Article
Biotechnology & Applied Microbiology
Ahmad Farhadi, Andrew G. Jeffs, Shane D. Lavery
Summary: This study investigates the genetic divergence and potential secondary contact patterns among geographically distant populations of the spiny lobster species complex. The analysis reveals strong regional structure and a complex evolutionary history of these populations, including a hybrid origin of one population. The findings suggest that alternating periods of divergence and gene flow have shaped the current genetic patterns in this lobster species.
Article
Biotechnology & Applied Microbiology
Zsolt Banfai, Erzsebet Koevesdi, Katalin Suemegi, Gergely Bueki, Andras Szabo, Lili Magyari, Valerian adam, Ferenc Palos, Attila Miseta, Miklos Kasler, Bela Melegh
Summary: This study provides the first analysis of the genetic composition of the Danube Swabians based on genome-wide autosomal data. The results suggest that they have significant German and other West European ancestry, with a prominent Hungarian ancestry.
Article
Biochemistry & Molecular Biology
Wibhu Kutanan, Dang Liu, Jatupol Kampuansai, Metawee Srikummool, Suparat Srithawong, Rasmi Shoocongdej, Sukrit Sangkhano, Sukhum Ruangchai, Pittayawat Pittayaporn, Leonardo Arias, Mark Stoneking
Summary: The study revealed genetic structure among different ethnolinguistic groups in Thailand and Laos, with heterogeneity in certain language families and populations reflecting population interactions and genetic drift. Some Thai groups show admixture from South Asia, likely associated with intensive international trade networks around 600-1000 years ago.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Jiawen Wang, Jun Wu, Qiuxia Sun, Qian Wu, Youjing Li, Shuhan Duan, Lin Yang, Wenxin Wu, Zheng Wang, Yan Liu, Renkuan Tang, Junbao Yang, Chuanchao Wang, Chao Liu, Jianwei Xu, Mengge Wang, Guanglin He
Summary: This study comprehensively investigated the genetic characteristics of Tai-Kadai-speaking Zhuang and Dong populations in the Yungui Plateau of Southwest China. It revealed close genetic affinity between these populations and geographically close Tai-Kadai and Han populations, as well as genetic evidence supporting a common origin hypothesis between Tai-Kadai and Austronesian populations. The study also identified specific selection candidate signatures associated with human immune systems and neurological disorders, providing evolutionary evidence for the frequency distribution pattern of genetic risk loci.
Article
Genetics & Heredity
Erin Calfee, Daniel Gates, Anne Lorant, M. Taylor Perkins, Graham Coop, Jeffrey Ross-Ibarra
Summary: Hybridization between maize and its wild teosinte relative mexicana may have facilitated maize's global range expansion, particularly to challenging high elevation regions. While recent hybrids are commonly observed and mexicana shows fine-scale local adaptation, the majority of mexicana ancestry introgressed into maize over 1000 generations ago, maintaining its diversity and likely coming from a common ancestral source.
Article
Evolutionary Biology
Tram Vi, Yves Vigouroux, Philippe Cubry, Pierre Marraccini, Ha Viet Phan, Giang Ngan Khong, Valerie Poncet
Summary: Humans have played a significant role in spreading crops beyond their native range, creating new opportunities for hybridization. Analyzing admixed genomes can provide valuable information about the adaptive history of crops and their impact on current varietal diversity.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Microbiology
Chanenath Sriaporn, Kathleen A. Campbell, Martin J. Van Kranendonk, Kim M. Handley
Summary: This study analyzed the genomes of Acidithiobacillus strains from hot springs in the Taupo Volcanic Zone of New Zealand, revealing four distinct species, including three novel ones. The findings suggest that these Acidithiobacillus have undergone genome streamlining to adapt to high temperatures in geothermal environments.
