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Qi D, Zheng T, Yang M, Huang Z, Wang T, Wang Q, Chen B. Bile Acid Composition and Transcriptome Analysis of the Liver and Small Intestine in Different Species. Metabolites 2024; 14:451. [PMID: 39195547 DOI: 10.3390/metabo14080451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 07/25/2024] [Accepted: 08/10/2024] [Indexed: 08/29/2024] Open
Abstract
Bile, a crucial fluid produced continuously by the liver, plays an essential role in digestion within the small intestine. Beyond its primary function in lipid digestion, bile also acts as a pathway for the elimination of various endogenous and exogenous substances. There have been limited studies focusing on interspecies differences. This study offers a comprehensive analysis of bile acid (BA) composition and its correlation with gene expression patterns across six different species, including mammals and poultry, through combining Liquid Chromatography-Mass Spectrometry (LC-MS) and transcriptome sequencing. The BA profiles revealed distinct metabolite clusters: D-glucuronic acid (GLCA) and glycochenodeoxycholic acid (GCDCA) were predominant in mammals, while taurolithocholic acid (TLCA) and T-alpha-MCA were prevalent in poultry, highlighting species-specific BA compositions. Differentially abundant metabolites, particularly GDCA, glycohyodeoxycholic acid (GHDCA) and taurodeoxycholic acid (TDCA) showed significant variations across species, with pigs showing the highest BA content. Transcriptome analysis of the liver and small intestine tissues of 56 cDNA libraries across the six species revealed distinct mRNA expression patterns. These patterns clustered samples into broad categories based on tissue type and phylogenetic relationships. Furthermore, the correlation between gene expression and BA content was examined, identifying the top 20 genes with significant associations. These genes potentially serve as biomarkers for BA regulation.
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Affiliation(s)
- Dongming Qi
- College of Animal Science, Xichang University, Xichang 615000, China
| | - Tingting Zheng
- School of Life Sciences, China West Normal University, Nanchong 637009, China
| | - Maosen Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Zhiying Huang
- College of Animal Science, Shanxi Agricultural University, Taiyuan 030801, China
| | - Tao Wang
- School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Qiang Wang
- Ningnan County Bureau of Agriculture and Rural Affairs, Xichang 615400, China
| | - Binlong Chen
- College of Animal Science, Xichang University, Xichang 615000, China
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2
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Semik-Gurgul E, Pawlina-Tyszko K, Gurgul A, Szmatoła T, Rybińska J, Ząbek T. In search of epigenetic hallmarks of different tissues: an integrative omics study of horse liver, lung, and heart. Mamm Genome 2024:10.1007/s00335-024-10057-0. [PMID: 39143382 DOI: 10.1007/s00335-024-10057-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 08/01/2024] [Indexed: 08/16/2024]
Abstract
DNA methylation and microRNA (miRNA) expression are epigenetic mechanisms essential for regulating tissue-specific gene expression and metabolic processes. However, high-resolution transcriptome, methylome, or miRNAome data is only available for a few model organisms and selected tissues. Up to date, only a few studies have reported on gene expression, DNA methylation, or miRNA expression in adult equine tissues at the genome-wide level. In the present study, we used RNA-Seq, miRNA-seq, and reduced representation bisulfite sequencing (RRBS) data from the heart, lung, and liver tissues of healthy cold-blooded horses to identify differentially expressed genes (DEGs), differentially expressed miRNA (DE miRNA) and differentially methylated sites (DMSs) between three types of horse tissues. Additionally, based on integrative omics analysis, we described the observed interactions of epigenetic mechanisms with tissue-specific gene expression alterations. The obtained data allowed identification from 4067 to 6143 DMSs, 9733 to 11,263 mRNAs, and 155 to 185 microRNAs, differentially expressed between various tissues. We pointed out specific genes whose expression level displayed a negative correlation with the level of CpG methylation and miRNA expression and revealed biological processes that they enrich. Furthermore, we confirmed and validated the accuracy of the Next-Generation Sequencing (NGS) results with bisulfite sequencing PCR (BSP) and quantitative PCR (qPCR). This comprehensive analysis forms a strong foundation for exploring the epigenetic mechanisms involved in tissue differentiation, especially the growth and development of the equine heart, lungs, and liver.
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Affiliation(s)
- Ewelina Semik-Gurgul
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland.
| | - Klaudia Pawlina-Tyszko
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland
| | - Artur Gurgul
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Redzina 1c, Krakow, 30-248, Poland
| | - Tomasz Szmatoła
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Redzina 1c, Krakow, 30-248, Poland
| | - Justyna Rybińska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland
| | - Tomasz Ząbek
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland
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3
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Wu Z, Chai Z, Cai X, Wang J, Wang H, Yue B, Zhang M, Wang J, Wang H, Zhong J, Xin J. Protein Lactylation Profiles Provide Insights into Molecular Mechanisms Underlying Metabolism in Yak. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38850252 DOI: 10.1021/acs.jafc.4c01800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2024]
Abstract
Protein lysine lactylation, a recently discovered post-translational modification (PTM), is prevalent across tissues and cells of diverse species, serving as a regulator of glycolytic flux and biological metabolism. The yak (Bos grunniens), a species that has inhabited the Qinghai-Tibetan Plateau for millennia, has evolved intricate adaptive mechanisms to cope with the region's unique geographical and climatic conditions, exhibiting remarkable energy utilization and metabolic efficiency. Nonetheless, the specific landscape of lysine lactylation in yaks remains poorly understood. Herein, we present the first comprehensive lactylome profile of the yak, effectively identifying 421, 308, and 650 lactylated proteins in the heart, muscles, and liver, respectively. These lactylated proteins are involved in glycolysis/gluconeogenesis, the tricarboxylic acid cycle, oxidative phosphorylation, and metabolic process encompassing carbohydrates, lipids, and proteins during both anaerobic and aerobic glucose bio-oxidation, implying their crucial role in material and energy metabolism, as well as in maintaining homeostasis in yaks.
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Affiliation(s)
- Zhijuan Wu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Zhixin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Xin Cai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Hui Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Binglin Yue
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Ming Zhang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Jikun Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Haibo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Jinwei Xin
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850000, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850009, China
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4
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Yang J, Wang DF, Huang JH, Zhu QH, Luo LY, Lu R, Xie XL, Salehian-Dehkordi H, Esmailizadeh A, Liu GE, Li MH. Structural variant landscapes reveal convergent signatures of evolution in sheep and goats. Genome Biol 2024; 25:148. [PMID: 38845023 PMCID: PMC11155191 DOI: 10.1186/s13059-024-03288-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution. RESULTS We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats. CONCLUSIONS Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.
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Affiliation(s)
- Ji Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Jia-Hui Huang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qiang-Hui Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ling-Yun Luo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ran Lu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, Iran
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, 20705, USA
| | - Meng-Hua Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Lan D, Fu W, Ji W, Mipam TD, Xiong X, Ying S, Xiong Y, Sheng P, Ni J, Bai L, Shan T, Kong X, Li J. Pangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks. J Anim Sci Biotechnol 2024; 15:64. [PMID: 38706000 PMCID: PMC11071219 DOI: 10.1186/s40104-024-01027-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/18/2024] [Indexed: 05/07/2024] Open
Abstract
BACKGROUND The genetic diversity of yak, a key domestic animal on the Qinghai-Tibetan Plateau (QTP), is a vital resource for domestication and breeding efforts. This study presents the first yak pangenome obtained through the de novo assembly of 16 yak genomes. RESULTS We discovered 290 Mb of nonreference sequences and 504 new genes. Our pangenome-wide presence and absence variation (PAV) analysis revealed 5,120 PAV-related genes, highlighting a wide range of variety-specific genes and genes with varying frequencies across yak populations. Principal component analysis (PCA) based on binary gene PAV data classified yaks into three new groups: wild, domestic, and Jinchuan. Moreover, we proposed a 'two-haplotype genomic hybridization model' for understanding the hybridization patterns among breeds by integrating gene frequency, heterozygosity, and gene PAV data. A gene PAV-GWAS identified a novel gene (BosGru3G009179) that may be associated with the multirib trait in Jinchuan yaks. Furthermore, an integrated transcriptome and pangenome analysis highlighted the significant differences in the expression of core genes and the mutational burden of differentially expressed genes between yaks from high and low altitudes. Transcriptome analysis across multiple species revealed that yaks have the most unique differentially expressed mRNAs and lncRNAs (between high- and low-altitude regions), especially in the heart and lungs, when comparing high- and low-altitude adaptations. CONCLUSIONS The yak pangenome offers a comprehensive resource and new insights for functional genomic studies, supporting future biological research and breeding strategies.
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Affiliation(s)
- Daoliang Lan
- Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China.
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China.
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China.
| | - Wei Fu
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Wenhui Ji
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Tserang-Donko Mipam
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Xianrong Xiong
- Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Shi Ying
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Yan Xiong
- Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Peng Sheng
- Jiguang Gene Biotechnology Co., Ltd., Nanjing, China
| | - Jiangping Ni
- Jiguang Gene Biotechnology Co., Ltd., Nanjing, China
| | - Lijun Bai
- Chengdu Genepre Technology Co., Ltd., Chengdu, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | | | - Jian Li
- Ministry of Education of Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource and Utilization, Southwest Minzu University, Chengdu, China
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
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6
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Wang W, Dong Y, Guo W, Zhang X, Degen AA, Bi S, Ding L, Chen X, Long R. Linkages between rumen microbiome, host, and environment in yaks, and their implications for understanding animal production and management. Front Microbiol 2024; 15:1301258. [PMID: 38348184 PMCID: PMC10860762 DOI: 10.3389/fmicb.2024.1301258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/03/2024] [Indexed: 02/15/2024] Open
Abstract
Livestock on the Qinghai-Tibetan Plateau is of great importance for the livelihood of the local inhabitants and the ecosystem of the plateau. The natural, harsh environment has shaped the adaptations of local livestock while providing them with requisite eco-services. Over time, unique genes and metabolic mechanisms (nitrogen and energy) have evolved which enabled the yaks to adapt morphologically and physiologically to the Qinghai-Tibetan Plateau. The rumen microbiota has also co-evolved with the host and contributed to the host's adaptation to the environment. Understanding the complex linkages between the rumen microbiota, the host, and the environment is essential to optimizing the rumen function to meet the growing demands for animal products while minimizing the environmental impact of ruminant production. However, little is known about the mechanisms of host-rumen microbiome-environment linkages and how they ultimately benefit the animal in adapting to the environment. In this review, we pieced together the yak's adaptation to the Qinghai-Tibetan Plateau ecosystem by summarizing the natural selection and nutritional features of yaks and integrating the key aspects of its rumen microbiome with the host metabolic efficiency and homeostasis. We found that this homeostasis results in higher feed digestibility, higher rumen microbial protein production, higher short-chain fatty acid (SCFA) concentrations, and lower methane emissions in yaks when compared with other low-altitude ruminants. The rumen microbiome forms a multi-synergistic relationship among the rumen microbiota services, their communities, genes, and enzymes. The rumen microbial proteins and SCFAs act as precursors that directly impact the milk composition or adipose accumulation, improving the milk or meat quality, resulting in a higher protein and fat content in yak milk and a higher percentage of protein and abundant fatty acids in yak meat when compared to dairy cow or cattle. The hierarchical interactions between the climate, forage, rumen microorganisms, and host genes have reshaped the animal's survival and performance. In this review, an integrating and interactive understanding of the host-rumen microbiome environment was established. The understanding of these concepts is valuable for agriculture and our environment. It also contributes to a better understanding of microbial ecology and evolution in anaerobic ecosystems and the host-environment linkages to improve animal production.
