Article
Cell Biology
Zhen Wang, Ruolan Wang, Chuanying Pan, Hong Chen, Lei Qu, Lian Wu, Zhengang Guo, Haijing Zhu, Xianyong Lan
Summary: Dynein Axonemal Heavy Chain 1 (DNAH1) encodes proteins that are crucial for the structural support and function of sperm and ova. This study identified several genetic variations within DNAH1 that were significantly associated with litter size in Shaanbei white cashmere goats. These genetic variations can be used as molecular markers for selecting reproductive traits in goats.
Article
Microbiology
Luz Helena Patino, Marina Munoz, Angie Lorena Ramirez, Norida Velez, Patricia Escandon, Claudia-Marcela Parra-Giraldo, Juan David Ramirez
Summary: By sequencing and analyzing the genomic architecture of 29 Colombian C. neoformans isolates, it was found that the majority belonged to the VNI molecular type. The study also revealed some SNP differences among these strains, but a low number of gene copy number variations and no changes in karyotype. These findings suggest that Colombian C. neoformans isolates may not require significant structural changes for host adaptation.
Article
Ecology
Yong-Meng He, Qiong-Hua Hong, Dong-Ke Zhou, Shi-Zhi Wang, Bai-Gao Yang, Ying Yuan, Wei-Yi Zhang, Yong-Fu Huang, E. Guang-Xin
Summary: The study on goats revealed that Mile red-bone goats have a unique bone structure and red bones related to specific genetic variants and signaling pathways. This research contributes to understanding the genetic basis of the unique bone phenotype of Mile red-bone goats.
ECOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Lyubov Getmantseva, Maria Kolosova, Kseniia Fede, Anna Korobeinikova, Anatoly Kolosov, Elena Romanets, Faridun Bakoev, Timofey Romanets, Vladimir Yudin, Anton Keskinov, Siroj Bakoev
Summary: This study focuses on the problem of leg defects in pigs and identifies candidate genetic variants associated with this trait. Functional analysis suggests that these variants may act as potential predictors of the hock joint phenotype of pigs, related to immune response, liver functions, intramuscular fat content, and animal fatness.
Article
Microbiology
Sarah Hendrickx, Joao Luis Reis-Cunha, Sarah Forrester, Daniel C. Jeffares, Guy Caljon
Summary: The study identified potential genetic variations associated with paromomycin resistance in Leishmania, including genes involved in transcription, translation, protein turnover, virulence, mitochondrial function, signaling, and vesicular trafficking. These results suggest that paromomycin affects protein translational processes and highlights the complex and multifactorial origin of resistance in Leishmania.
Article
Medicine, Research & Experimental
Xinlin Chen, Yulin Jiang, Ruiguo Chen, Qingwei Qi, Xiujuan Zhang, Sheng Zhao, Chaoshi Liu, Weiyun Wang, Yuezhen Li, Guoqiang Sun, Jieping Song, Hui Huang, Chen Cheng, Jianguang Zhang, Longxian Cheng, Juntao Liu
Summary: This study investigates the efficiency of simultaneous CNV-seq and WES in diagnosing fetal anomalies based on a large Chinese cohort. The results show that simultaneous CNV-seq and WES analysis contributes to fetal anomaly diagnosis and plays a vital role in elucidating complex anomalies with compound causes.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Genetics & Heredity
Wei Zhang, Xiaojin Li, Yao Jiang, Mei Zhou, Linqing Liu, Shiguang Su, Chengliang Xu, Xueting Li, Chonglong Wang
Summary: This study analyzed the genetic diversity and population structure of pig populations in Anhui Province through genome resequencing. Two distinct types of pigs were identified based on ancestral descent, and potential selective sweep regions associated with domestication characteristics were also identified. These findings provide valuable insights for future genetic studies and genome-assisted breeding of pigs and other domesticated animals.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Pradeep Ruperao, Nepolean Thirunavukkarasu, Prasad Gandham, Sivasubramani Selvanayagam, Mahalingam Govindaraj, Baloua Nebie, Eric Manyasa, Rajeev Gupta, Roma Rani Das, Damaris A. Odeny, Harish Gandhi, David Edwards, Santosh P. Deshpande, Abhishek Rathore
Summary: The study constructed the sorghum pan-genome, revealing its structural and functional characteristics, and analyzing its role in genetic gain and drought adaptation. Results showed that the sorghum genome has rich gene diversity that can be utilized in crop improvement.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Xinyu Xu, Bihua Chen, Juan Zhang, Siren Lan, Shasha Wu
Summary: This study evaluated the genomic characteristics of Gardenia jasminoides by re-sequencing wild and cultivated materials. The results showed that Gardenia jasminoides has rich genetic diversity and identified numerous SNPs and other gene variations. Additionally, the study further explored gene variations in the biosynthetic pathway of the main medicinal substances in Gardenia jasminoides.