Article
Allergy
Yadu Gautam, Julie Caldwell, Leah Kottyan, Mirna Chehade, Evan S. Dellon, Marc E. Rothenberg, Tesfaye B. Mersha
Summary: This study conducted admixture mapping (AM) and genome-wide association study (GWAS) of EoE using participants from African American (AA) populations, and identified 3 significant loci associated with EoE. The findings indicate that there are ancestry-specific genetic susceptibility loci for EoE.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2023)
Article
Genetics & Heredity
Tingting Gong, Weerachai Jaratlerdsiri, Jue Jiang, Cali Willet, Tracy Chew, Sean M. Patrick, Ruth J. Lyons, Anne-Maree Haynes, Gabriela Pasqualim, Ilma Simoni Brum, Phillip D. Stricker, Shingai B. A. Mutambirwa, Rosemarie Sadsad, Anthony T. Papenfuss, Riana M. S. Bornman, Eva K. F. Chan, Vanessa M. Hayes
Summary: This study conducted a comprehensive analysis of structural variations in high-risk prostate cancer and found ethnic disparities between African and European populations. African-derived tumors exhibited a higher frequency of duplication events and hyper-structural variation subtypes. Novel African-specific mutations were identified in African male patients with prostate cancer.
Article
Allergy
Ayobami T. Akenroye, Tonya Brunetti, Karina Romero, Michelle Daya, Kanika Kanchan, Gautam Shankar, Sameer Chavan, Meher Preethi Boorgula, Elizabeth A. Ampleford, Hellen Freitas Fonseca, Gregory A. Hawkins, Helena Mariana Pitangueira Teixeira, Monica Campbell, Nicholas Rafaels, Alexandra Winters, Eugene R. Bleecker, Alvaro A. Cruz, Mauricio L. Barreto, Deborah A. Meyers, Victor E. Ortega, Camila A. Figueiredo, Kathleen C. Barnes, William Checkley, Nadia N. Hansel, Rasika A. Mathias
Summary: This study aimed to evaluate the impact of ancestry on asthma, total serum IgE level, and lung function outcomes in Peruvian children. The results showed a correlation between indigenous ancestry and higher IgE levels and FEV1 values, while European ancestry was associated with lower IgE levels. Additionally, genetic variants in the HLA-DR/DQ region and a novel locus on chromosome 19 were identified as influencing these outcomes.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2021)
Article
Clinical Neurology
Maria Carolina Dalmasso, Itziar de Rojas, Natividad Olivar, Carolina Muchnik, Barbara Angel, Sergio Gloger, Mariana Soledad Sanchez Abalos, Maria Victoria Chacon, Rafael Aranguiz, Paulina Orellana, Carolina Cuesta, Pablo Galeano, Lorenzo Campanelli, Gisela Vanina Novack, Luis Eduardo Martinez, Nancy Medel, Julieta Lisso, Zulma Sevillano, Nicolas Irureta, Eduardo Miguel Castano, Laura Montrreal, Michaela Thoenes, Claudia Hanses, Stefanie Heilmann-Heimbach, Claudia Kairiyama, Ines Mintz, Ivana Villella, Fabiana Rueda, Amanda Romero, Nancy Wukitsevits, Ivana Quiroga, Cristian Gona, Jean-Charles Lambert, Patricia Solis, Daniel Gustavo Politis, Carlos Alberto Mangone, Christian Gonzalez-Billault, Merce Boada, Lluis Tarraga, Andrea Slachevsky, Cecilia Albala, Patricio Fuentes, Silvia Kochen, Luis Ignacio Brusco, Agustin Ruiz, Laura Morelli, Alfredo Ramirez
Summary: This study is the first GWAS on Alzheimer's disease in a population from Argentina and Chile. A trans-ethnic meta-analysis revealed four new loci involving lysosomal function in AD. The genetic risk score developed in Europeans performed well in this population, but the score diminished with increasing Native American ancestry.