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Affiliation(s)
- Weiwei Wang
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, Guizhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yuntao Dong
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, Guizhou, China
| | - Wei Guo
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, Guizhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiao Zhang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - A. Allan Degen
- Desert Animal Adaptations and Husbandry, Wyler Department of Dryland Agriculture, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sisi Bi
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Luming Ding
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiang Chen
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, Guizhou, China
| | - Ruijun Long
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
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An L, Li Y, Yaq L, Wang Y, Dai Q, Du S, Ru Y, Zhoucuo Q, Wang J. Transcriptome analysis reveals molecular regulation mechanism of Tibet sheep tolerance to high altitude oxygen environment. Anim Biotechnol 2023; 34:5097-5112. [PMID: 37729444 DOI: 10.1080/10495398.2023.2258953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
As one of the most important livestock breeds on the Qinghai-Tibet Plateau, Tibetan sheep are of great importance to the local economy, agriculture and culture. Its adaptive mechanism in low temperature and low oxygen at highland altitudes has not been reported. In this study, transcriptome sequencing was used to analyze the heart, liver, spleen, lung, kidney, and muscle tissue of sheep at low and highland altitudes. LOC101112291, SELENOW, COL3A1, GPX1, TMSB4X and HSF4 were selected as candidate genes for adapting to plateau characteristics in Tibet Sheep. Besides, glutathione metabolism, arachidonic acid metabolism, nucleotide excision repair, regulation of actin cytoskeleton, protein digestion and absorption, thyroid hormone synthesis, relaxation signaling pathways may play important roles in the adaptation to plateau hypoxia, and cold tolerance. Structural analysis also showed that sequencing genes related to the adaptation mechanism of Tibet sheep to highland altitude. This study will lay a certain foundation for Tibet sheep research.
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Affiliation(s)
- Li An
- College of Life Science and Biotechnology, Mianyang Teacher's College, Mianyang, China
- Key Laboratory of Qinghai-Tibet Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest University for Nationalities, Chengdu, China
- College of Animal & Veterinary Science, Southwest Minzu University, Chengdu, China
| | - Yanyan Li
- Key Laboratory of Qinghai-Tibet Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest University for Nationalities, Chengdu, China
- College of Animal & Veterinary Science, Southwest Minzu University, Chengdu, China
| | - Lin Yaq
- Key Laboratory of Qinghai-Tibet Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest University for Nationalities, Chengdu, China
- College of Animal & Veterinary Science, Southwest Minzu University, Chengdu, China
| | - Yong Wang
- Key Laboratory of Qinghai-Tibet Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest University for Nationalities, Chengdu, China
- College of Animal & Veterinary Science, Southwest Minzu University, Chengdu, China
| | - Qilin Dai
- School of Life Science and Engineering, Southwest University of Science and Technology, Mian Yang, China
| | - Shizhang Du
- College of Life Science and Biotechnology, Mianyang Teacher's College, Mianyang, China
| | - Yi Ru
- Ruo'ergai Bureau of Agriculture and Animal Husbandry, Ruo'ergai, China
| | - Qi Zhoucuo
- Huzhu Tu Autonomous County of Comprehensive Law Enforcement Brigade of Agricultural Administration, Huzhu Tu Autonomous County, China
| | - Jinling Wang
- College of Life Science and Biotechnology, Mianyang Teacher's College, Mianyang, China
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8
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Gao H, Zang Y, Zhang Y, Zhao H, Ma W, Chen X, Wang J, Zhao D, Wang X, Huang Y, Zhang F. Transcriptome analysis revealed that short-term stress in Blattella germanica to β-cypermethrin can reshape the phenotype of resistance adaptation. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 197:105703. [PMID: 38072557 DOI: 10.1016/j.pestbp.2023.105703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/11/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023]
Abstract
Previous studies on insect resistance have primarily focused on resistance monitoring and the molecular mechanisms involved, while overlooking the process of phenotype formation induced by insecticide stress. In this study, we compared the expression profiles of a beta-cypermethrin (β-CYP) resistant strain (R) and a susceptible strain (S) of Blattella germanica after β-CYP induction using transcriptome sequencing. In the short-term stress experiment, we identified a total of 792 and 622 differentially expressed genes (DEGs) in the S and R strains. Additionally, 893 DEGs were identified in the long-term adaptation experiment. To validate the RNA-Seq data, we performed qRT-PCR on eleven selected DEGs, and the results were consistent with the transcriptome sequencing data. These DEGs exhibited down-regulation in the short-term stress group and up-regulation in the long-term adaptation group. Among the validated DEGs, CUO8 and Cyp4g19 were identified and subjected to knockdown using RNA interference. Subsequent insecticide bioassays revealed that the mortality rate of cockroaches treated with β-CYP increased by 69.3% and 66.7% after silencing the CUO8 and Cyp4g19 genes (P<0.05). Furthermore, the silencing of CUO8 resulted in a significant thinning of the cuticle by 59.3% and 53.4% (P<0.05), as observed through transmission electron microscopy and eosin staining, in the S and R strains, respectively. Overall, our findings demonstrate that the phenotypic plasticity in response to short-term stress can reshape the adaptive mechanisms of genetic variation during prolonged exposure to insecticides. And the identified resistance-related genes, CUO8 and Cyp4g19, could serve as potential targets for controlling these pest populations.
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Affiliation(s)
- Huiyuan Gao
- Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Science, Shandong Normal University, Jinan 250014, China; Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, Dongying 257000, China
| | - Yanan Zang
- Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Science, Shandong Normal University, Jinan 250014, China; Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, Dongying 257000, China
| | - Yuting Zhang
- Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Science, Shandong Normal University, Jinan 250014, China; Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, Dongying 257000, China
| | - Haizheng Zhao
- Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Science, Shandong Normal University, Jinan 250014, China; Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, Dongying 257000, China
| | - Wenxiao Ma
- Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Science, Shandong Normal University, Jinan 250014, China; Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, Dongying 257000, China
| | - Xingyu Chen
- Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Science, Shandong Normal University, Jinan 250014, China; Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, Dongying 257000, China
| | - Jingjing Wang
- Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Science, Shandong Normal University, Jinan 250014, China; Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, Dongying 257000, China
| | - Dongqin Zhao
- Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Science, Shandong Normal University, Jinan 250014, China; Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, Dongying 257000, China
| | - Xuejun Wang
- Shandong Center for Disease Control and Prevention, Jinan 250013, China
| | - Yanhong Huang
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China
| | - Fan Zhang
- Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Science, Shandong Normal University, Jinan 250014, China; Dongying Key Laboratory of Salt Tolerance Mechanism and Application of Halophytes, Dongying Institute, Shandong Normal University, Dongying 257000, China.
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9
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Jiang YF, Wang S, Wang CL, Xu RH, Wang WW, Jiang Y, Wang MS, Jiang L, Dai LH, Wang JR, Chu XH, Zeng YQ, Fang LZ, Wu DD, Zhang Q, Ding XD. Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs. iScience 2023; 26:106119. [PMID: 36852268 PMCID: PMC9958381 DOI: 10.1016/j.isci.2023.106119] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/21/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Long-read sequencing (LRS) facilitates both the genome assembly and the discovery of structural variants (SVs). Here, we built a graph-based pig pangenome by incorporating 11 LRS genomes with an average of 94.01% BUSCO completeness score, revealing 206-Mb novel sequences. We discovered 183,352 nonredundant SVs (63% novel), representing 12.12% of the reference genome. By genotyping SVs in an additional 196 short-read sequencing samples, we identified thousands of population stratified SVs. Particularly, we detected 7,568 Tibetan specific SVs, some of which demonstrate significant population differentiation between Tibetan and low-altitude pigs, which might be associated with the high-altitude hypoxia adaptation in Tibetan pigs. Further integrating functional genomic data, the most promising candidate genes within the SVs that might contribute to the high-altitude hypoxia adaptation were discovered. Overall, our study generates a benchmark pangenome resource for illustrating the important roles of SVs in adaptive evolution, domestication, and genetic improvement of agronomic traits in pigs.
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Affiliation(s)
- Yi-Fan Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Chong-Long Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Ru-Hai Xu
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wen-Wen Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian 271001, China
| | - Yao Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Li Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Li-He Dai
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jie-Ru Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiao-Hong Chu
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yong-Qing Zeng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian 271001, China
| | - Ling-Zhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian 271001, China
| | - Xiang-Dong Ding
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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10
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Nan J, Yang S, Zhang X, Leng T, Zhuoma J, Zhuoma R, Yuan J, Pi J, Sheng Z, Li S. Identification of candidate genes related to highland adaptation from multiple Chinese local chicken breeds by whole genome sequencing analysis. Anim Genet 2023; 54:55-67. [PMID: 36305422 DOI: 10.1111/age.13268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/30/2022] [Accepted: 09/20/2022] [Indexed: 01/07/2023]
Abstract
Understanding the genetic mechanism of highland adaptation is of great importance for breeding improvement of Tibetan chickens (TBC). Some studies of TBC have identified some candidate genes and pathways from multiple subgroups, but the related genetic mechanisms remain largely unknown. Different genetic backgrounds and the independent genetic basis of highland adaptation make it difficult to identity the selective region of highland adaptation with all TBC samples. In this study, we conducted pre-analysis in a large-scale population to select a TBC subgroup with the purest and highest level of highland-specific lineage for the further analysis. Finally, the 37 samples from a TBC subgroup and 19 Lahsa White chickens were used to represent the highland group for further analysis with 80 samples from five Chinese local lowland breeds as controls. Population structure analysis revealed that highland adaptation significantly affected population stratification in Chinese local chicken breeds. Genome-wide selection signal analysis identified 201 candidate genes associated with highland adaptation of TBC, and these genes were significantly enriched in calcium signaling, vascular smooth muscle contraction and the cellular response to oxidative stress pathways. Additionally, we identified a narrow 1.76 kb region containing an overlapping region between HBZ and an active enhancer, and our identified region showed a highly significant signal. The highland group selected the haplotype with high activity to improve the oxygen-carrying capacity, thus being adapted to a hypoxic environment. We also found that STX2 was significantly selected in the highland group, thus potentially reducing the oxidative stress caused by hypoxia, and that STX2 exhibited the opposite effects on highland adaptation and reproductive traits. Our findings advance our understanding of extreme environment adaptation of highland chickens, and provide some variants and genes beneficial to TBC genetic breeding improvement.
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Affiliation(s)
- Jiuhong Nan
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sendong Yang
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaojian Zhang
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tianze Leng
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Joan Zhuoma
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Neighborhood Committee Office, Xigaze City, China
| | - Rensang Zhuoma
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Luomai Township People's Government of Seni District, Naqu City, China
| | - Jingwei Yuan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinsong Pi
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan, China
| | - Zheya Sheng
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shijun Li
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Smart Farming for Agricultural Animals, Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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11
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Zhu P, Liu W, Zhang X, Li M, Liu G, Yu Y, Li Z, Li X, Du J, Wang X, Grueter CC, Li M, Zhou X. Correlated evolution of social organization and lifespan in mammals. Nat Commun 2023; 14:372. [PMID: 36720880 PMCID: PMC9889386 DOI: 10.1038/s41467-023-35869-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 01/05/2023] [Indexed: 02/02/2023] Open
Abstract
Discerning the relationship between sociality and longevity would permit a deeper understanding of how animal life history evolved. Here, we perform a phylogenetic comparative analysis of ~1000 mammalian species on three states of social organization (solitary, pair-living, and group-living) and longevity. We show that group-living species generally live longer than solitary species, and that the transition rate from a short-lived state to a long-lived state is higher in group-living than non-group-living species, altogether supporting the correlated evolution of social organization and longevity. The comparative brain transcriptomes of 94 mammalian species identify 31 genes, hormones and immunity-related pathways broadly involved in the association between social organization and longevity. Further selection features reveal twenty overlapping pathways under selection for both social organization and longevity. These results underscore a molecular basis for the influence of the social organization on longevity.
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Affiliation(s)
- Pingfen Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Weiqiang Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiao Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meng Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Yang Yu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Zihao Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuanjing Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Du
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Cyril C Grueter
- School of Human Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Centre for Evolutionary Biology, School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,International Center of Biodiversity and Primate Conservation, Dali University, Dali, Yunnan, 671003, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.
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12
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Lyu T, Zhou S, Fang J, Wang L, Shi L, Dong Y, Zhang H. Convergent Genomic Signatures of High-Altitude Adaptation among Six Independently Evolved Mammals. Animals (Basel) 2022; 12:ani12243572. [PMID: 36552492 PMCID: PMC9774524 DOI: 10.3390/ani12243572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/08/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
The species living in the Qinghai-Tibet Plateau provide an excellent model system for studying the relationship between molecular convergent evolution and adaptation. Distant species experiencing the same selection pressure (i.e., hypoxia, low temperature and strong ultraviolet radiation) are likely to evolve similar genetic adaptations independently. Here, we performed comparative genomics studies on six independently evolved high-altitude species. The results also showed that the convergent evolution of the six species was mainly reflected at the level of rapidly evolving genes, and the functions of these rapidly evolving genes were mainly related to hypoxia response and DNA damage repair. In addition, we found that high-altitude species had more gene family changes than their low-altitude relatives, except for the order Lagomorpha. The results also show that the convergence of the gene family contraction of high-altitude species is much greater than that of expansion, revealing a possible pattern of species in adapting to high-altitude. Furthermore, we detected a positive selection signature in four genes related to hypoxia response and ultraviolet radiation damage in these six species (FYCO1, ERBIN, SCAMP1 and CXCL10). Our study reveals that hypoxia response might play an important role in the adaptation of independently evolved species to a high-altitude environment, providing a basic perspective for further exploring the high-altitude adaptation mechanism of different related species in the future.
