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Jain K, Panigrahi M, Nayak SS, Rajawat D, Sharma A, Sahoo SP, Bhushan B, Dutt T. The evolution of contemporary livestock species: Insights from mitochondrial genome. Gene 2024; 927:148728. [PMID: 38944163 DOI: 10.1016/j.gene.2024.148728] [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] [Received: 04/16/2024] [Revised: 06/05/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
The domestication of animals marks a pivotal moment in human history, profoundly influencing our demographic and cultural progress. This process has led to significant genetic, behavioral, and physical changes in livestock species compared to their wild ancestors. Understanding the evolutionary history and genetic diversity of livestock species is crucial, and mitochondrial DNA (mtDNA) has emerged as a robust marker for investigating molecular diversity in animals. Its highly conserved gene content across animal species, minimal duplications, absence of introns, and short intergenic regions make mtDNA analysis ideal for such studies. Mitochondrial DNA analysis has uncovered distinct cattle domestication events dating back to 8000 years BC in Southwestern Asia. The sequencing of water buffalo mtDNA in 2004 provided important insights into their domestication history. Caprine mtDNA analysis identified three haplogroups, indicating varied maternal origins. Sheep, domesticated 12,000 years ago, exhibit diverse mtDNA lineages, suggesting multiple domestication events. Ovine mtDNA studies revealed clades A, B, C, and a fourth lineage, group D. The origins of domestic pigs were traced to separate European and Asian events followed by interbreeding. In camels, mtDNA elucidated the phylogeographic structure and genetic differentiation between wild and domesticated species. Horses, domesticated around 3500 BC, show significant mtDNA variability, highlighting their diverse origins. Yaks exhibit unique adaptations for high-altitude environments, with mtDNA analysis providing insights into their adaptation. Chicken mtDNA studies supported a monophyletic origin from Southeast Asia's red jungle fowl, with evidence of multiple origins. This review explores livestock evolution and diversity through mtDNA studies, focusing on cattle, water buffalo, goat, sheep, pig, camel, horse, yak and chicken. It highlights mtDNA's significance in unraveling maternal lineages, genetic diversity, and domestication histories, concluding with insights into its potential application in improving livestock production and reproduction dynamics.
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Affiliation(s)
- Karan Jain
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | | | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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Manee MM, Al-Shomrani BM, Alqahtani FH. Mitochondrial DNA of the Arabian Camel Camelus dromedarius. Animals (Basel) 2024; 14:2460. [PMID: 39272245 PMCID: PMC11394021 DOI: 10.3390/ani14172460] [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: 07/30/2024] [Revised: 08/21/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
The Camelidae family, ranging from southwest Asia to north Africa, South America, and Australia, includes key domesticated species adapted to diverse environments. Among these, the Arabian camel (Camelus dromedarius) is vital to the cultural and economic landscape of the Arabian Peninsula. This review explores the mitochondrial DNA of the dromedary camel, focusing on the D-loop region to understand its genetic diversity, maternal inheritance, and evolutionary history. We aim to investigate the unique characteristics of Arabian camel mtDNA, analyze the D-loop for genetic diversity and maternal lineage patterns, and explore the implications of mitochondrial genomic studies for camel domestication and adaptation. Key findings on mtDNA structure and variation highlight significant genetic differences and adaptive traits. The D-loop, essential for mtDNA replication and transcription, reveals extensive polymorphisms and haplotypes, providing insights into dromedary camel domestication and breeding history. Comparative analyses with other camelid species reveal unique genetic signatures in the Arabian camel, reflecting its evolutionary and adaptive pathways. Finally, this review integrates recent advancements in mitochondrial genomics, demonstrating camel genetic diversity and potential applications in conservation and breeding programs. Through comprehensive mitochondrial genome analysis, we aim to enhance the understanding of Camelidae genetics and contribute to the preservation and improvement of these vital animals.