ALZHEIMERS & DEMENTIA
(2023)
Article
Ecology
Guanglin He, Atif Adnan, Wedad Saeed Al-Qahtani, Fatmah Ahmed Safhi, Hui-Yuan Yeh, Sibte Hadi, Chuan-Chao Wang, Mengge Wang, Chao Liu, Jun Yao
Summary: The fine-scale patterns of population genetic structure and diversity of ethnolinguistically diverse populations are important for various applications, such as biogeographical ancestry inference, kinship testing, and the development and validation of forensic personal identification kits. This study conducted comprehensive genetic analyses to explore the genetic structure, admixture history, and forensic features of the Qiang people, a Tibeto-Burman-speaking population residing in the Tibetan Plateau. The results revealed their close genetic relationship with lowland Tibetan-Yi corridor populations and their genetic admixture with Tibetan and Neolithic Yellow River farmers.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Agriculture, Dairy & Animal Science
Mary Kate Hollifield, Matias Bermann, Daniela Lourenco, Ignacy Misztal
Summary: Previous research in genomics explored the concept of independent chromosome segments and found that genomic prediction is based on capturing segment effects rather than LD to individual QTL. This study aimed to determine if physical segments are approximately consecutive haplotype blocks of length 1/4 M, with the number of haplotype blocks for each physical location equal to Ne. Simulated population data was used to analyze the accuracies of segment effects compared to true breeding values and traditional genomic estimated breeding values (GEBV). The results suggested that genomic selection acts partially on 1/4 M long chromosome segments and using the statistical definition of segments moderately explains the accuracy, but more complex simulations are needed for further investigation.
Article
Genetics & Heredity
Jing Xiao, Yang Zhou, Shu He, Wen-Long Ren
Summary: The newly proposed method ScoreEB combines score test and Empirical Bayes, improving computational efficiency in multi-locus GWAS. Applied to quantitative trait analysis in plants and animals, ScoreEB can detect new genes and accurately control false positive rate.
FRONTIERS IN GENETICS
(2021)
Article
Plant Sciences
Liuchun Feng, Yu Chen, Min Xu, Ying Yang, Haoran Yue, Qiao Su, Chenhui Zhou, Guoli Feng, Nijiang Ai, Ningshan Wang, Baoliang Zhou
Summary: This study developed G. arboreum chromosome segment introgression lines in G. hirsutum and identified multiple QTLs for yield and fiber quality. While most QTLs showed negative additive effects, suggesting domestication in G. hirsutum, some QTLs with positive additive effects indicate G. arboreum's potential to improve fiber quality in G. hirsutum.
FRONTIERS IN PLANT SCIENCE
(2021)
Letter
Gastroenterology & Hepatology
Haiyi Lou, Bo Xie, Yimin Wang, Yang Gao, Shuhua Xu
Article
Genetics & Heredity
Chunyu Liu, Ying Shen, Shuyan Tang, Jiaxiong Wang, Yiling Zhou, Shixiong Tian, Huan Wu, Jiangshan Cong, Xiaojin He, Li Jin, Yunxia Cao, Yihong Yang, Feng Zhang
Summary: In this study, we investigated a group of Han Chinese men with asthenoteratozoospermia, a common type of male infertility. Through whole-exome sequencing, we identified AKAP3 as a novel gene associated with multiple morphological abnormalities of the sperm flagella (MMAF). Two different deleterious variants of AKAP3 were found in unrelated MMAF-affected men, and subsequent experiments confirmed the impact of these variants on AKAP3 expression in spermatozoa. Interestingly, the clinical outcomes after intracytoplasmic sperm injection (ICSI) were different between these two cases, suggesting that AKAP3 dosage may influence the prognosis of ICSI treatment.
JOURNAL OF MEDICAL GENETICS
(2023)
Article
Clinical Neurology
Yingzhe Wang, Yanfeng Jiang, Wanqing Wu, Kelin Xu, Qianhua Zhao, Ziyi Tan, Xiaoniu Liang, Min Fan, Zhenxu Xiao, Li Zheng, Saineng Ding, Qiang Dong, Zhen Hong, Li Jin, Xingdong Chen, Ding Ding, Mei Cui
Summary: The study found that older adults with higher educational attainment showed slower cognitive decline. Education is especially important for maintaining cognitive health in disadvantaged living environments.