Article
Genetics & Heredity
Long Zhao, Meiling Zou, Sirong Jiang, Xiaorui Dong, Ke Deng, Tiancang Na, Jian Wang, Zhiqiang Xia, Fang Wang
Summary: In this study, genome-wide association analysis was performed for plant height traits in 370 potato cultivars. A total of 92 significant SNP loci associated with plant height were identified. These loci were mainly found in specific haplotypes on chromosome 1 and chromosome 5, and were related to 35 candidate genes involved in hormone signal transduction pathways. The discovery of PIF3 and GID1a genes on chromosome 1 provides more effective genetic loci for marker-assisted breeding and precise localization and cloning of plant height genes in potatoes.
Article
Oncology
Roberta Giordo, Rida Gulsha, Sarah Kalla, George A. Calin, Leonard Lipovich
Summary: The genome-wide association study identified six genetic variants significantly associated with both type 2 diabetes and cancer in non-coding regions, including lncRNA genes. These variants provide evidence of a shared genetic architecture between the two diseases and may serve as potential drug targets.
Article
Plant Sciences
H. B. Mahesh, M. K. Prasannakumar, K. G. Manasa, Sampath Perumal, Yogendra Khedikar, Sateesh Kagale, Raju Y. Soolanayakanahally, H. C. Lohithaswa, Annabathula Mohan Rao, Shailaja Hittalmani
Summary: This study successfully sequenced the horsegram genome and identified a series of important genes and transcription factors. The genome is rich in Bowman-Birk protease inhibitors, suggesting its potential as a functional food ingredient. Key genes related to powdery mildew resistance were identified through a genome-wide association study.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
Ting Sun, Shengwei Pei, Yangkai Liu, Quratulain Hanif, Haiyue Xu, Ningbo Chen, Chuzhao Lei, Xiangpeng Yue
Summary: In this study, high sperm motility (HSM) and poor sperm motility (PSM) Simmental bulls were analyzed for genetic variations (SNPs and CNVs) using high-coverage short-read next generation sequencing and single-molecule long reads sequencing data. The study identified a large number of SNPs and CNVs in Simmental bulls, as well as positive selected genes (PSGs) and CNVRs overlapping with quantitative trait loci (QTLs) related to immunity, muscle development, and reproduction. Moreover, the study discovered two new variants in LEPR, potentially related to artificial breeding for improving economic traits, and identified genes and pathways related to male fertility. Notably, a CNV on SPAG16 was found to be completely deleted in all PSM bulls and half of HSM bulls, suggesting a crucial role in bull fertility.
Review
Biochemistry & Molecular Biology
Ludmila Volozonoka, Anna Miskova, Linda Gailite
Summary: This review provides insight into the performance and drawbacks of WGA techniques such as DOP-PCR, MDA, MALBAC, and hybrid techniques in PGT. The advantages of MDA-based solutions for comprehensive genome coverage and PCR-based solutions for uniformity of coverage are highlighted. The choice of WGA technique should take into consideration the influence of MPS parameters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Indrajit Saha, Nimisha Ghosh, Ayan Pradhan, Nikhil Sharma, Debasree Maity, Kaushik Mitra
Summary: Whole genome analysis of SARS-CoV-2 was conducted to identify genetic diversity globally and in individual countries. Unique mutations were determined for each country and common mutations were also identified. The most frequent mutation points were found in specific genes across different populations and countries.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Agriculture, Dairy & Animal Science
Tao Zhong, Xinlu Wang, Chunhua Huang, Liu Yang, Qianjun Zhao, Xiaoyong Chen, Aline Freitas -de -Melo, Siyuan Zhan, Linjie Wang, Dinghui Dai, Jiaxue Cao, Jiazhong Guo, Li Li, Hongping Zhang, Lili Niu
Summary: This study conducted a comprehensive analysis of the genomic diversity and selection signatures of indigenous goats in China, revealing high genetic differentiation and loss of genetic diversity among the breeds. Additionally, signature genes related to high-altitude adaptation and prolificity were identified. This research provides a valuable resource for future genome-wide studies on Chinese indigenous goats.
Article
Agriculture, Dairy & Animal Science
Xujia Zhang, Xin Liu, Tingting Jiang, Siyuan Zhan, Tao Zhong, Jiazhong Guo, Jiaxue Cao, Li Li, Hongping Zhang, Linjie Wang
Summary: In this study, circZEB1, a circular RNA derived from exon 2 and exon 3 of goat ZEB1 gene, was found to promote brown adipocytes differentiation and thermogenesis. The results also showed that circZEB1 could bind to miR-326-3p and regulate lipid accumulation in brown adipocytes.
