneumoniae</i> strains. <i>M. hyopneumoniae</i> adhesion activated several pathways, including nuclear factor kappa-light-chain-enhancer of activated B, mitogen-activated protein kinase, cell apoptosis, T helper 1 and T helper 2 cell differentiation, tumor necrosis factor signaling, interleukin-6/janus kinase 2/signal transducer and activator of transcription signaling, and response to reactive oxygen species, leading to cilium loss, epithelial cell‒cell barrier disruption, and lung tissue lesions. Finally, we observed the similar phylogenetic compositions of the lung microbiome between humans with <i>Mycoplasma pneumoniae</i> and pigs infected with <i>M. hyopneumoniae</i>. The results provided important insights into pig lower respiratory tract microbiome and its relationship with lung health.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":"e258"},"PeriodicalIF":23.7,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling the diversity dynamics and network stability of alkaline phosphomonoesterase-producing bacteria in modulating maize yield.","authors":"Lijun Chen, Guofan Zhu, Alberto Pascual-Garcia, Francisco Dini-Andreote, Jie Zheng, Xiaoyue Wang, Shungui Zhou, Yuji Jiang","doi":"10.1002/imt2.260","DOIUrl":"10.1002/imt2.260","url":null,"abstract":"<p><p>Phosphorus, as a nonrenewable resource, plays a crucial role in crop development and productivity. However, the extent to which straw amendments contribute to the dynamics of soil alkaline phosphomonoesterase (ALP)-producing bacterial community and functionality over an extended period remains elusive. Here, we conducted a 7-year long-term field experiment consisting of a no-fertilizer control, a chemical fertilizer treatment, and three straw (straw, straw combined with manure, and straw biochar) treatments. Our results indicated that straw amendments significantly improved the succession patterns of the ALP-producing bacterial diversity. Simultaneously, straw amendments significantly increased the network stability of the ALP-producing bacteria over time, as evidenced by higher network robustness, a higher ratio of negative to positive cohesion, and lower network vulnerability. High dynamic and stability of ALP-producing bacterial community generated high ALP activity which further increased soil Phosphorus (P) availability as well as maize productivity.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":"e260"},"PeriodicalIF":23.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683463/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome-wide association identifies <i>KLC1</i> as a regulator of mitophagy in non-syndromic cleft lip with or without palate.","authors":"Shu Lou, Guirong Zhu, Changyue Xing, Shushu Hao, Junyan Lin, Jiayi Xu, Dandan Li, Yifei Du, Congbo Mi, Lian Sun, Lin Wang, Meilin Wang, Mulong Du, Yongchu Pan","doi":"10.1002/imt2.262","DOIUrl":"10.1002/imt2.262","url":null,"abstract":"<p><p>This study investigated pathogenic genes associated with non-syndromic cleft lip with or without cleft palate (NSCL/P) through transcriptome-wide association studies (TWAS). By integrating expression quantitative trait loci (eQTL) data with genome-wide association study (GWAS) data, we identified key susceptibility genes, including <i>KLC1</i>. Notably, the variant rs12884809 G>A was associated with an increased risk of NSCL/P by enhancing the binding of the transcription factor ELK1 to the <i>KLC1</i> promoter, thereby activating its expression. This alteration in <i>KLC1</i> expression subsequently impacted mitophagy, leading to significant changes in cellular behavior and zebrafish morphology. Our findings illuminate the genetic mechanisms underlying NSCL/P and provide valuable insights for future prevention strategies and a deeper understanding of this condition.