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Affiliation(s)
- Manee M Manee
- National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
- Advanced Agricultural and Food Technologies Institute, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Badr M Al-Shomrani
- National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
- Advanced Agricultural and Food Technologies Institute, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Fahad H Alqahtani
- National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
- Advanced Agricultural and Food Technologies Institute, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
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3
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Tian H, Zhang H, Shi X, Ma W, Zhang J. Population genetic diversity and environmental adaptation of Tamarix hispida in the Tarim Basin, arid Northwestern China. Heredity (Edinb) 2024:10.1038/s41437-024-00714-0. [PMID: 39138378 DOI: 10.1038/s41437-024-00714-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 08/06/2024] [Accepted: 08/06/2024] [Indexed: 08/15/2024] Open
Abstract
Arid ecosystems, characterized by severe water scarcity, play a crucial role in preserving Earth's biodiversity and resources. The Tarim Basin in Northwestern China, a typical arid region isolated by the Tianshan Mountains and expansive deserts, provides a special study area for investigating how plant response and adaptation to such environments. Tamarix hispida, a species well adapted to saline-alkaline and drought conditions, dominates in the saline-alkali lands of the Tarim Basin. This study aims to examine the genetic diversity and environmental adaptation of T. hispida in the Tarim Basin. Genomic SNPs for a total of 160 individuals from 17 populations were generated using dd-RAD sequencing approach. Population genetic structure and genetic diversity were analyzed by methods including ADMIXTURE, PCA, and phylogenetic tree. Environmental association analysis (EAA) was performed using LFMM and RDA analyses. The results revealed two major genetic lineages with geographical substitution patterns from west to east, indicating significant gene flow and hybridization. Environmental factors such as Precipitation Seasonality (bio15) and Topsoil Sand Fraction (T_SAND) significantly shaped allele frequencies, supporting the species' genetic adaptability. Several genes associated with environmental adaptation were identified and annotated, highlighting physiological and metabolic processes crucial for survival in arid conditions. The study highlights the role of geographical isolation and environmental factors in shaping genetic structure and adaptive evolution. The identified adaptive genes related to stress tolerance emphasize the species' resilience and highlight the importance of specific physiological and metabolic pathways.
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Affiliation(s)
- Haowen Tian
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China
- Xinjiang Key Laboratory of Conservation and Utilization of Gene Resources, Urumqi, Xinjiang, China
- Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Hongxiang Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China.
- Xinjiang Key Laboratory of Conservation and Utilization of Gene Resources, Urumqi, Xinjiang, China.
- Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China.
| | - Xiaojun Shi
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi, Xinjiang, China.
| | - Wenhui Ma
- College of Ecology and Environment, Xinjiang University, Urumqi, 830046, China
| | - Jian Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China
- Xinjiang Key Laboratory of Conservation and Utilization of Gene Resources, Urumqi, Xinjiang, China
- Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China
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Blumstein D, MacManes M. The multi-tissue gene expression and physiological responses of water deprived Peromyscus eremicus. BMC Genomics 2024; 25:770. [PMID: 39118009 PMCID: PMC11308687 DOI: 10.1186/s12864-024-10629-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 07/17/2024] [Indexed: 08/10/2024] Open
Abstract
The harsh and dry conditions of desert environments have resulted in genomic adaptations, allowing for desert organisms to withstand prolonged drought, extreme temperatures, and limited food resources. Here, we present a comprehensive exploration of gene expression across five tissues (kidney, liver, lung, gastrointestinal tract, and hypothalamus) and 19 phenotypic measurements to explore the whole-organism physiological and genomic response to water deprivation in the desert-adapted cactus mouse (Peromyscus eremicus). The findings encompass the identification of differentially expressed genes and correlative analysis between phenotypes and gene expression patterns across multiple tissues. Specifically, we found robust activation of the vasopressin renin-angiotensin-aldosterone system (RAAS) pathways, whose primary function is to manage water and solute balance. Animals reduced food intake during water deprivation, and upregulation of PCK1 highlights the adaptive response to reduced oral intake via its actions aimed at maintained serum glucose levels. Even with such responses to maintain water balance, hemoconcentration still occurred, prompting a protective downregulation of genes responsible for the production of clotting factors while simultaneously enhancing angiogenesis which is thought to maintain tissue perfusion. In this study, we elucidate the complex mechanisms involved in water balance in the desert-adapted cactus mouse, P. eremicus. By prioritizing a comprehensive analysis of whole-organism physiology and multi-tissue gene expression in a simulated desert environment, we describe the complex response of regulatory processes.