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Affiliation(s)
- Tianshu Lyu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150000, China
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Shengyang Zhou
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Jiaohui Fang
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Lidong Wang
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Lupeng Shi
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Yuehuan Dong
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu 273165, China
- Correspondence:
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13
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Mu D, Wu X, Feijó A, Wu W, Wen Z, Cheng J, Xia L, Yang Q, Shan W, Ge D. Transcriptome analysis of pika heart tissue reveals mechanisms underlying the adaptation of a keystone species on the roof of the world. Front Genet 2022; 13:1020789. [PMID: 36506315 PMCID: PMC9728954 DOI: 10.3389/fgene.2022.1020789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022] Open
Abstract
High-altitude environments impose intense stresses on living organisms and drive striking phenotypic and genetic adaptations, such as hypoxia resistance, cold tolerance, and increases in metabolic capacity and body mass. As one of the most successful and dominant mammals on the Qinghai-Tibetan Plateau (QHTP), the plateau pika (Ochotona curzoniae) has adapted to the extreme environments of the highest altitudes of this region and exhibits tolerance to cold and hypoxia, in contrast to closely related species that inhabit the peripheral alpine bush or forests. To explore the potential genetic mechanisms underlying the adaptation of O. curzoniae to a high-altitude environment, we sequenced the heart tissue transcriptomes of adult plateau pikas (comparing specimens from sites at two different altitudes) and Gansu pikas (O. cansus). Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were used to identify differentially expressed genes (DEGs) and their primary functions. Key genes and pathways related to high-altitude adaptation were identified. In addition to the biological processes of signal transduction, energy metabolism and material transport, the identified plateau pika genes were mainly enriched in biological pathways such as the negative regulation of smooth muscle cell proliferation, the apoptosis signalling pathway, the cellular response to DNA damage stimulus, and ossification involved in bone maturation and heart development. Our results showed that the plateau pika has adapted to the extreme environments of the QHTP via protection against cardiomyopathy, tissue structure alterations and improvements in the blood circulation system and energy metabolism. These adaptations shed light on how pikas thrive on the roof of the world.
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Affiliation(s)
- Danping Mu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xinlai Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China,Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wei Wu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wenjuan Shan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China,*Correspondence: Wenjuan Shan, ; Deyan Ge,
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China,*Correspondence: Wenjuan Shan, ; Deyan Ge,
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14
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Li C, Wu Y, Chen B, Cai Y, Guo J, Leonard AS, Kalds P, Zhou S, Zhang J, Zhou P, Gan S, Jia T, Pu T, Suo L, Li Y, Zhang K, Li L, Purevdorj M, Wang X, Li M, Wang Y, Liu Y, Huang S, Sonstegard T, Wang MS, Kemp S, Pausch H, Chen Y, Han JL, Jiang Y, Wang X. Markhor-derived Introgression of a Genomic Region Encompassing PAPSS2 Confers High-altitude Adaptability in Tibetan Goats. Mol Biol Evol 2022; 39:6830663. [PMID: 36382357 PMCID: PMC9728798 DOI: 10.1093/molbev/msac253] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding the genetic mechanism of how animals adapt to extreme conditions is fundamental to determine the relationship between molecular evolution and changing environments. Goat is one of the first domesticated species and has evolved rapidly to adapt to diverse environments, including harsh high-altitude conditions with low temperature and poor oxygen supply but strong ultraviolet radiation. Here, we analyzed 331 genomes of domestic goats and wild caprid species living at varying altitudes (high > 3000 m above sea level and low < 1200 m), along with a reference-guided chromosome-scale assembly (contig-N50: 90.4 Mb) of a female Tibetan goat genome based on PacBio HiFi long reads, to dissect the genetic determinants underlying their adaptation to harsh conditions on the Qinghai-Tibetan Plateau (QTP). Population genomic analyses combined with genome-wide association studies (GWAS) revealed a genomic region harboring the 3'-phosphoadenosine 5'-phosphosulfate synthase 2 (PAPSS2) gene showing strong association with high-altitude adaptability (PGWAS = 3.62 × 10-25) in Tibetan goats. Transcriptomic data from 13 tissues revealed that PAPSS2 was implicated in hypoxia-related pathways in Tibetan goats. We further verified potential functional role of PAPSS2 in response to hypoxia in PAPSS2-deficient cells. Introgression analyses suggested that the PAPSS2 haplotype conferring the high-altitude adaptability in Tibetan goats originated from a recent hybridization between goats and a wild caprid species, the markhor (Capra falconeri). In conclusion, our results uncover a hitherto unknown contribution of PAPSS2 to high-altitude adaptability in Tibetan goats on QTP, following interspecific introgression and natural selection.
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Affiliation(s)
| | | | | | | | | | | | - Peter Kalds
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Shiwei Zhou
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China,College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Jingchen Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China,State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Shangqu Gan
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China,State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Ting Jia
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing 100044, China
| | - Tianchun Pu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing 100044, China
| | - Langda Suo
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China
| | - Yan Li
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ke Zhang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Lan Li
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Myagmarsuren Purevdorj
- Lab of Animal Genetics and Animal Reproductive Technology, Research Institute of Animal Husbandry, Mongolian University of Life Sciences, Ulaanbaatar 17024, Mongolia
| | - Xihong Wang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ming Li
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yu Wang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yao Liu
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Shuhong Huang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | | | - Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 94720
| | - Stephen Kemp
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi 30709-00100, Kenya
| | - Hubert Pausch
- Animal Genomics, ETH Zürich, 8092 Zürich, Switzerland
| | - Yulin Chen
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | | | - Yu Jiang
- Corresponding authors: E-mails: ; ;
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15
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Wang Y, Wang X, Sun S, Jin C, Su J, Wei J, Luo X, Wen J, Wei T, Sahu SK, Zou H, Chen H, Mu Z, Zhang G, Liu X, Xu X, Gram L, Yang H, Wang E, Liu H. GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet. Nat Commun 2022; 13:5913. [PMID: 36207301 PMCID: PMC9546826 DOI: 10.1038/s41467-022-33238-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 09/09/2022] [Indexed: 11/09/2022] Open
Abstract
Genetic and environmental factors collectively determine plant growth and yield. In the past 20 years, genome-wide association studies (GWAS) have been conducted on crops to decipher genetic loci that contribute to growth and yield, however, plant genotype appears to be insufficient to explain the trait variations. Here, we unravel the associations between genotypic, phenotypic, and rhizoplane microbiota variables of 827 foxtail millet cultivars by an integrated GWAS, microbiome-wide association studies (MWAS) and microbiome genome-wide association studies (mGWAS) method. We identify 257 rhizoplane microbial biomarkers associated with six key agronomic traits and validated the microbial-mediated growth effects on foxtail millet using marker strains isolated from the field. The rhizoplane microbiota composition is mainly driven by variations in plant genes related to immunity, metabolites, hormone signaling and nutrient uptake. Among these, the host immune gene FLS2 and transcription factor bHLH35 are widely associated with the microbial taxa of the rhizoplane. We further uncover a plant genotype-microbiota interaction network that contributes to phenotype plasticity. The microbial-mediated growth effects on foxtail millet are dependent on the host genotype, suggesting that precision microbiome management could be used to engineer high-yielding cultivars in agriculture systems.
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Grants
- Statens Naturvidenskabelige Forskningsrad (Danish National Science Foundation)
- This research was supported by the Funding of Joint Research on Agricultural Variety Improvement of Henan Province (No. 2022010401, H. Z.), the Major Science and Technology Projects of Yunnan Province (Digitalization, development and application of biotic resource, No. 860 202002AA100007, H. L.), the National Science Foundation (32088102, 31730103, 31825003, E. W.), the Specialty Industry for Key Research and Development Program in Shanxi Academy of Agricultural Sciences (No. YCX2019T01, Z. M.) and Key R&D Program of ShanXi Province (No. 201903D211003, Z. M.). This work was also supported by China National GeneBank (CNGB), Key Laboratory of Genomics, Ministry of Agriculture, BGI-Shenzhen.
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Affiliation(s)
- Yayu Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Xiaolin Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Shuai Sun
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, Qingdao, 266555, China
| | - Canzhi Jin
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianmu Su
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jinpu Wei
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Xinyue Luo
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiawen Wen
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tong Wei
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongfeng Zou
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongyun Chen
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhixin Mu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, China
| | - Gengyun Zhang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518083, China
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs, Lyngby, Denmark
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China.
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16
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Wang D, Li Y, Li M, Yang W, Ma X, Zhang L, Wang Y, Feng Y, Zhang Y, Zhou R, Sanderson BJ, Keefover-Ring K, Yin T, Smart LB, DiFazio SP, Liu J, Olson M, Ma T. Repeated turnovers keep sex chromosomes young in willows. Genome Biol 2022; 23:200. [PMID: 36151581 PMCID: PMC9502649 DOI: 10.1186/s13059-022-02769-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 09/08/2022] [Indexed: 01/10/2023] Open
Abstract
Background Salicaceae species have diverse sex determination systems and frequent sex chromosome turnovers. However, compared with poplars, the diversity of sex determination in willows is poorly understood, and little is known about the evolutionary forces driving their turnover. Here, we characterized the sex determination in two Salix species, S. chaenomeloides and S. arbutifolia, which have an XY system on chromosome 7 and 15, respectively. Results Based on the assemblies of their sex determination regions, we found that the sex determination mechanism of willows may have underlying similarities with poplars, both involving intact and/or partial homologs of a type A cytokinin response regulator (RR) gene. Comparative analyses suggested that at least two sex turnover events have occurred in Salix, one preserving the ancestral pattern of male heterogamety, and the other changing heterogametic sex from XY to ZW, which could be partly explained by the “deleterious mutation load” and “sexually antagonistic selection” theoretical models. We hypothesize that these repeated turnovers keep sex chromosomes of willow species in a perpetually young state, leading to limited degeneration. Conclusions Our findings further improve the evolutionary trajectory of sex chromosomes in Salicaceae species, explore the evolutionary forces driving the repeated turnovers of their sex chromosomes, and provide a valuable reference for the study of sex chromosomes in other species. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02769-w.
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Affiliation(s)
- Deyan Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yiling Li
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Mengmeng Li
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Wenlu Yang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Xinzhi Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Lei Zhang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yubo Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yanlin Feng
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yuanyuan Zhang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Ran Zhou
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Brian J Sanderson
- Department of Biology, West Virginia University, Morgantown, WV, USA.,Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin-Madison, Madison, WI, USA
| | - Tongming Yin
- The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, China
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Jianquan Liu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China.
| | - Matthew Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
| | - Tao Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China.
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17
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Lyu T, Yang X, Zhao C, Wang L, Zhou S, Shi L, Dong Y, Dou H, Zhang H. Comparative transcriptomics of high-altitude Vulpes and their low-altitude relatives. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.999411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The harsh environment of Qinghai-Tibet Plateau (QTP) imposes strong selective stresses (e.g., hypoxia, high UV-radiation, and extreme temperature) to the native species, which have driven striking phenotypic and genetic adaptations. Although the mechanisms of high-altitude adaptation have been explored for many plateau species, how the phylogenetic background contributes to genetic adaption to high-altitude of Vulpes is largely unknown. In this study, we sequenced transcriptomic data across multiple tissues of two high-altitude Vulpes (Vulpes vulpes montana and Vulpes ferrilata) and their low-altitude relatives (Vulpes corsac and Vulpes lagopus) to search the genetic and gene expression changes caused by high-altitude environment. The results indicated that the positive selection genes (PSGs) identified by both high-altitude Vulpes are related to angiogenesis, suggesting that angiogenesis may be the result of convergent evolution of Vulpes in the face of hypoxic selection pressure. In addition, more PSGs were detected in V. ferrilata than in V. v. montana, which may be related to the longer adaptation time of V. ferrilata to plateau environment and thus more genetic changes. Besides, more PSGs associated with high-altitude adaptation were identified in V. ferrilata compared with V. v. montana, indicating that the longer the adaptation time to the high-altitude environment, the more genetic alterations of the species. Furthermore, the result of expression profiles revealed a tissue-specific pattern between Vulpes. We also observed that differential expressed genes in the high-altitude group exhibited species-specific expression patterns, revealed a convergent expression pattern of Vulpes in high-altitude environment. In general, our research provides a valuable transcriptomic resource for further studies, and expands our understanding of high-altitude adaptation within a phylogenetic context.