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":"e262"},"PeriodicalIF":23.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683466/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Short-term probiotic supplementation affects the diversity, genetics, growth, and interactions of the native gut microbiome.","authors":"Xin Shen, Hao Jin, Feiyan Zhao, Lai-Yu Kwok, Zhixin Zhao, Zhihong Sun","doi":"10.1002/imt2.253","DOIUrl":"10.1002/imt2.253","url":null,"abstract":"<p><p>The precise mechanisms through which probiotics interact with and reshape the native gut microbiota, especially at the species and genetic levels, remain underexplored. This study employed a high-dose probiotic regimen of <i>Bifidobacterium animalis</i> subsp. <i>lactis</i> [200 billion colony forming units (CFU)/day] over 7 days among healthy participants. Weekly fecal samples were collected for metagenomic sequencing analysis. We found that probiotic intake can significantly enhance the diversity of the gut microbiome and impact single nucleotide variations, growth rates, and network interactions of the resident intestinal bacteria. These adaptive changes in the gut microbiota indicate the swift evolutionary responses of native bacteria to the ecological disturbance presented by probiotic supplementation. Notably, the microbial community appears to undergo rapid and multifaceted ecological adjustments, potentially preceding longer-term evolutionary changes. This knowledge lays the groundwork for further exploration into the mechanisms underlying probiotic-mediated modulation of the gut microbiome, highlighting the necessity of encompassing ecological and evolutionary perspectives in the design and optimization of probiotic applications.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":"e253"},"PeriodicalIF":23.7,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683461/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The long-term intake of milk fat does not significantly increase the blood lipid burden in normal and high-fat diet-fed mice.","authors":"Guang-Xu Ren, Liang He, Yong-Xin Liu, Yu-Ke Fei, Xiao-Fan Liu, Qiu-Yi Lu, Xin Chen, Zhi-Da Song, Jia-Qi Wang","doi":"10.1002/imt2.256","DOIUrl":"10.1002/imt2.256","url":null,"abstract":"<p><p>After 10 weeks of feeding C57BL/6J mice with a normal diet (ND) or a high-fat diet (HFD), a 7-week intervention with milk fat and whole milk was conducted to assess their long-term effects on host blood lipid levels. The results showed that milk fat and whole milk did not significantly elevate low-density lipoprotein cholesterol (LDL-C) in either ND- or HFD-fed mice. In ND mice, milk fat and whole milk improved gut microbiota diversity and Amplicon Sequence Variants. Key bacterial genera, such as <i>Blautia</i>, <i>Romboutsia</i>, and <i>Prevotellaceae_NK3B31_group</i>, were identified as bidirectional regulators of LDL-C and high-density lipoprotein cholesterol (HDL-C). Six unique metabolites were also linked to LDL-C and HDL-C regulation. Furthermore, an optimized machine learning model accurately predicted LDL-C (<i>R</i>² = 0.96) and HDL-C (<i>R</i>² = 0.89) based on gut microbiota data, with 80% of the top predictive features being gut metabolites influenced by milk fat and whole milk. These findings indicate that the long-term intake of milk fat does not significantly increase the blood lipid burden, and machine learning algorithms based on gut microbiota and metabolites offer novel insights for early lipid assessment and personalized nutrition strategies.