ALZHEIMERS & DEMENTIA
(2023)
Article
Biochemistry & Molecular Biology
Yimin Wang, Yunchao Ling, Jiao Gong, Xiaohan Zhao, Hanwen Zhou, Bo Xie, Haiyi Lou, Xinhao Zhuang, Li Jin, Shaohua Fan, Guoqing Zhang, Shuhua Xu
Summary: PGG.SV is a practical platform that provides large-scale structural variation data, including 1030 long-read sequencing genomes representing 177 global populations. The database offers high-quality SVs with precise genomic locations, estimates of SV prevalence in different geographical populations, informative annotations of related genes, and an analysis platform and visualization tools for association studies.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Hanni Ke, Shuyan Tang, Ting Guo, Dong Hou, Xue Jiao, Shan Li, Wei Luo, Bingying Xu, Shidou Zhao, Guangyu Li, Xiaoxi Zhang, Shuhua Xu, Lingbo Wang, Yanhua Wu, Jiucun Wang, Feng Zhang, Yingying Qin, Li Jin, Zi-Jiang Chen
Summary: Whole-exome sequencing in a cohort of 1,030 patients with POI identified new likely pathogenic variants and revealed different genetic architectures between primary and secondary amenorrhea. This study expands our understanding of the genetic landscape underlying POI and provides insights that have the potential to improve diagnostic genetic screenings.
Article
Oncology
Huangbo Yuan, Tao Qing, Sibo Zhu, Xiaorong Yang, Weicheng Wu, Kelin Xu, Hui Chen, Yanfeng Jiang, Chengkai Zhu, Ziyu Yuan, Tiejun Zhang, Li Jin, Chen Suo, Ming Lu, Xingdong Chen, Weimin Ye
Summary: Defects in DNA damage repair pathways can lead to genomic instability and oncogenesis. DDR alterations in esophageal squamous cell carcinoma (ESCC) affect mutational processes and tumor immune microenvironment.
Editorial Material
Multidisciplinary Sciences
Yongsen Ruan, Haijun Wen, Mei Hou, Weiwei Zhai, Shuhua Xu, Xuemei Lu
NATIONAL SCIENCE REVIEW
(2023)
Editorial Material
Multidisciplinary Sciences
Yanan Cao, Lingling Chen, Hua Chen, Yupeng Cun, Xiaofeng Dai, Hongli Du, Feng Gao, Fengbiao Guo, Yalong Guo, Pei Hao, Shunmin He, Shunping He, XiongLei He, Zheng Hu, Boon-Peng Hoh, Xin Jin, Qian Jiang, Qinghua Jiang, Asifullah Khan, Hong-Zhi Kong, Jinchen Li, Shuai Cheng Li, Ying Li, Qiang Lin, Jianquan Liu, Qi Liu, Jian Lu, Xuemei Lu, Shujin Luo, Qinghua Nie, Zilong Qiu, Tieliu Shi, Xiaofeng Song, Jianzhong Su, Sheng-ce Tao, Chaolong Wang, Chuan-Chao Wang, Guo-Dong Wang, Jiguang Wang, Qi Wu, Shaoyuan Wu, Shuhua Xu, Yu Xue, Wenjun Yang, Zhaohui Yang, Kai Ye, Yuan-Nong Ye, Li Yu, Fangqing Zhao, Yiqiang Zhao, Weiwei Zhai, Dandan Zhang, Liye Zhang, Houfeng Zheng, Qi Zhou, Tianqi Zhu, Ya-ping Zhang
NATIONAL SCIENCE REVIEW
(2023)
Editorial Material
Multidisciplinary Sciences
Yi Li, Meng Hao, Zixin Hu, Yanyun Ma, Kun Wang, Xiaoyu Liu, Xianhong Yin, Menghan Zhang, Yi Wang, Meng Liang, Yuan Guo, Lei Bao, Shixuan Zhang, Shiguan Le, Chenyuan Wu, Dayan Sun, Yang Wei, Fei Wu, Rui Zhang, Lingxian Zhu, Hui Zhang, Shuai Jiang, Xingdong Chen, Xiaofeng Wang, Yao Zhang, Longli Kang, Wenyuan Duan, Bin Qiao, Jiucun Wang, Li Jin
NATIONAL SCIENCE REVIEW
(2023)
Review
Genetics & Heredity
Tong Wu, Shuhua Xu
Summary: The topic of obesity is gaining global attention. It is believed that the main cause of high obesity rates is the mismatch between environment and genes after the shift towards a high-calorie diet. The debate on how obesity-related genes become prevalent worldwide has been ongoing for over 60 years. This review examines three influential hypotheses or viewpoints, namely the thrifty gene hypothesis, the drifty gene hypothesis, and the maladaptation viewpoint. Recent genome-wide association studies have provided valuable findings and evidence to better understand the evolutionary genetic mechanisms of obesity. This brief review is expected to guide further studies and inspire the future application of precision medicine in obesity treatment.