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18
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Genome sequence assembly algorithms and misassembly identification methods. Mol Biol Rep 2022; 49:11133-11148. [PMID: 36151399 DOI: 10.1007/s11033-022-07919-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022]
Abstract
The sequence assembly algorithms have rapidly evolved with the vigorous growth of genome sequencing technology over the past two decades. Assembly mainly uses the iterative expansion of overlap relationships between sequences to construct the target genome. The assembly algorithms can be typically classified into several categories, such as the Greedy strategy, Overlap-Layout-Consensus (OLC) strategy, and de Bruijn graph (DBG) strategy. In particular, due to the rapid development of third-generation sequencing (TGS) technology, some prevalent assembly algorithms have been proposed to generate high-quality chromosome-level assemblies. However, due to the genome complexity, the length of short reads, and the high error rate of long reads, contigs produced by assembly may contain misassemblies adversely affecting downstream data analysis. Therefore, several read-based and reference-based methods for misassembly identification have been developed to improve assembly quality. This work primarily reviewed the development of DNA sequencing technologies and summarized sequencing data simulation methods, sequencing error correction methods, various mainstream sequence assembly algorithms, and misassembly identification methods. A large amount of computation makes the sequence assembly problem more challenging, and therefore, it is necessary to develop more efficient and accurate assembly algorithms and alternative algorithms.
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19
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Dubey A, Malla MA, Kumar A. Taxonomical and functional bacterial community profiling in disease-resistant and disease-susceptible soybean cultivars. Braz J Microbiol 2022; 53:1355-1370. [PMID: 35415800 PMCID: PMC9433584 DOI: 10.1007/s42770-022-00746-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/28/2022] [Indexed: 12/13/2022] Open
Abstract
Highly varied bacterial communities inhabiting the soybean rhizosphere perform important roles in its growth and production; nevertheless, little is known about the changes that occur in these communities under disease-stress conditions. The present study investigated the bacterial diversity and their metabolic profile in the rhizosphere of disease-resistant (JS-20-34) and disease-susceptible (JS-335) soybean (Glycine max (L.) Merr.) cultivars using 16S rRNA amplicon sequencing and community-level physiological profiling (CLPP). In disease-resistant soybean (AKADR) samples, the most dominating phyla were Actinobacteria (40%) followed by Chloroflexi (24%), Proteobacteria (20%), and Firmicutes (12%), while in the disease-susceptible (AKADS) sample, the most dominating phyla were Proteobacteria (35%) followed by Actinobacteria (27%) and Bacteroidetes (17%). Functional profiling of bacterial communities was done using the METAGENassist, and PICRUSt2 software, which shows that AKADR samples have more ammonifying, chitin degrading, nitrogen-fixing, and nitrite reducing bacteria compared to AKADS rhizosphere samples. The bacterial communities present in disease-resistant samples were significantly enriched with genes involved in nitrogen fixation, carbon fixation, ammonification, denitrification, and antibiotic production. Furthermore, the CLPP results show that carbohydrates and carboxylic acids were the most frequently utilized nutrients by the microbes. The principal component analysis (PCA) revealed that the AKADR soils had higher functional activity (strong association with the Shannon-Wiener index, richness index, and hydrocarbon consumption) than AKADS rhizospheric soils. Overall, our findings suggested that the rhizosphere of resistant varieties of soybean comprises of beneficial bacterial population over susceptible varieties.
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Affiliation(s)
- Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, 470003, Madhya Pradesh, India
| | - Muneer Ahmad Malla
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, 470003, Madhya Pradesh, India
- Department of Zoology, Dr. Harisingh Gour University (A Central University), Sagar, 470003, Madhya Pradesh, India
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, 470003, Madhya Pradesh, India.
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20
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Ahn J, Lee J, Kim DH, Hwang IS, Park MR, Cho IC, Hwang S, Lee K. Loss of Monoallelic Expression of IGF2 in the Adult Liver Via Alternative Promoter Usage and Chromatin Reorganization. Front Genet 2022; 13:920641. [PMID: 35938007 PMCID: PMC9355166 DOI: 10.3389/fgene.2022.920641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
In mammals, genomic imprinting operates via gene silencing mechanisms. Although conservation of the imprinting mechanism at the H19/IGF2 locus has been generally described in pigs, tissue-specific imprinting at the transcript level, monoallelic-to-biallelic conversion, and spatio-temporal chromatin reorganization remain largely uninvestigated. Here, we delineate spatially regulated imprinting of IGF2 transcripts, age-dependent hepatic mono- to biallelic conversion, and reorganization of topologically associating domains at the porcine H19/IGF2 locus for better translation to human and animal research. Whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) of normal and parthenogenetic porcine embryos revealed the paternally hypermethylated H19 differentially methylated region and paternal expression of IGF2. Using a polymorphism-based approach and omics datasets from chromatin immunoprecipitation sequencing (ChIP–seq), whole-genome sequencing (WGS), RNA-seq, and Hi-C, regulation of IGF2 during development was analyzed. Regulatory elements in the liver were distinguished from those in the muscle where the porcine IGF2 transcript was monoallelically expressed. The IGF2 transcript from the liver was biallelically expressed at later developmental stages in both pigs and humans. Chromatin interaction was less frequent in the adult liver compared to the fetal liver and skeletal muscle. The duration of genomic imprinting effects within the H19/IGF2 locus might be reduced in the liver with biallelic conversion through alternative promoter usage and chromatin remodeling. Our integrative omics analyses of genome, epigenome, and transcriptome provided a comprehensive view of imprinting status at the H19/IGF2 cluster.
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Affiliation(s)
- Jinsoo Ahn
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH, United States
| | - Joonbum Lee
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH, United States
- The Ohio State University Interdisciplinary Human Nutrition Program, The Ohio State University, Columbus, OH, United States
| | - Dong-Hwan Kim
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH, United States
| | - In-Sul Hwang
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Jeonbuk, South Korea
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, Columbia University, New York, NY, United States
| | - Mi-Ryung Park
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Jeonbuk, South Korea
| | - In-Cheol Cho
- National Institute of Animal Science, Rural Development Administration, Jeju, South Korea
| | - Seongsoo Hwang
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Jeonbuk, South Korea
| | - Kichoon Lee
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH, United States
- The Ohio State University Interdisciplinary Human Nutrition Program, The Ohio State University, Columbus, OH, United States
- *Correspondence: Kichoon Lee,
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21
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Curry KD, Wang Q, Nute MG, Tyshaieva A, Reeves E, Soriano S, Wu Q, Graeber E, Finzer P, Mendling W, Savidge T, Villapol S, Dilthey A, Treangen TJ. Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data. Nat Methods 2022; 19:845-853. [PMID: 35773532 PMCID: PMC9939874 DOI: 10.1038/s41592-022-01520-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 05/10/2022] [Indexed: 12/12/2022]
Abstract
16S ribosomal RNA-based analysis is the established standard for elucidating the composition of microbial communities. While short-read 16S rRNA analyses are largely confined to genus-level resolution at best, given that only a portion of the gene is sequenced, full-length 16S rRNA gene amplicon sequences have the potential to provide species-level accuracy. However, existing taxonomic identification algorithms are not optimized for the increased read length and error rate often observed in long-read data. Here we present Emu, an approach that uses an expectation-maximization algorithm to generate taxonomic abundance profiles from full-length 16S rRNA reads. Results produced from simulated datasets and mock communities show that Emu is capable of accurate microbial community profiling while obtaining fewer false positives and false negatives than alternative methods. Additionally, we illustrate a real-world application of Emu by comparing clinical sample composition estimates generated by an established whole-genome shotgun sequencing workflow with those returned by full-length 16S rRNA gene sequences processed with Emu.
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Affiliation(s)
- Kristen D. Curry
- Rice University, Department of Computer Science, Houston, TX, USA,Corresponding authors: , ,
| | - Qi Wang
- Rice University, Department of Systems, Synthetic, and Physical Biology Science, Houston, TX, USA
| | - Michael G. Nute
- Rice University, Department of Computer Science, Houston, TX, USA
| | - Alona Tyshaieva
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Elizabeth Reeves
- Rice University, Department of Computer Science, Houston, TX, USA
| | - Sirena Soriano
- Houston Methodist Research Institute, Center for Neuroregeneration, Houston, TX, USA
| | - Qinglong Wu
- Baylor College of Medicine, Department of Pathology and Immunology, Houston, TX, USA,Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Enid Graeber
- Rice University, Department of Systems, Synthetic, and Physical Biology Science, Houston, TX, USA
| | - Patrick Finzer
- Rice University, Department of Systems, Synthetic, and Physical Biology Science, Houston, TX, USA
| | - Werner Mendling
- German Center for Infections in Gynaecology and Obstetrics at Helios University Clinic Wuppertal, Wuppertal, Germany
| | - Tor Savidge
- Baylor College of Medicine, Department of Pathology and Immunology, Houston, TX, USA,Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Sonia Villapol
- Houston Methodist Research Institute, Center for Neuroregeneration, Houston, TX, USA
| | - Alexander Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Todd J. Treangen
- Rice University, Department of Computer Science, Houston, TX, USA,Corresponding authors: , ,
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22
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Dickson ZW, Golding GB. Low complexity regions in mammalian proteins are associated with low protein abundance and high transcript abundance. Mol Biol Evol 2022; 39:6575407. [PMID: 35482425 PMCID: PMC9070799 DOI: 10.1093/molbev/msac087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Low Complexity Regions (LCRs) are present in a surprisingly large number of eukaryotic proteins. These highly repetitive and compositionally biased sequences are often structurally disordered, bind promiscuously, and evolve rapidly. Frequently studied in terms of evolutionary dynamics, little is known about how LCRs affect the expression of the proteins which contain them. It would be expected that rapidly evolving LCRs are unlikely to be tolerated in strongly conserved, highly abundant proteins, leading to lower overall abundance in proteins which contain LCRs. To test this hypothesis and examine the associations of protein abundance and transcript abundance with the presence of LCRs, we have integrated high-throughput data from across mammals. We have found that LCRs are indeed associated with reduced protein abundance, but are also associated with elevated transcript abundance. These associations are qualitatively consistent across 12 human tissues and nine mammalian species. The differential impacts of LCRs on abundance at the protein and transcript level are not explained by differences in either protein degradation rates or the inefficiency of translation for LCR containing proteins. We suggest that rapidly evolving LCRs are a source of selective pressure on the regulatory mechanisms which maintain steady-state protein abundance levels.
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Affiliation(s)
- Zachery W Dickson
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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23
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Zhang T, Wang T, Niu Q, Xu L, Chen Y, Gao X, Gao H, Zhang L, Liu GE, Li J, Xu L. Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle. BMC Biol 2022; 20:79. [PMID: 35351103 PMCID: PMC8966188 DOI: 10.1186/s12915-022-01269-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 03/03/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND A comprehensive analysis of gene expression profiling across tissues can provide necessary information for an in-depth understanding of their biological functions. We performed a large-scale gene expression analysis and generated a high-resolution atlas of the transcriptome in beef cattle. RESULTS Our transcriptome atlas was generated from 135 bovine tissues in adult beef cattle, covering 51 tissue types of major organ systems (e.g., muscular system, digestive system, immune system, reproductive system). Approximately 94.76% of sequencing reads were successfully mapped to the reference genome assembly ARS-UCD1.2. We detected a total of 60,488 transcripts, and 32% of them were not reported before. We identified 2654 housekeeping genes (HKGs) and 477 tissue-specific genes (TSGs) across tissues. Using weighted gene co-expression network analysis, we obtained 24 modules with 237 hub genes (HUBGs). Functional enrichment analysis showed that HKGs mainly maintain the basic biological activities of cells, while TSGs were involved in tissue differentiation and specific physiological processes. HKGs in bovine tissues were more conserved in terms of expression pattern as compared to TSGs and HUBGs among multiple species. Finally, we obtained a subset of tissue-specific differentially expressed genes (DEGs) between beef and dairy cattle and several functional pathways, which may be involved in production and health traits. CONCLUSIONS We generated a large-scale gene expression atlas across the major tissues in beef cattle, providing valuable information for enhancing genome assembly and annotation. HKGs, TSGs, and HUBGs further contribute to better understanding the biology and evolution of multiple tissues in cattle. DEGs between beef and dairy cattle also fill in the knowledge gaps about differential transcriptome regulation of bovine tissues underlying economically important traits.