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":"e256"},"PeriodicalIF":23.7,"publicationDate":"2024-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683457/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>iMeta</i> Conference 2024: Building an innovative scientific research ecosystem for microbiome and One Health.","authors":"Yao Wang, Huiyu Hou, Hao Luo, Jiani Xun, Chuang Ma, Haifei Yang, Defeng Bai, Salsabeel Yousuf, Hujie Lyu, Tianyuan Zhang, Xiulin Wan, Xiaofang Yao, Tengfei Ma, Yuanping Zhou, Zhihao Zhu, Meiyin Zeng, Sanqi An, Qing Bai, Yao Bai, Guodong Cao, Tingting Cao, Yongkai Cao, Chihmin Chang, Lijia Chang, Bo Chen, Dai Chen, Dijun Chen, Hanqing Chen, Jiali Chen, Jinfeng Chen, Wei-Hua Chen, Xinhai Chen, Yue Chen, Zhangran Chen, Cheng Cheng, Quan Cheng, Xi-Jian Dai, Chaowen Deng, Feilong Deng, Jingwen Deng, Chang-Sheng Dong, Lei Dong, Lianhui Duan, Yi Duan, Qingjie Fan, Chao Fang, Tingyu Fang, Wensheng Fang, Zhencheng Fang, Min Fu, Minjie Fu, Cong Gao, Hao Gao, Weiwei Gao, Xinrui Gao, Yi-Zhou Gao, Yan Geng, Wenping Gong, Shaohua Gu, Xia Gu, Zhengquan Gu, Jian-Wei Guo, Junjie Guo, Qiuyan Guo, Xiang Guo, Xiaoqian Guo, Dongfei Han, Ziyi Han, Yanan Hao, Jiale He, Jianquan He, Jianyu He, Ruolin He, Guosen Hou, Bin Hu, Haibo Hu, Yi Hu, Yongfei Hu, Yucan Hu, Guanyin Huang, Haiyun Huang, Jiaomei Huang, Shenghui Huang, Baolei Jia, Xingxing Jian, Chao Jiang, Kun Jiang, Lanyan Jiang, Shuaiming Jiang, Jian-Yu Jiao, Hao Jin, Jiajia Jin, Siyuan Kong, Xinxing Lai, Yuxin Leng, Bang Li, Bing Li, Fang Li, Hao Li, Huanjie Li, Jing Li, Kai Li, Lanqi Li, Leyuan Li, Minghan Li, Pengsong Li, Wei Li, Wei Li, Xianyu Li, Li Xuemeng, Yafei Li, Yuantao Li, Zhi Li, Liqin Liang, Rong Liang, Zhuobin Liang, Qingya Liu, Dejian Liu, Huiheng Liu, Jinchao Liu, Li Liu, Lihui Liu, Moyang Liu, Ran Liu, Shuai Liu, Tianyang Liu, Wei Liu, Wenjuan Liu, Xiaomin Liu, Yang Liu, Yichen Liu, Yina Liu, Yuan Liu, Zhe Liu, Zhipeng Liu, Zhiquan Liu, Chunhao Long, Yun Long, Changying Lu, Chao Lu, Cheng Lu, Qi Lu, Yaning Luan, Peng Luo, Sheng Luo, Ning Ma, Xiao-Ya Ma, Yan Ma, Wenjun Mao, Yuanfa Meng, Yan Ni, Yawen Ni, Kang Ning, Dongze Niu, Kai Peng, Zhengwu Peng, Xubo Qian, Zhiguang Qiu, Hui Qu, Zepeng Qu, Yan Ren, Zhigang Ren, Youming Shen, Lin Shi, Linlin Shi, Wenxuan Shi, Yongpeng Shi, Tianyuan Song, Xiaohui Song, Xiaoming Song, Xiaowei Song, Qi Su, Yufan Su, Lifang Sun, Qiang Sun, Tiefeng Sun, Yunke Sun, Hua Tang, Wenjing Tang, Tao Yu, Simon Tian, Shuo Wang, Bowen Wang, Cheng Wang, Wang Jin, Leli Wang, Liangliang Wang, Lixiao Wang, Mingbang Wang, Ming-Ke Wang, Pingyi Wang, Shaolin Wang, Shaopu Wang, Xinxia Wang, Xueqiang Wang, Mi Wei, Yan Wei, Yanxia Wei, Yongjun Wei, Chaoliang Wen, Xin Wen, Linkun Wu, Shengru Wu, Yuting Wu, Shuting Xia, Xiaodong Xia, Yu Xia, Xionggen Xiang, Chuanxing Xiao, Weihua Xiao, Yingping Xiao, Ruohan Xie, Rui Xing, Hui Xu, Wei Xu, Zhimin Xu, Hongliang Xue, Chao Yan, Qiu-Long Yan, Shaofei Yan, Xiuchuan Yan, Mengli Yang, Yufan Yang, Zhipeng Yang, Ziyuan Yang, Guixiang Yao, Yanlai Yao, Xianfu Yi, Chong Yin, Mingliang Yin, Shicheng Yu, Ying Yu, Yongyao Yu, Fusong Yuan, Shao-Lun Zhai, Bo Zhang, Chen Zhang, Fang Zhang, Feng-Li Zhang, Hengguo Zhang, Jinping Zhang, Junya Zhang, Kun Zhang, Li Zhang, Lin Zhang, Lingxuan Zhang, Meng Zhang, Qian Zhang, Runan Zhang, Tongtong Zhang, Tongxue Zhang, Weipeng Zhang, Yong Zhang, Yuchao Zhang, Yujun Zhang, Zeng Zhang, Zhengxiao Zhang, Zhi-Feng Zhang, Boxi Zhao, Yanyan Zhao, Yibing Zhao, Ziwei Zhao, Diwei Zheng, Ying Zheng, Wenqiang Zhi, Jixin Zhong, Xiangjian Zhong, Wei Zhou, Xin Zhou, Zhemin Zhou, Zhichao Zhou, Congmin Zhu, Feiying Zhu, Xiaodie Zhu, Yutian Zou, Hongling Zhou, Lei Lei, Yanliang Bi, Hubing Shi, Hui-Zeng Sun, Shuangxia Jin, Wenkai Ren, Lei Dai, Xin Wang, Canhui Lan, Hongwei Liu, Shuang-Jiang Liu, Yulong Yin, Chun-Lin Shi, Ren-You Gan, Fangqing Zhao, Jun Yu, Tong Chen, Xin Hong, Hua Yang, Bangzhou Zhang, Shifu Chen, Xiaodong Li, Yunyun