SMALL RUMINANT RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yanjin Sun, Siyuan Zhan, Sen Zhao, Tao Zhong, Linjie Wang, Jiazhong Guo, Dinghui Dai, Dandan Li, Jiaxue Cao, Li Li, Hongping Zhang
Summary: HuR is highly expressed in goat skeletal muscle and plays a crucial role in promoting muscle differentiation by increasing the stability of Myomaker mRNA. Overexpression of HuR accelerates muscle cell differentiation and formation of myotubes, while knockdown of HuR has the opposite effects. HuR binds to Myomaker, increasing its mRNA stability and positively regulating its expression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Chenyu Yang, Xinyi Zhou, Yanan Xue, Dandan Li, Linjie Wang, Tao Zhong, Dinghui Dai, Jiaxue Cao, Jiazhong Guo, Li Li, Hongping Zhang, Siyuan Zhan
Summary: This study investigates the expression profiles of long non-coding RNAs (lncRNAs) during the proliferation and differentiation of skeletal muscle satellite cells (MuSCs) in goats. A total of 1001 lncRNAs were identified, and 314 differentially expressed lncRNAs were screened. Functional analysis revealed that these lncRNAs were significantly associated with muscle development-related genes and pathways. Additionally, a competing endogenous RNA (ceRNA) network analysis showed the interaction between lncRNAs, microRNAs, and mRNAs. These findings provide valuable insights into the role of lncRNAs during skeletal muscle development in goats.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Emmanuel Odame, Li Li, Joshua Abdulai Nabilla, He Cai, Miao Xiao, Jiangfeng Ye, Yuan Chen, Bismark Kyei, Dinghui Dai, Siyuan Zhan, Jiaxue Cao, Jiazhong Guo, Tao Zhong, Linjie Wang, Hongping Zhang
Summary: Muscle growth and injury-induced regeneration in postnatal animals are controlled by skeletal muscle satellite cells (MuSCs) through myogenesis. However, the molecular mechanisms involving non-coding RNAs, including circRNAs and miRNAs, are still unclear. In this study, the role of miR-145-3p and MYBL1 in muscle development and mitochondrial mass was investigated. The overexpression of miR-145-3p inhibited MuSCs proliferation, while its deficiency retarded MuSCs differentiation. miR-145-3p altered the mitochondrial mass in MuSCs and negatively regulated the expression of CDR1as and MYBL1. Knockdown of MYBL1 simulated the inhibitory function of miR-145-3p on cell proliferation. These findings confirm the importance of mitochondrial mass and the regulatory role of miR-145-3p and MYBL1 in muscle development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Jing Tang, Xin Liu, Duo Su, Tingting Jiang, Siyuan Zhan, Tao Zhong, Jiazhong Guo, Jiaxue Cao, Li Li, Hongping Zhang, Linjie Wang
Summary: In this study, a BAT-enriched lncRNA called MSTRG.310246.1 was identified. It was found to be localized in both nuclear and cytoplasmic compartments and its expression was upregulated during brown adipocyte differentiation. Overexpression of MSTRG.310246.1 promoted the differentiation and thermogenesis of goat brown adipocytes, while its knockdown inhibited these processes. However, MSTRG.310246.1 had no effect on goat white adipocyte differentiation and thermogenesis.
Article
Biochemistry & Molecular Biology
Xinlu Wang, Lili Niu, Yaxuan Wang, Siyuan Zhan, Linjie Wang, Dinghui Dai, Jiaxue Cao, Jiazhong Guo, Li Li, Hongping Zhang, Tao Zhong
Summary: This study investigated the association between diarrhea occurrence and changes in gut microbiota, metabolism, and immunity in goat kids and lambs. The results showed dominant phyla in goat kids and lambs, as well as the presence of certain families in both diarrheic goat kids and lambs. Functional prediction of microbiota revealed its involvement in cell motility and cancer pathways. Lambs had significant differences in immunoglobulins and cytokines compared to goat kids. Weighted gene co-expression network analysis identified modules positively associated with immune factors and triglycerides. Overall, this study characterized the gut microbiota, metabolism, and immune status of lambs and goat kids with diarrhea.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Li Li, Xiaoli Xu, Miao Xiao, Chunhua Huang, Jiaxue Cao, Siyuan Zhan, Jiazhong Guo, Tao Zhong, Linjie Wang, Liu Yang, Hongping Zhang
Summary: High-altitude environments have a significant impact on the genetic evolution of vertebrates. The role of RNA editing in high-altitude adaptation in non-model species remains underexplored. In this study, we investigated the RNA editing sites in the goat species living at different altitudes and found that RNA editing plays a crucial role in the adaptation to high-altitude environments. Our findings provide valuable insights into the adaptive evolution of goats and the study of plateau-related diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)