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Affiliation(s)
- Tianliu Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - Tianzhen Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - Qunhao Niu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - Lei Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705 USA
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
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24
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Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation. iScience 2022; 25:103899. [PMID: 35243257 PMCID: PMC8873613 DOI: 10.1016/j.isci.2022.103899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/12/2021] [Accepted: 02/07/2022] [Indexed: 11/20/2022] Open
Abstract
The phenotypic plasticity in responses to short-term stress can provide clues for understanding the adaptive fixation mechanism of genetic variation during long-term exposure to extreme environments. However, few studies have compared short-term stress responses with long-term evolutionary patterns; in particular, no interactions between the two processes have been evaluated in high-altitude environment. We performed RNA sequencing in embryo fibroblasts derived from great tits and mice to explore transcriptional responses after exposure to simulated high-altitude environmental stresses. Transcriptional changes of genes associated with metabolic pathways were identified in both bird and mice cells after short-term stress responses. Genomic comparisons among long-term highland tits and mammals and their lowland relatives revealed similar pathways (e.g., metabolic pathways) with that initiated under short-term stress transcriptional responses in vitro. These findings highlight the indicative roles of short-term stress in the long-term adaptation, and adopt common paths to molecular adaptation in mouse and bird cells. Short-term stress and long-term adaptations share the common metabolic pathways Phenotypic plasticity can promote adaptive evolution Adopt common paths to molecular adaptation in mouse and bird cells
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25
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Liu Z, Roberts R, Mercer TR, Xu J, Sedlazeck FJ, Tong W. Towards accurate and reliable resolution of structural variants for clinical diagnosis. Genome Biol 2022; 23:68. [PMID: 35241127 PMCID: PMC8892125 DOI: 10.1186/s13059-022-02636-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 02/15/2022] [Indexed: 12/17/2022] Open
Abstract
Structural variants (SVs) are a major source of human genetic diversity and have been associated with different diseases and phenotypes. The detection of SVs is difficult, and a diverse range of detection methods and data analysis protocols has been developed. This difficulty and diversity make the detection of SVs for clinical applications challenging and requires a framework to ensure accuracy and reproducibility. Here, we discuss current developments in the diagnosis of SVs and propose a roadmap for the accurate and reproducible detection of SVs that includes case studies provided from the FDA-led SEquencing Quality Control Phase II (SEQC-II) and other consortium efforts.
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Affiliation(s)
- Zhichao Liu
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Ruth Roberts
- ApconiX, BioHub at Alderley Park, Alderley Edge, SK10 4TG, UK
- University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Joshua Xu
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Weida Tong
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
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Du Z, Lin W, Yu B, Zhu J, Li J. Integrated Metabolomic and Transcriptomic Analysis of the Flavonoid Accumulation in the Leaves of Cyclocarya paliurus at Different Altitudes. FRONTIERS IN PLANT SCIENCE 2022; 12:794137. [PMID: 35211131 PMCID: PMC8860981 DOI: 10.3389/fpls.2021.794137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Cyclocarya paliurus is a medicinal plant containing flavonoids, triterpenoids, polyphenolics, polysaccharides, and other compounds with diverse biological functions. C. paliurus is distributed across altitudes ranging from 400 to 1,000 m. However, little is known about the effect of altitude on metabolite accumulation in C. paliurus. Also, the biosynthetic pathway involved in flavonoid accumulation in C. paliurus has not been fully elucidated. In this study, mature leaves of C. paliurus growing at low altitude (280 m) and high altitude (920 m) were sampled and subjected to metabolomic and transcriptomic analyses. The flavonoid content and composition were higher in the leaves of C. paliurus collected at high altitude than in those collected at low altitude. Most of the differentially accumulated metabolites (DAMs) were enriched in "flavone and flavonol biosynthesis." The significant differentially expressed genes (DEGs) between low and high altitudes were mainly enriched in "biological process." The most heavily enriched KEGG pathway was related to the subcategory "Oxidative phosphorylation," indicating that complicated biological processes are involved in the response of C. paliurus to harsh environmental factors. High UV-light might be the main influencing factor among the harsh environmental factors found in high altitudes. Integrated analysis of metabolomic and transcriptomic data showed that 31 flavonoids were significantly correlated with 227 DEGs, resulting in 412 related pairs (283 positive and 129 negative) between the DEGs and flavonoids. The possible mechanisms underlying the differentially accumulation of flavonoids at different altitude might be due to variations in transport and relocation of flavonoids in C. paliurus leaves, but not different flavonoid biosynthesis pathways. The up-regulation of genes related to energy and protein synthesis might contribute to flavonoid accumulation at high altitudes. This study broadens our understanding of the effect of altitude on metabolite accumulation and biosynthesis in C. paliurus.
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Affiliation(s)
- Zhaokui Du
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Weida Lin
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- Taizhou Vocational College of Science and Technology, Taizhou, China
| | - Binbin Yu
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Jinxing Zhu
- Suichang County Bureau of Agriculture and Rural Affairs, Lishui, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
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Ma J, Zhang T, Wang W, Chen Y, Cai W, Zhu B, Xu L, Gao H, Zhang L, Li J, Gao X. Comparative Transcriptome Analyses of Gayal (Bos frontalis), Yak (Bos grunniens), and Cattle (Bos taurus) Reveal the High-Altitude Adaptation. Front Genet 2022; 12:778788. [PMID: 35087567 PMCID: PMC8789257 DOI: 10.3389/fgene.2021.778788] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Gayal and yak are well adapted to their local high-altitude environments, yet the transcriptional regulation difference of the plateau environment among them remains obscure. Herein, cross-tissue and cross-species comparative transcriptome analyses were performed for the six hypoxia-sensitive tissues from gayal, yak, and cattle. Gene expression profiles for all single-copy orthologous genes showed tissue-specific expression patterns. By differential expression analysis, we identified 3,020 and 1,995 differentially expressed genes (DEGs) in at least one tissue of gayal vs. cattle and yak vs. cattle, respectively. Notably, we found that the adaptability of the gayal to the alpine canyon environment is highly similar to the yak living in the Qinghai-Tibet Plateau, such as promoting red blood cell development, angiogenesis, reducing blood coagulation, immune system activation, and energy metabolism shifts from fatty acid β-oxidation to glycolysis. By further analyzing the common and unique DEGs in the six tissues, we also found that numerous expressed regulatory genes related to these functions are unique in the gayal and yak, which may play important roles in adapting to the corresponding high-altitude environment. Combined with WGCNA analysis, we found that UQCRC1 and COX5A are the shared differentially expressed hub genes related to the energy supply of myocardial contraction in the heart-related modules of gayal and yak, and CAPS is a shared differential hub gene among the hub genes of the lung-related module, which is related to pulmonary artery smooth muscle contraction. Additionally, EDN3 is the unique differentially expressed hub gene related to the tracheal epithelium and pulmonary vasoconstriction in the lung of gayal. CHRM2 is a unique differentially expressed hub gene that was identified in the heart of yak, which has an important role in the autonomous regulation of the heart. These results provide a basis for further understanding the complex transcriptome expression pattern and the regulatory mechanism of high-altitude domestication of gayal and yak.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Junya Li
- *Correspondence: Junya Li, ; Xue Gao,
| | - Xue Gao
- *Correspondence: Junya Li, ; Xue Gao,
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Huang M, Zhang X, Yan W, Liu J, Wang H. Metabolomics reveals potential plateau adaptability by regulating
inflammatory response and oxidative stress-related metabolism and energy
metabolism pathways in yak. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2021; 64:97-109. [PMID: 35174345 PMCID: PMC8819316 DOI: 10.5187/jast.2021.e129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/14/2021] [Accepted: 11/30/2021] [Indexed: 11/23/2022]
Abstract
Species are facing strong selection pressures to adapt to inhospitable
high-altitude environments. Yaks are a valuable species and an iconic symbol of
the Qinghai-Tibet Plateau. Extensive studies of high-altitude adaptation have
been conducted, but few have focused on metabolism. In the present study, we
determined the differences in the serum metabolomics between yaks and the
closely related species of low-altitude yellow cattle and dairy cows. We
generated high-quality metabolite profiling data for 36 samples derived from the
three species, and a clear separation trend was obtained between yaks and the
other animals from principal component analysis. In addition, we identified a
total of 63 differentially expressed metabolites among the three species.
Functional analysis revealed that differentially expressed metabolites were
related to the innate immune activation, oxidative stress-related metabolism,
and energy metabolism in yaks, which indicates the important roles of
metabolites in high-altitude adaptation in yaks. The results provide new
insights into the mechanism of adaptation or acclimatization to high-altitude
environments in yaks and hypoxia-related diseases in humans.
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Affiliation(s)
- Meizhou Huang
- Department of Toxicology, School of Public
Health, Lanzhou University, Gansu 730000, China
- Academician (Expert) Workstation of
Sichuan Province, The Affiliated Hospital of Southwest Medical
University, Sichuan 646000, China
| | - Xin Zhang
- Department of Toxicology, School of Public
Health, Lanzhou University, Gansu 730000, China
| | - Wenjun Yan
- Agricultural and Rural Integrated Service
Center of Dachaigou Town, Tianzhu Tibetan Autonomous County,
Gansu 733202, China
| | - Jingjing Liu
- Department of Toxicology, School of Public
Health, Lanzhou University, Gansu 730000, China
| | - Hui Wang
- Department of Toxicology, School of Public
Health, Lanzhou University, Gansu 730000, China
- Corresponding author: Hui Wang, Department of
Toxicology, School of Public Health, Lanzhou University, Gansu 730000, China.
Tel: +86-13919330832, E-mail:
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Yang P, Wang D, Kang L. Alternative splicing level related to intron size and organism complexity. BMC Genomics 2021; 22:853. [PMID: 34819032 PMCID: PMC8614042 DOI: 10.1186/s12864-021-08172-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 11/12/2021] [Indexed: 12/25/2022] Open
Abstract
Background Alternative splicing is the process of selecting different combinations of splice sites to produce variably spliced mRNAs. However, the relationships between alternative splicing prevalence and level (ASP/L) and variations of intron size and organism complexity (OC) remain vague. Here, we developed a robust protocol to analyze the relationships between ASP/L and variations of intron size and OC. Approximately 8 Tb raw RNA-Seq data from 37 eumetazoan species were divided into three sets of species based on variations in intron size and OC. Results We found a strong positive correlation between ASP/L and OC, but no correlation between ASP/L and intron size across species. Surprisingly, ASP/L displayed a positive correlation with mean intron size of genes within individual genomes. Moreover, our results revealed that four ASP/L-related pathways contributed to the differences in ASP/L that were associated with OC. In particular, the spliceosome pathway displayed distinct genomic features, such as the highest gene expression level, conservation level, and fraction of disordered regions. Interestingly, lower or no obvious correlations were observed among these genomic features. Conclusions The positive correlation between ASP/L and OC ubiquitously exists in eukaryotes, and this correlation is not affected by the mean intron size of these species. ASP/L-related splicing factors may play an important role in the evolution of OC. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08172-2.