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Affiliation(s)
- Danielle Blumstein
- Biomedical Sciences Department, University of New Hampshire, Molecular, Cellular, Durham, NH, DMB, 03824, USA.
| | - Matthew MacManes
- Biomedical Sciences Department, University of New Hampshire, Molecular, Cellular, Durham, NH, DMB, 03824, USA
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Li Z, Fang B, Dong P, Shan W. Selective sweep analysis of the adaptability of the Yarkand hare (Lepus yarkandensis) to hot arid environments using SLAF-seq. Anim Genet 2024; 55:681-686. [PMID: 38722026 DOI: 10.1111/age.13440] [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] [Received: 03/06/2023] [Revised: 03/06/2024] [Accepted: 04/22/2024] [Indexed: 07/04/2024]
Abstract
The Yarkand hare (Lepus yarkandensis) inhabits arid desert areas and is endemic to China. It has evolved various adaptations to survive in hot arid environments, including stress responses, the ability to maintain water homeostasis and heat tolerance. Here, we performed a selective sweep analysis to identify the candidate genes for adaptation to hot arid environments in the Yarkand hare. A total of 397 237 single-nucleotide polymorphisms were obtained from 80 Yarkand hares, which inhabit hot arid environments, and 36 Tolai hares (Lepus tolai), which inhabit environments with a mild climate, via specific-locus amplified fragment sequencing. We identified several candidate genes that were associated with the heat stress response (HSPE1), oxidative stress response (SLC23A and GLRX2), immune response (IL1R1 and IRG1), central nervous system development (FGF13, THOC2, FMR1 and MECP2) and regulation of water homeostasis (CDK1) according to fixation index values and θπ ratios in the selective sweep analysis, and six of these genes (GLRX2, IRG1, FGF13, FMR1, MECP2 and CDK1) are newly discovered genes. To the best of our knowledge, this is the first study to identify candidate genes for adaptation to hot arid environments in the Yarkand hare. The results of this study enhance our understanding of the adaptation of the Yarkand hare to hot arid environments and will aid future studies aiming to functionally verify these candidate genes.
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Affiliation(s)
- Zurui Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Bingwa Fang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Pengcheng Dong
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Wenjuan Shan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
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Bahbahani H. Long-range linkage disequilibrium events on the genome of dromedary camels as a signal of epistatic and directional positive selection. Heliyon 2024; 10:e34343. [PMID: 39100441 PMCID: PMC11295981 DOI: 10.1016/j.heliyon.2024.e34343] [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: 06/27/2024] [Accepted: 07/08/2024] [Indexed: 08/06/2024] Open
Abstract
The genome of dromedary camels has been subjected to various evolutionary forces, such as genetic admixture, natural positive selection, and epistatic selection. These forces are considered as main factors associated with the formation of long-range linkage disequilibrium (LRLD) events. We have analyzed whole-genome data of 56 dromedary camel samples from different geographical regions across the Arabian Peninsula for two main purposes: first, to assess the level of linkage disequilibrium, and second, to identify autosomal LRLD events. The analysis revealed a mean r 2 value of 0.25 (±0.028) over the dromedary autosomes, with a continuous decay until reaching a plateau at inter-variant distances >400 kb. A total of 1847 LRLD events were identified within the dromedary autosomes, which harbor 36 prevalent haplotypes. A level of genetic admixture was observed among the dromedary populations analyzed, which might be a source for the observed LRLD events. Four functional interactions were revealed among the genes found within the LRLD events, with some genes overlapping with prevalent haplotypes, indicative of potential epistatic selection. Genes related to renal function, fertility, thermal regulation, bone structure, and insulin regulation were found among the LRLD genes. These genes, along with the defined prevalent haplotypes, can be considered as hotspots for natural positive selection associated with the LRLD distribution on dromedary genomes. In this study, we have for the first time analyzed the genome of dromedary camels for LRLD events possibly influenced by forces including genetic admixture, epistatic and positive selection. The revealed LRLD elements and prevalent haplotypes should be accounted for when designing breeding programmes to conserve the genetic stock of this well-adapted domestic species.