Article
Multidisciplinary Sciences
Qi Liu, Ke Yang, Bo Xie, Yang Gao, Shuhua Xu, Yan Lu
Summary: Ticks, as the second most common vector after mosquitoes, pose an increasing threat to public health and cause economic losses. This study conducted the first whole-genome sequencing-based analysis of structural variation (SV) in ticks, identifying numerous SVs in two tick species. The study also revealed distinct geographic populations in one tick species and identified genetic variations associated with vector-pathogen adaptation. This research provides valuable insights into the biology and evolution of ticks and may contribute to the prevention and control of tick-related diseases.
Article
Biochemical Research Methods
Qi Liu, Bo Xie, Yang Gao, Shuhua Xu, Yan Lu
Summary: This article presents a protocol for accurately detecting high-differentiated structural variations (SVs) using low-coverage next-generation sequencing data of Rhipicephalus microplus. It also outlines its use in investigating population/species-specific genetic structures, local adaptation, and transcriptional function.
Article
Medicine, Research & Experimental
Wenjing Wang, Yoichi Miyamoto, Biaobang Chen, Juanzi Shi, Feiyang Diao, Wei Zheng, Qun Li, Lan Yu, Lin Li, Yao Xu, Ling Wu, Xiaoyan Mao, Jing Fu, Bin Li, Zheng Yan, Rong Shi, Xia Xue, Jian Mu, Zhihua Zhang, Tianyu Wu, Lin Zhao, Weijie Wang, Zhou Zhou, Jie Dong, Qiaoli Li, Li Jin, Lin He, Xiaoxi Sun, Ge Lin, Yanping Kuang, Lei Wang, Qing Sang
Summary: By analyzing whole-exome sequencing data of 606 women with PREMBA, researchers have identified a candidate gene KPNA7, which may contribute to the development of PREMBA. The study further revealed that KPNA7 mutations reduce protein levels, impair its binding capacity to substrate RSL1D1, and affect nuclear transport activity. Furthermore, the study found that mouse KPNA2 plays a critical role in embryonic development and its deficiency leads to embryo arrest, similar to human PREMBA cases. These findings provide a mechanistic understanding of PREMBA and a diagnostic marker for PREMBA patients.
JOURNAL OF CLINICAL INVESTIGATION
(2023)
Correction
Biology
Zhaoqing Yang, Hao Chen, Yan Lu, Yang Gao, Hao Sun, Jiucun Wang, Li Jin, Jiayou Chu, Shuhua Xu
Article
Genetics & Heredity
Jialin Li, Qingxia Huang, Yingzhe Wang, Mei Cui, Kelin Xu, Chen Suo, Zhenqiu Liu, Yanpeng An, Li Jin, Huiru Tang, Xingdong Chen, Yanfeng Jiang
Summary: Cardiovascular health is linked to a lower risk of cognitive decline, and this association may be mediated by metabolic perturbations. The study found that better cardiovascular health was associated with a lower risk of concentration and orientation decline. Certain blood components, such as apolipoprotein-A1 and high-density lipoprotein cholesterol, were also associated with a lower risk of memory and orientation decline. Mediation analysis suggested that cholesterol ester and total lipids in medium-size HDL may partially mediate the negative association between health status and the risk of orientation decline. These findings highlight the potential of using lipoproteins as targets for early stage dementia screening and intervention.