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Affiliation(s)
- Pengcheng Yang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Depin Wang
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Le Kang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
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Zhang ZS, Zeng QY, Liu YJ. Frequent ploidy changes in Salicaceae indicates widespread sharing of the salicoid whole genome duplication by the relatives of Populus L. and Salix L. BMC PLANT BIOLOGY 2021; 21:535. [PMID: 34773988 PMCID: PMC8590345 DOI: 10.1186/s12870-021-03313-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUNDS Populus and Salix belong to Salicaceae and are used as models to investigate woody plant physiology. The variation of karyotype and nuclear DNA content can partly reflect the evolutionary history of the whole genome, and can provide critical information for understanding, predicting, and potentially ameliorating the woody plant traits. Therefore, it is essential to study the chromosome number (CN) and genome size in detail to provide information for revealing the evolutionary process of Salicaceae. RESULTS In this study, we report the somatic CNs of seventeen species from eight genera in Salicaceae. Of these, CNs for twelve species and for five genera are reported for the first time. Among the three subfamilies of Salicaceae, the available data indicate CN in Samydoideae is n = 21, 22, 42. The only two genera, Dianyuea and Scyphostegia, in Scyphostegioideae respectively have n = 9 and 18. In Salicoideae, Populus, Salix and five genera closely related to them (Bennettiodendron, Idesia, Carrierea, Poliothyrsis, Itoa) are based on relatively high CNs from n = 19, 20, 21, 22 to n = 95 in Salix. However, the other genera of Salicoideae are mainly based on relatively low CNs of n = 9, 10, 11. The genome sizes of 35 taxa belonging to 14 genera of Salicaceae were estimated. Of these, the genome sizes of 12 genera and all taxa except Populus euphratica are first reported. Except for Dianyuea, Idesia and Bennettiodendron, all examined species have relatively small genome sizes of less than 1 pg, although polyploidization exists. CONCLUSIONS The variation of CN and genome size across Salicaceae indicates frequent ploidy changes and a widespread sharing of the salicoid whole genome duplication (WGD) by the relatives of Populus and Salix. The shrinkage of genome size after WGD indicates massive loss of genomic components. The phylogenetic asymmetry in clade of Populus, Salix, and their close relatives suggests that there is a lag-time for the subsequent radiations after the salicoid WGD event. Our results provide useful data for studying the evolutionary events of Salicaceae.
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Affiliation(s)
- Zhong-Shuai Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091, Beijing, China
| | - Qing-Yin Zeng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091, Beijing, China
| | - Yan-Jing Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091, Beijing, China.
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Fu W, Wang R, Nanaei HA, Wang J, Hu D, Jiang Y. RGD v2.0: a major update of the ruminant functional and evolutionary genomics database. Nucleic Acids Res 2021; 50:D1091-D1099. [PMID: 34643708 PMCID: PMC8728256 DOI: 10.1093/nar/gkab887] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/10/2021] [Accepted: 10/05/2021] [Indexed: 12/26/2022] Open
Abstract
Ruminant Genome Database (RGD; http://animal.nwsuaf.edu.cn/RGD) provides visualization and analysis tools for ruminant comparative genomics and functional annotations. As more high-quality ruminant genome assemblies have become available, we have redesigned the user interface, integrated and expanded multi-omics data, and developed novel features to improve the database. The new version, RGD v2.0, houses 78 ruminant genomes; 110-species synteny alignments for major livestock (including cattle, sheep, goat) and wild ungulates; 21 012 orthologous gene clusters with Gene Ontology and pathway annotation; ∼8 600 000 conserved elements; and ∼1 000 000 cis-regulatory elements by utilizing 1053 epigenomic data sets. The transcriptome data in RGD v2.0 has nearly doubled, currently with 1936 RNA-seq data sets, and 155 174 phenotypic data sets have been newly added. New and updated features include: (i) The UCSC Genome Browser, BLAT, BLAST and Table Browser tools were updated for six available ruminant livestock species. (ii) The LiftOver tool was newly introduced into our browser to allow coordinate conversion between different ruminant assemblies. And (iii) tissue specificity index, tau, was calculated to facilitate batch screening of specifically expressed genes. The enhanced genome annotations and improved functionality in RGD v2.0 will be useful for study of genome evolution, environmental adaption, livestock breeding and biomedicine.
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Affiliation(s)
- Weiwei Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.,Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China
| | - Rui Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.,Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China
| | - Hojjat Asadollahpour Nanaei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.,Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China
| | - Jinxin Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.,Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China
| | - Dexiang Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.,Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.,Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China
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Using weighted gene co-expression network analysis (WGCNA) to identify the hub genes related to hypoxic adaptation in yak (Bos grunniens). Genes Genomics 2021; 43:1231-1246. [PMID: 34338989 DOI: 10.1007/s13258-021-01137-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/29/2021] [Indexed: 12/29/2022]
Abstract
BACKGROUND As a mammal living at the highest altitude in the world, the yak has strong adaptability to the harsh natural environment (such as low temperature, scarce food, especially low oxygen) of Qinghai-Tibet Plateau (QTP) after a long process of natural selection. OBJECTIVE Here, we used Weighted Correlation Network Analysis (WGCNA), a systematic biology method, to identify hypoxic adaptation-related modules and hub genes. The research of the adaptability of yak against hypoxia is of great significance to identify the genetic characteristics and yak breeding. METHODS Based on the transcriptome sequencing data (PRJNA362606), the R package DESeq2 and WGCNA were conducted to analyze differentially expressed genes (DEGs) and construct the gene co-expression network. The module hub genes were identified and characterized by the correlation of gene and trait, module membership (kME). In addition, GO and KEGG enrichment analyses were used to explore the functions of hub genes. RESULTS Our results revealed that 1098, 1429, and 1645 DEGs were identified in muscle, spleen, and lung, respectively. Besides, a total of 13 gene co-expression modules were detected, of which two hypoxic adaptation-related modules (saddlebrown and turquoise) were found. We identified 39 and 150 hub genes in these two modules. Functional enrichment analyses showed that 12 GO terms and 18 KEGG pathways were enriched in the saddlebrown module while 85 GO terms and 22 KEGG pathways were enriched in the turquoise module. The significant pathways related to hypoxia adaptation include FoxO signaling pathway, Thermogenesis pathway, and Retrograde endocannabinoid signaling pathway, etc. CONCLUSIONS: In this study, we obtained two hypoxia-related specific modules and identified hub genes based on the connectivity by constructing a weighted gene co-expression network. Function enrichment analysis of two modules revealed mitochondrion is the most important organelle for hypoxia adaptation. Moreover, the insulin-related pathways and thermogenic-related pathways played a major role. The results of this study provide theoretical guidance for further understanding the molecular mechanism of yak adaptation to hypoxia.
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Zhang J, Hou L, Zuo Z, Ji P, Zhang X, Xue Y, Zhao F. Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long. Nat Biotechnol 2021; 39:836-845. [PMID: 33707777 DOI: 10.1038/s41587-021-00842-6] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 02/08/2023]
Abstract
Reconstructing the sequence of circular RNAs (circRNAs) from short RNA sequencing reads has proved challenging given the similarity of circRNAs and their corresponding linear messenger RNAs. Previous sequencing methods were unable to achieve high-throughput detection of full-length circRNAs. Here we describe a protocol for enrichment and full-length sequencing of circRNA isoforms using nanopore technology. Circular reverse transcription and size selection achieves a 20-fold higher enrichment of circRNAs from total RNA compared to previous methods. We developed an algorithm, called circRNA identifier using long-read sequencing data (CIRI-long), to reconstruct the sequence of circRNAs. The workflow was validated with simulated data and by comparison to Illumina sequencing as well as quantitative real-time RT-PCR. We used CIRI-long to analyze adult mouse brain samples and systematically profile circRNAs, including mitochondria-derived and transcriptional read-through circRNAs. We identified a new type of intronic self-ligated circRNA that exhibits special splicing and expression patterns. Our method takes advantage of nanopore long reads and enables unbiased reconstruction of full-length circRNA sequences.
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Affiliation(s)
- Jinyang Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lingling Hou
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Zhenqiang Zuo
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Peifeng Ji
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xiaorong Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China. .,Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China.
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Wang H, Zhong J, Wang J, Chai Z, Zhang C, Xin J, Wang J, Cai X, Wu Z, Ji Q. Whole-Transcriptome Analysis of Yak and Cattle Heart Tissues Reveals Regulatory Pathways Associated With High-Altitude Adaptation. Front Genet 2021; 12:579800. [PMID: 34093634 PMCID: PMC8176224 DOI: 10.3389/fgene.2021.579800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 04/26/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The yak (Bos grunniens) is an important livestock species that can survive the extremely cold, harsh, and oxygen-poor conditions of the Qinghai-Tibetan Plateau and provide meat, milk, and transportation for the Tibetans living there. However, the regulatory network that drive this hypoxic adaptation remain elusive. RESULTS The heart tissues from LeiRoqi (LWQY) yak and their related cattle (Bos Taurus) breeds, which are two native cattle breeds located in high altitude (HAC) and low altitude (LAC) regions, respectively, were collected for RNA sequencing. A total of 178 co-differentially expressed protein-coding transcripts (co-DETs) were discovered in each of the LAC-vs-LWQY and LAC-vs-HAC comparison groups, including NFATC2, NFATC1, ENPP2, ACSL4, BAD, and many other genes whose functions were reported to be associated with the immune-system, endocrine-system, and lipid metabolism. Two and 230 lncRNA transcripts were differentially expressed in the LAC-vs-LWQY and LAC-vs-HAC comparisons' respectively, but no lncRNA transcripts that were co-differentially expressed. Among the 58 miRNAs that were co-differentially expressed, 18 were up-regulated and 40 were down-regulated. In addition, 640 (501 up-regulated and 139 down-regulated) and 152 (152 up-regulated and one down-regulated) circRNAs showed differential expression in LAC-vs-LWQY and LAC-vs-HAC comparison groups, respectively, and 53 up-regulated co-differentially expressed circRNAs were shared. Multiple co-DETs, which are the targets of miRNAs/lncRNAs, are significantly enriched in high-altitude adaptation related processes, such as, T cell receptor signaling, VEGF signaling, and cAMP signaling. A competing endogenous RNA (ceRNA) network was constructed by integrating the competing relationships among co-differentially expressed mRNAs, miRNAs, lncRNAs and circRNAs. Furthermore, the hypoxic adaptation related ceRNA network was constructed, and the six mRNAs (MAPKAPK3, PXN, NFATC2, ATP7A, DIAPH1, and F2R), the eight miRNAs (including miR-195), and 15 circRNAs (including novel-circ-017096 and novel-circ-018073) are proposed as novel and promising candidates for regulation of hypoxic adaptation in the heart. CONCLUSION In conclusion, the data recorded in the present study provides new insights into the molecular network of high-altitude adaptation along with more detailed information of protein-coding transcripts and non-coding transcripts involved in this physiological process, the detailed mechanisms behind how these transcripts "crosstalk" with each other during the plateau adaptation are worthy of future research efforts.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Jikun Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Zhixin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Chengfu Zhang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, China
| | - Jinwei Xin
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, China
| | - Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Xin Cai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Zhijuan Wu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Qiumei Ji
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, China
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Chen G, Yin Y, Lin Z, Wen H, Chen J, Luo W. Transcriptome profile analysis reveals KLHL30 as an essential regulator for myoblast differentiation. Biochem Biophys Res Commun 2021; 559:84-91. [PMID: 33933993 DOI: 10.1016/j.bbrc.2021.04.086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 04/20/2021] [Indexed: 11/29/2022]
Abstract
Skeletal muscle development is a sophisticated multistep process orchestrated by diverse myogenic transcription factors. Recent studies have suggested that Kelch-like genes play vital roles in muscle disease and myogenesis. However, it is still unclear how Kelch-like genes impact myoblast physiology. Here, through integrative analysis of the mRNA expression profile during chicken primary myoblast and C2C12 differentiation, many differentially expressed genes were found and suggested to be enriched in myoblast differentiation and muscle development. Interestingly, a little-known Kelch-like gene KLHL30 was screened as skeletal muscle-specific gene with essential roles in myogenic differentiation. Transcriptomic data and quantitative PCR analysis indicated that the expression of KLHL30 is upregulated under myoblast differentiation state. KLHL30 overexpression upregulated the protein expression of myogenic transcription factors (MYOD, MYOG, MEF2C) and induced myoblast differentiation and myotube formation, while knockdown of KLHL30 caused the opposite effect. Furthermore, KLHL30 was found to significantly decrease the numbers of cells in the S stage and thereby depress myoblast proliferation. Collectively, this study highlights that KLHL30 as a muscle-specific regulator plays essential roles in myoblast proliferation and differentiation.
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Affiliation(s)
- Genghua Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong Province, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, 510642, China
| | - Yunqian Yin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong Province, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, 510642, China
| | - Zetong Lin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong Province, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, 510642, China
| | - Huaqiang Wen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong Province, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, 510642, China
| | - Jiahui Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong Province, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, 510642, China
| | - Wen Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong Province, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, 510642, China.