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Affiliation(s)
- Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem Campus, Kuwait
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Bagiyal M, Parsad R, Ahlawat S, Gera R, Chhabra P, Sharma U, Arora R, Sharma R. Review on camel genetic diversity: ecological and economic perspectives. Mamm Genome 2024:10.1007/s00335-024-10054-3. [PMID: 39075281 DOI: 10.1007/s00335-024-10054-3] [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: 06/03/2024] [Accepted: 07/15/2024] [Indexed: 07/31/2024]
Abstract
Camels, known as the "Ship of the Desert," play a vital role in the ecosystems and economies of arid and semi-arid regions. They provide meat, milk, transportation, and other essential services, and their resilience to harsh environments makes them invaluable. Despite their similarities, camel breeds exhibit notable differences in size, color, and structure, with over 40 million camels worldwide. This number is projected to increase, underscoring their growing significance. Economically, camels are crucial for food production, tourism, and trade, with camel racing being particularly significant in Arab countries. Their unique physiological traits, such as low disease susceptibility and efficient water conservation, further enhance their value. Camel products, especially meat and milk, offer substantial nutritional and therapeutic benefits, contributing to their high demand. Genetic diversity studies have advanced our understanding of camels' adaptation to extreme environments. Functional genomics and whole-genome sequencing have identified genes responsible for these adaptations, aiding breeding programs and conservation efforts. High-throughput sequencing has revealed genetic markers linked to traits like milk production and disease resistance. The development of SNP chips has revolutionized genetic studies by providing a cost-effective alternative to whole-genome sequencing. These tools facilitate large-scale genotyping, essential for conserving genetic diversity and improving breeding strategies. To prevent the depletion of camel genetic diversity, it is crucial to streamline in situ and ex situ conservation efforts to maintain their ecological and economic value. A comprehensive approach to camel conservation and genetic preservation, involving advanced genomic technologies, reproductive biotechniques, and sustainable management practices, will ensure their continued contribution to human societies.
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Affiliation(s)
- Meena Bagiyal
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Ram Parsad
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
| | - Ritika Gera
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Upasna Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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Wang Z, Song B, Yao J, Li X, Zhang Y, Tang Z, Yi G. Whole-genome analysis reveals distinct adaptation signatures to diverse environments in Chinese domestic pigs. J Anim Sci Biotechnol 2024; 15:97. [PMID: 38982489 PMCID: PMC11234542 DOI: 10.1186/s40104-024-01053-0] [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: 02/07/2024] [Accepted: 05/20/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Long-term natural and artificial selection has resulted in many genetic footprints within the genomes of pig breeds across distinct agroecological zones. Nevertheless, the mechanisms by which these signatures contribute to phenotypic diversity and facilitate environmental adaptation remain unclear. RESULTS Here, we leveraged whole-genome sequencing data from 82 individuals from 6 domestic pig breeds originating in tropical, high-altitude, and frigid regions. Population genetic analysis suggested that habitat isolation significantly shaped the genetic diversity and contributed to population stratification in local Chinese pig breeds. Analysis of selection signals revealed regions under selection for adaptation in tropical (55.5 Mb), high-altitude (43.6 Mb), and frigid (17.72 Mb) regions. The potential functions of the selective sweep regions were linked to certain complex traits that might play critical roles in different geographic environments, including fat coverage in frigid environments and blood indicators in tropical and high-altitude environments. Candidate genes under selection were significantly enriched in biological pathways involved in environmental adaptation. These pathways included blood circulation, protein degradation, and inflammation for adaptation to tropical environments; heart and lung development, hypoxia response, and DNA damage repair for high-altitude adaptation; and thermogenesis, cold-induced vasodilation (CIVD), and the cell cycle for adaptation to frigid environments. By examining the chromatin state of the selection signatures, we identified the lung and ileum as two candidate functional tissues for environmental adaptation. Finally, we identified a mutation (chr1: G246,175,129A) in the cis-regulatory region of ABCA1 as a plausible promising variant for adaptation to tropical environments. CONCLUSIONS In this study, we conducted a genome-wide exploration of the genetic mechanisms underlying the adaptability of local Chinese pig breeds to tropical, high-altitude, and frigid environments. Our findings shed light on the prominent role of cis-regulatory elements in environmental adaptation in pigs and may serve as a valuable biological model of human plateau-related disorders and cardiovascular diseases.
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Affiliation(s)
- Zhen Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China
| | - Bangmin Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- Shenzhen Research Institute of Henan University, Shenzhen, 518000, China
| | - Jianyu Yao
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong SAR, China
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China
| | - Yan Zhang
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China.