Gao, Yong-Xin Liu","doi":"10.1002/imt2.251","DOIUrl":"10.1002/imt2.251","url":null,"abstract":"<p><p>The <i>iMeta</i> Conference 2024 provides a platform to promote the development of an innovative scientific research ecosystem for microbiome and One Health. The four key components - Technology, Research (Biology), Academic journals, and Social media - form a synergistic ecosystem. Advanced technologies drive biological research, which generates novel insights that are disseminated through academic journals. Social media plays a crucial role in engaging the public and facilitating scientific communication, thus amplifying the impact of research. Together, these elements create a self-sustaining loop that fosters continuous innovation and collaboration in the field of bioinformatics, biotechnology and microbiome research.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":"e251"},"PeriodicalIF":23.7,"publicationDate":"2024-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683455/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive multi-tissue epigenome atlas in sheep: A resource for complex traits, domestication, and breeding.","authors":"Deyin Zhang, Jiangbo Cheng, Xiaolong Li, Kai Huang, Lvfeng Yuan, Yuan Zhao, Dan Xu, Yukun Zhang, Liming Zhao, Xiaobin Yang, Zongwu Ma, Quanzhong Xu, Chong Li, Xiaojuan Wang, Chen Zheng, Defu Tang, Fang Nian, Xiangpeng Yue, Wanhong Li, Huibin Tian, Xiuxiu Weng, Peng Hu, Yuanqing Feng, Peter Kalds, Zhihua Jiang, Yunxia Zhao, Xiaoxue Zhang, Fadi Li, Weimin Wang","doi":"10.1002/imt2.254","DOIUrl":"10.1002/imt2.254","url":null,"abstract":"<p><p>Comprehensive functional genome annotation is crucial to elucidate the molecular mechanisms of agronomic traits in livestock, yet systematic functional annotation of the sheep genome is lacking. Here, we generated 92 transcriptomic and epigenomic data sets from nine major tissues, along with whole-genome data from 2357 individuals across 29 breeds worldwide, and 4006 phenotypic data related to tail fat weight. We constructed the first multi-tissue epigenome atlas in terms of functional elements, chromatin states, and their functions and explored the utility of the functional elements in interpreting phenotypic variation during sheep domestication and improvement. Particularly, we identified a total of 753,723 nonredundant functional elements, with over 60% being novel. We found tissue-specific promoters and enhancers related to sensory abilities and immune response that were highly enriched in genomic regions influenced by domestication, while <i>longissimus dorsi</i> tissue-specific active enhancers and tail fat tissue-specific active promoters were highly enriched in genomic regions influenced by breeding and improvement. Notably, a variant, Chr13:51760995A>C, located in an enhancer region, was identified as a causal variant for tail fat deposition based on multi-layered data sets. Overall, this research provides foundational resources and a successful case for future investigations of complex traits in sheep through the integration of multi-omics data sets.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":"e254"},"PeriodicalIF":23.7,"publicationDate":"2024-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to \"<i>Lepidium meyenii</i> Walp (Maca)-derived extracellular vesicles ameliorate depression by promoting 5-HT synthesis via the modulation of gut-brain axis\".","authors":"","doi":"10.1002/imt2.259","DOIUrl":"10.1002/imt2.259","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1002/imt2.116.].</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":"e259"},"PeriodicalIF":23.7,"publicationDate":"2024-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683467/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}