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Wang T, Guo Y, Liu S, Zhang C, Cui T, Ding K, Wang P, Wang X, Wang Z. KLF4, a Key Regulator of a Transitive Triplet, Acts on the TGF-β Signaling Pathway and Contributes to High-Altitude Adaptation of Tibetan Pigs. Front Genet 2021; 12:628192. [PMID: 33936161 PMCID: PMC8082500 DOI: 10.3389/fgene.2021.628192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/10/2021] [Indexed: 11/13/2022] Open
Abstract
Tibetan pigs are native mammalian species on the Tibetan Plateau that have evolved distinct physiological traits that allow them to tolerate high-altitude hypoxic environments. However, the genetic mechanism underlying this adaptation remains elusive. Here, based on multitissue transcriptional data from high-altitude Tibetan pigs and low-altitude Rongchang pigs, we performed a weighted correlation network analysis (WGCNA) and identified key modules related to these tissues. Complex network analysis and bioinformatics analysis were integrated to identify key genes and three-node network motifs. We found that among the six tissues (muscle, liver, heart, spleen, kidneys, and lungs), lung tissue may be the key organs for Tibetan pigs to adapt to hypoxic environment. In the lung tissue of Tibetan pigs, we identified KLF4, BCL6B, EGR1, EPAS1, SMAD6, SMAD7, KDR, ATOH8, and CCN1 genes as potential regulators of hypoxia adaption. We found that KLF4 and EGR1 genes might simultaneously regulate the BCL6B gene, forming a KLF4-EGR1-BCL6B complex. This complex, dominated by KLF4, may enhance the hypoxia tolerance of Tibetan pigs by mediating the TGF-β signaling pathway. The complex may also affect the PI3K-Akt signaling pathway, which plays an important role in angiogenesis caused by hypoxia. Therefore, we postulate that the KLF4-EGR1-BCL6B complex may be beneficial for Tibetan pigs to survive better in the hypoxia environments. Although further molecular experiments and independent large-scale studies are needed to verify our findings, these findings may provide new details of the regulatory architecture of hypoxia-adaptive genes and are valuable for understanding the genetic mechanism of hypoxic adaptation in mammals.
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Affiliation(s)
- Tao Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Yuanyuan Guo
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Shengwei Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Chaoxin Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Tongyan Cui
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Kun Ding
- College of Computer Science and Technology, Inner Mongolia Normal University, Hohhot, China
| | - Peng Wang
- HeiLongJiang Provincial Husbandry Department, Harbin, China
| | - Xibiao Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Zhipeng Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
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37
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Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing. Nat Methods 2021; 18:491-498. [PMID: 33820988 PMCID: PMC8107137 DOI: 10.1038/s41592-021-01109-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 03/03/2021] [Indexed: 01/09/2023]
Abstract
Bacterial DNA methylation occurs at diverse sequence contexts and plays important functional roles in cellular defense and gene regulation. Existing methods for detecting DNA modification from nanopore sequencing data do not effectively support de novo study of unknown bacterial methylomes. In this work, we observed that a nanopore sequencing signal displays complex heterogeneity across methylation events of the same type. To enable nanopore sequencing for broadly applicable methylation discovery, we generated a training dataset from an assortment of bacterial species and developed a method, named nanodisco ( https://github.com/fanglab/nanodisco ), that couples the identification and fine mapping of the three forms of methylation into a multi-label classification framework. We applied it to individual bacteria and the mouse gut microbiome for reliable methylation discovery. In addition, we demonstrated the use of DNA methylation for binning metagenomic contigs, associating mobile genetic elements with their host genomes and identifying misassembled metagenomic contigs.
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38
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Chen Y, Chen H, Zhong Q, Yun YH, Chen W, Chen W. Determination of Microbial Diversity and Community Composition in Unfermented and Fermented Washing Rice Water by High-Throughput Sequencing. Curr Microbiol 2021; 78:1730-1740. [PMID: 33704531 DOI: 10.1007/s00284-021-02400-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/10/2021] [Indexed: 11/28/2022]
Abstract
Washing rice water (WRW) refers to the sewage produced by rice washing in China and other parts of Asia people's daily life. As in the WRW is rich a variety of nutrients, microorganisms are prone to multiply and pollute the environment. In this article, high-throughput sequencing is used to describe the microbial diversity in different fermentation time WRW. The results showed that the sequencing depth effectively covered the microbial species in the samples, and the bacterial community structure in the samples of WRW at different fermentation periods was rich in diversity. Preominant taxa included Proteobacteria (62%), Firmicutes (28%), approximately Cyanobacteria (10%) and Bacteroidetes (0.5%). The core WRW microbiome comprises Trabulsiella, Pseudomonas, Serratia, Lactobacillus, Erwinia, Enterobacter, Clostridium and Acinetobacter, some of which are potential beneficial microbes. The change of microbial community composition with the change of habitat was assessed. It was found that environmental factors had significant influence on the assembly structure of microbial community.
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Affiliation(s)
- Youlin Chen
- College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou, 570228, China
| | - Haiming Chen
- College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou, 570228, China
| | - Qiuping Zhong
- College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou, 570228, China
| | - Yong-Huan Yun
- College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou, 570228, China
| | - Weijun Chen
- College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou, 570228, China. .,Chunguang Agro-Product Processing Institute, Wenchang, 571333, China.
| | - Wenxue Chen
- College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou, 570228, China.
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39
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Cui J, Lu Z, Wang T, Chen G, Mostafa S, Ren H, Liu S, Fu C, Wang L, Zhu Y, Lu J, Chen X, Wei Z, Jin B. The genome of Medicago polymorpha provides insights into its edibility and nutritional value as a vegetable and forage legume. HORTICULTURE RESEARCH 2021; 8:47. [PMID: 33642569 PMCID: PMC7917105 DOI: 10.1038/s41438-021-00483-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/12/2020] [Accepted: 12/17/2020] [Indexed: 05/20/2023]
Abstract
Medicago polymorpha is a nutritious and palatable forage and vegetable plant that also fixes nitrogen. Here, we reveal the chromosome-scale genome sequence of M. polymorpha using an integrated approach including Illumina, PacBio and Hi-C technologies. We combined PacBio full-length RNA-seq, metabolomic analysis, structural anatomy analysis and related physiological indexes to elucidate the important agronomic traits of M. polymorpha for forage and vegetable usage. The assembled M. polymorpha genome consisted of 457.53 Mb with a long scaffold N50 of 57.72 Mb, and 92.92% (441.83 Mb) of the assembly was assigned to seven pseudochromosomes. Comparative genomic analysis revealed that expansion and contraction of the photosynthesis and lignin biosynthetic gene families, respectively, led to enhancement of nutritious compounds and reduced lignin biosynthesis in M. polymorpha. In addition, we found that several positively selected nitrogen metabolism-related genes were responsible for crude protein biosynthesis. Notably, the metabolomic results revealed that a large number of flavonoids, vitamins, alkaloids, and terpenoids were enriched in M. polymorpha. These results imply that the decreased lignin content but relatively high nutrient content of M. polymorpha enhance its edibility and nutritional value as a forage and vegetable. Our genomic data provide a genetic basis that will accelerate functional genomic and breeding research on M. polymorpha as well as other Medicago and legume plants.
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Affiliation(s)
- Jiawen Cui
- College of Horticulture and Plant Protection, Yangzhou University, 225009, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, China
| | - Zhaogeng Lu
- College of Horticulture and Plant Protection, Yangzhou University, 225009, Yangzhou, China
| | - Tianyi Wang
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Gang Chen
- College of Bioscience and Biotechnology, Yangzhou University, 225009, Yangzhou, China
| | - Salma Mostafa
- College of Horticulture and Plant Protection, Yangzhou University, 225009, Yangzhou, China
| | - Hailong Ren
- College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, China
| | - Sian Liu
- College of Horticulture and Plant Protection, Yangzhou University, 225009, Yangzhou, China
| | - Chunxiang Fu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, China
| | - Li Wang
- College of Horticulture and Plant Protection, Yangzhou University, 225009, Yangzhou, China
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 475001, Kaifeng, China
| | - Jinkai Lu
- College of Horticulture and Plant Protection, Yangzhou University, 225009, Yangzhou, China
| | - Xiang Chen
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Zhenwu Wei
- College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, China.
| | - Biao Jin
- College of Horticulture and Plant Protection, Yangzhou University, 225009, Yangzhou, China.
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40
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Duan M, Wang Z, Guo X, Wang K, Liu S, Zhang B, Shang P. Integrated analysis of transcriptomic and proteomic analyses reveals different metabolic patterns in the livers of Tibetan and Yorkshire pigs. Anim Biosci 2020; 34:922-930. [PMID: 33152227 PMCID: PMC8100475 DOI: 10.5713/ajas.20.0342] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 09/13/2020] [Indexed: 11/27/2022] Open
Abstract
Objective Tibetan pigs, predominantly originating from the Tibetan Plateau, have been subjected to long-term natural selection in an extreme environment. To characterize the metabolic adaptations to hypoxic conditions, transcriptomic and proteomic expression patterns in the livers of Tibetan and Yorkshire pigs were compared. Methods RNA and protein were extracted from liver tissue of Tibetan and Yorkshire pigs (n = 3, each). Differentially expressed genes and proteins were subjected to gene ontology and Kyoto encyclopedia of genes and genomes functional enrichment analyses. Results In the RNA-Seq and isobaric tags for relative and absolute quantitation analyses, a total of 18,791 genes and 3,390 proteins were detected and compared. Of these, 273 and 257 differentially expressed genes and proteins were identified. Evidence from functional enrichment analysis showed that many genes were involved in metabolic processes. The combined transcriptomic and proteomic analyses revealed that small molecular biosynthesis, metabolic processes, and organic hydroxyl compound metabolic processes were the major processes operating differently in the two breeds. The important genes include retinol dehydrogenase 16, adenine phosphoribosyltransferase, prenylcysteine oxidase 1, sorbin and SH3 domain containing 2, ENSSSCG00000036224, perilipin 2, ladinin 1, kynurenine aminotransferase 1, and dimethylarginine dimethylaminohydrolase 1. Conclusion The findings of this study provide novel insight into the high-altitude metabolic adaptation of Tibetan pigs.
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Affiliation(s)
- Mengqi Duan
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Xizang 86000, China
| | - Zhenmei Wang
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Xizang 86000, China
| | - Xinying Guo
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Xizang 86000, China
| | - Kejun Wang
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Siyuan Liu
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Xizang 86000, China
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Peng Shang
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Xizang 86000, China
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41
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Sun HZ, Zhu Z, Zhou M, Wang J, Dugan MER, Guan LL. Gene co-expression and alternative splicing analysis of key metabolic tissues to unravel the regulatory signatures of fatty acid composition in cattle. RNA Biol 2020; 18:854-862. [PMID: 32931715 DOI: 10.1080/15476286.2020.1824060] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Increasing the healthy/unhealthy fatty acid (FA) ratio in meat is one of the urgent tasks required to address consumer concerns. However, the regulatory mechanisms ultimately resulting in FA profiles vary among animals and remain largely unknown. In this study, using ~1.2 Tb high-quality RNA-Seq-based transcriptomic data of 188 samples from four key metabolic tissues (rumen, liver, muscle, and backfat) together with the contents of 49 FAs in backfat, the molecular regulatory mechanisms of these tissues contributing to FA formation in cattle were explored. Using this large dataset, the alternative splicing (AS) events, one of the transcriptional regulatory mechanisms in four tissues were identified. The highly conserved and absent AS events were detected in rumen tissue, which may contribute to its functional differences compared with the other three tissues. In addition, the healthy/unhealthy FA ratio related AS events, differential expressed (DE) genes, co-expressed genes, and their functions in four tissues were analysed. Eight key genes were identified from the integrated analysis of DE, co-expressed, and AS genes between animals with high and low healthy/unhealthy FA ratios. This study provides an applicable pipeline for AS events based on comprehensive RNA-Seq analysis and improves our understanding of the regulatory mechanism of FAs in beef cattle.
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Affiliation(s)
- Hui-Zeng Sun
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China.,Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhi Zhu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Department of Animal Science, Southwest University, Chongqing, P.R. China
| | - Mi Zhou
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Jian Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Michael E R Dugan
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
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42
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Müller NA, Kersten B, Leite Montalvão AP, Mähler N, Bernhardsson C, Bräutigam K, Carracedo Lorenzo Z, Hoenicka H, Kumar V, Mader M, Pakull B, Robinson KM, Sabatti M, Vettori C, Ingvarsson PK, Cronk Q, Street NR, Fladung M. A single gene underlies the dynamic evolution of poplar sex determination. NATURE PLANTS 2020; 6:630-637. [PMID: 32483326 DOI: 10.1038/s41477-020-0672-9] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 04/22/2020] [Indexed: 05/20/2023]
Abstract
Although hundreds of plant lineages have independently evolved dioecy (that is, separation of the sexes), the underlying genetic basis remains largely elusive1. Here we show that diverse poplar species carry partial duplicates of the ARABIDOPSIS RESPONSE REGULATOR 17 (ARR17) orthologue in the male-specific region of the Y chromosome. These duplicates give rise to small RNAs apparently causing male-specific DNA methylation and silencing of the ARR17 gene. CRISPR-Cas9-induced mutations demonstrate that ARR17 functions as a sex switch, triggering female development when on and male development when off. Despite repeated turnover events, including a transition from the XY system to a ZW system, the sex-specific regulation of ARR17 is conserved across the poplar genus and probably beyond. Our data reveal how a single-gene-based mechanism of dioecy can enable highly dynamic sex-linked regions and contribute to maintaining recombination and integrity of sex chromosomes.
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Affiliation(s)
- Niels A Müller
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany.
| | - Birgit Kersten
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | | | - Niklas Mähler
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå, Sweden
| | - Carolina Bernhardsson
- Department of Plant Biology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Katharina Bräutigam
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | | | - Hans Hoenicka
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | - Vikash Kumar
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå, Sweden
| | - Malte Mader
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | - Birte Pakull
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | | | - Maurizio Sabatti
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Viterbo, Italy
| | - Cristina Vettori
- Institute of Biosciences and BioResources, Division of Florence, National Research Council, Sesto Fiorentino, Italy
| | - Pär K Ingvarsson
- Department of Plant Biology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Quentin Cronk
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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43
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Tang AD, Soulette CM, van Baren MJ, Hart K, Hrabeta-Robinson E, Wu CJ, Brooks AN. Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns. Nat Commun 2020; 11:1438. [PMID: 32188845 PMCID: PMC7080807 DOI: 10.1038/s41467-020-15171-6] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/06/2020] [Indexed: 01/01/2023] Open
Abstract
While splicing changes caused by somatic mutations in SF3B1 are known, identifying full-length isoform changes may better elucidate the functional consequences of these mutations. We report nanopore sequencing of full-length cDNA from CLL samples with and without SF3B1 mutation, as well as normal B cell samples, giving a total of 149 million pass reads. We present FLAIR (Full-Length Alternative Isoform analysis of RNA), a computational workflow to identify high-confidence transcripts, perform differential splicing event analysis, and differential isoform analysis. Using nanopore reads, we demonstrate differential 3' splice site changes associated with SF3B1 mutation, agreeing with previous studies. We also observe a strong downregulation of intron retention events associated with SF3B1 mutation. Full-length transcript analysis links multiple alternative splicing events together and allows for better estimates of the abundance of productive versus unproductive isoforms. Our work demonstrates the potential utility of nanopore sequencing for cancer and splicing research.
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Affiliation(s)
- Alison D Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95062, USA
| | - Cameron M Soulette
- Department of Molecular Cell & Developmental Biology, University of California, Santa Cruz, CA, 95062, USA
| | - Marijke J van Baren
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95062, USA
| | - Kevyn Hart
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95062, USA
| | - Eva Hrabeta-Robinson
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95062, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institiute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95062, USA.
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Small non-coding RNA transcriptome of four high-altitude vertebrates and their low-altitude relatives. Sci Data 2019; 6:192. [PMID: 31586122 PMCID: PMC6778140 DOI: 10.1038/s41597-019-0204-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/16/2019] [Indexed: 12/19/2022] Open
Abstract
Animals that lived at high altitudes have evolved distinctive physiological traits that allow them to tolerate extreme high-altitude environment, including higher hemoglobin concentration, increased oxygen saturation of blood and a high energy metabolism. Although previous investigations performed plenty of comparison between high- and low-altitude mammals at the level of morphology, physiology and genomics, mechanism underlying high-altitude adaptation remains largely unknown. Few studies provided comparative analyses in high-altitude adaptation, such as parallel analysis in multiple species. In this study, we generated high-quality small RNA sequencing data for six tissues (heart, liver, spleen, lung, kidney and muscle) from low- and high-altitude populations of four typical livestock animals, and identified comparable numbers of miRNAs in each species. This dataset will provide valuable information for understanding the molecular mechanism of high-altitude adaptation in vertebrates.
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45
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E GX, Basang WD, Zhu YB. Whole-genome analysis identifying candidate genes of altitude adaptive ecological thresholds in yak populations. J Anim Breed Genet 2019; 136:371-377. [PMID: 31062447 DOI: 10.1111/jbg.12403] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 12/30/2022]
Abstract
The domestic yak (Bos grunniens) is an iconic symbol of animal husbandry on the Qinghai-Tibet Plateau. Long-term domestication and natural selection have led to a wide distribution of yak, forming many ecological populations to adapt to the local ecological environment. High altitude is closely related to oxygen density, and it is an important environmental ecological factor for biological survival and livestock production. The aim of the present study was to perform a preliminary analysis to identify the candidate genes of altitude distribution adapted ecological thresholds in yak using next-generation sequence technology. A total of 15,762,829 SNPs were obtained from 29 yaks with high- and low-altitude distribution by genome-wide sequencing. According to the results of the selective sweep analysis with FST and ZHp, 21 candidate genes were identified. 14 genes (serine/threonine protein kinase TNNI3K, TEN1, DYM, ITPR1, ZC4H2, KNTC1, ADGRB3, CLYBL, TANGO6, ASCC3, KLHL3, PDE4D, DEPDC1B and AGBL4) were grouped into 32 Gene Ontology terms, and four genes (RPS6KA6, ITPR1, GNAO1 and PDE4D) annotated in 35 pathways, including seven environmental information processing and one environmental adaptation. Therefore, the novel candidate genes found in the current study do not only support new theories about high-altitude adaptation, but also further explain the molecular mechanisms of altitude adaptation threshold in yaks.
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Affiliation(s)
- Guang-Xin E
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wang-Dui Basang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement (Tibet Academy of Agricultural and Animal Husbandry Sciences (TAAAS)), Lhasa, China.,Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Yan-Bin Zhu
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
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46
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Zhang B, Ban D, Gou X, Zhang Y, Yang L, Chamba Y, Zhang H. Genome-wide DNA methylation profiles in Tibetan and Yorkshire pigs under high-altitude hypoxia. J Anim Sci Biotechnol 2019; 10:25. [PMID: 30867905 PMCID: PMC6397503 DOI: 10.1186/s40104-019-0316-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 01/04/2019] [Indexed: 12/21/2022] Open
Abstract
Background Tibetan pigs, which inhabit the Tibetan Plateau, exhibit distinct phenotypic and physiological characteristics from those of lowland pigs and have adapted well to the extreme conditions at high altitude. However, the genetic and epigenetic mechanisms of hypoxic adaptation in animals remain unclear. Methods Whole-genome DNA methylation data were generated for heart tissues of Tibetan pigs grown in the highland (TH, n = 4) and lowland (TL, n = 4), as well as Yorkshire pigs grown in the highland (YH, n = 4) and lowland (YL, n = 4), using methylated DNA immunoprecipitation sequencing. Results We obtained 480 million reads and detected 280679, 287224, 259066, and 332078 methylation enrichment peaks in TH, YH, TL, and YL, respectively. Pairwise TH vs. YH, TL vs. YL, TH vs. TL, and YH vs. YL comparisons revealed 6829, 11997, 2828, and 1286 differentially methylated regions (DMRs), respectively. These DMRs contained 384, 619, 192, and 92 differentially methylated genes (DMGs), respectively. DMGs that were enriched in the hypoxia-inducible factor 1 signaling pathway and pathways involved in cancer and hypoxia-related processes were considered to be important candidate genes for high-altitude adaptation in Tibetan pigs. Conclusions This study elucidates the molecular and epigenetic mechanisms involved in hypoxic adaptation in pigs and may help further understand human hypoxia-related diseases.
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Affiliation(s)
- Bo Zhang
- 1National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Dongmei Ban
- 1National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xiao Gou
- 2College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Yawen Zhang
- 1National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Lin Yang
- 1National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Yangzom Chamba
- 3College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, 860000 Tibet China
| | - Hao Zhang
- 1National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, 100193 China
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47
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Liu R, Jin L, Long K, Tang Q, Ma J, Wang X, Zhu L, Jiang A, Tang G, Jiang Y, Li X, Li M. Analysis of mitochondrial DNA sequence and copy number variation across five high-altitude species and their low-altitude relatives. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:847-851. [PMID: 33474342 PMCID: PMC7799994 DOI: 10.1080/23802359.2018.1501285] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
High-altitude inhospitable environments impose a formidable life challenge for the local animals. Training and exposure to high-altitude environments produce both distinct physiological and phenotypic characteristics. The mitochondrion, an organelle crucial for the energy production, plays an important role in hypoxia adaptation. In this study, we investigated the mitochondrial DNA (mtDNA) polymorphism and copy number variation between the population pairs from distinct altitudes across the multi-species. Higher mitochondrial DNA control region's genetic diversity is conspicuous in high-altitude animals versus low-altitude relatives. We also found an accordant decrease of mtDNA copy number in most of the tissues from high-altitude animals. Compared to mammals, chickens have significantly distinct mitogenomic characteristics, and more significant changes in the skeletal muscle mtDNA copy number between high- and low-altitude individuals. Our study catches a snapshot of the biological similarities and differences in the mitochondrial high-altitude acclimation across the species.
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Affiliation(s)
- Rui Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Long Jin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Keren Long
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qianzi Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jideng Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xun Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - An'an Jiang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Guoqing Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yanzhi Jiang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xuewei Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingzhou Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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48
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Tang Q, Gu Y, Zhou X, Jin L, Guan J, Liu R, Li J, Long K, Tian S, Che T, Hu S, Liang Y, Yang X, Tao X, Zhong Z, Wang G, Chen X, Li D, Ma J, Wang X, Mai M, Jiang A, Luo X, Lv X, Gladyshev VN, Li X, Li M. Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives. Gigascience 2018; 6:1-9. [PMID: 29149296 PMCID: PMC5729692 DOI: 10.1093/gigascience/gix105] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 10/24/2017] [Indexed: 01/22/2023] Open
Abstract
Background Species living at high altitude are subject to strong selective pressures due to inhospitable environments (e.g., hypoxia, low temperature, high solar radiation, and lack of biological production), making these species valuable models for comparative analyses of local adaptation. Studies that have examined high-altitude adaptation have identified a vast array of rapidly evolving genes that characterize the dramatic phenotypic changes in high-altitude animals. However, how high-altitude environment shapes gene expression programs remains largely unknown. Findings We generated a total of 910 Gb of high-quality RNA-seq data for 180 samples derived from 6 tissues of 5 agriculturally important high-altitude vertebrates (Tibetan chicken, Tibetan pig, Tibetan sheep, Tibetan goat, and yak) and their cross-fertile relatives living in geographically neighboring low-altitude regions. Of these, ∼75% reads could be aligned to their respective reference genomes, and on average ∼60% of annotated protein coding genes in each organism showed FPKM expression values greater than 0.5. We observed a general concordance in topological relationships between the nucleotide alignments and gene expression-based trees. Tissue and species accounted for markedly more variance than altitude based on either the expression or the alternative splicing patterns. Cross-species clustering analyses showed a tissue-dominated pattern of gene expression and a species-dominated pattern for alternative splicing. We also identified numerous differentially expressed genes that could potentially be involved in phenotypic divergence shaped by high-altitude adaptation. Conclusions These data serve as a valuable resource for examining the convergence and divergence of gene expression changes between species as they adapt or acclimatize to high-altitude environments.
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Affiliation(s)
- Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yiren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, 02115 USA
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiuqiang Guan
- Yak Research Institute, Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Rui Liu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Kereng Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Shilin Tian
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tiandong Che
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Liang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Xuemei Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Xuan Tao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Zhijun Zhong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Guosong Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Department of Animal Science, Texas A & M University, College Station, Texas, 77843 USA
| | - Xiaohui Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xun Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Miaomiao Mai
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - An'an Jiang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaolin Luo
- Yak Research Institute, Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Xuebin Lv
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, 02115 USA
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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