- Bama Yao Autonomous County Rural Revitalization Research Institute, Bama, 547500, China.
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China.
- Bama Yao Autonomous County Rural Revitalization Research Institute, Bama, 547500, China.
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Liang Z, Yue X, Liu Y, Ye M, Zhong L, Luan Y, Wang Q. Genome-Wide Identification of Specific Genetic Loci Common to Sheep and Goat. Biomolecules 2024; 14:638. [PMID: 38927042 PMCID: PMC11201639 DOI: 10.3390/biom14060638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 06/28/2024] Open
Abstract
Sheep and goat may become carriers of some zoonotic diseases. They are important livestock and experimental model animals for human beings. The fast and accurate identification of genetic materials originating from sheep and goat can prevent and inhibit the spread of some zoonotic diseases, monitor market product quality, and maintain the stability of animal husbandry and food industries. This study proposed a methodology for identifying sheep and goat common specific sites from a genome-wide perspective. A total of 150 specific sites were selected from three data sources, including the coding sequences of single copy genes from nine species (sheep, goat, cow, pig, dog, horse, human, mouse, and chicken), the dbSNPs for these species, and human 100-way alignment data. These 150 sites exhibited low intraspecific heterogeneity in the resequencing data of 1450 samples from five species (sheep, goat, cow, pig, and chicken) and high interspecific divergence in the human 100-way alignment data after quality control. The results were proven to be reliable at the data level. Using the process proposed in this study, specific sites of other species can be screened, and genome-level species identification can be performed using the screened sites.
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Affiliation(s)
- Zuoxiang Liang
- State Key Laboratory of Animal Biotech Breeding, 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; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
| | - Xiaoyu Yue
- State Key Laboratory of Animal Biotech Breeding, 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; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
| | - Yangxiu Liu
- State Key Laboratory of Animal Biotech Breeding, 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; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
| | - Mengyan Ye
- State Key Laboratory of Animal Biotech Breeding, 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; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
| | - Ling Zhong
- State Key Laboratory of Animal Biotech Breeding, 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; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
| | - Yue Luan
- State Key Laboratory of Animal Biotech Breeding, 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; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
| | - Qin Wang
- State Key Laboratory of Animal Biotech Breeding, 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; (Z.L.); (X.Y.); (Y.L.); (M.Y.); (L.Z.); (Y.L.)
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10
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Mohanta TK, Mohanta YK, Kaushik P, Kumar J. Physiology, genomics, and evolutionary aspects of desert plants. J Adv Res 2024; 58:63-78. [PMID: 37160225 PMCID: PMC10982872 DOI: 10.1016/j.jare.2023.04.019] [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] [Received: 11/17/2022] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Despite the exposure to arid environmental conditions across the globe ultimately hampering the sustainability of the living organism, few plant species are equipped with several unique genotypic, biochemical, and physiological features to counter such harsh conditions. Physiologically, they have evolved with reduced leaf size, spines, waxy cuticles, thick leaves, succulent hydrenchyma, sclerophyll, chloroembryo, and photosynthesis in nonfoliar and other parts. At the biochemical level, they are evolved to perform efficient photosynthesis through Crassulacean acid metabolism (CAM) and C4 pathways with the formation of oxaloacetic acid (Hatch-Slack pathway) instead of the C3 pathway. Additionally, comparative genomics with existing data provides ample evidence of the xerophytic plants' positive selection to adapt to the arid environment. However, adding more high-throughput sequencing of xerophyte plant species is further required for a comparative genomic study toward trait discovery related to survival. Learning from the mechanism to survive in harsh conditions could pave the way to engineer crops for future sustainable agriculture. AIM OF THE REVIEW The distinct physiology of desert plants allows them to survive in harsh environments. However, the genomic composition also contributes significantly to this and requires great attention. This review emphasizes the physiological and genomic adaptation of desert plants. Other important parameters, such as desert biodiversity and photosynthetic strategy, are also discussed with recent progress in the field. Overall, this review discusses the different features of desert plants, which prepares them for harsh conditions intending to translate knowledge to engineer plant species for sustainable agriculture. KEY SCIENTIFIC CONCEPTS OF REVIEW This review comprehensively presents the physiology, molecular mechanism, and genomics of desert plants aimed towards engineering a sustainable crop.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 611, Oman.
| | - Yugal Kishore Mohanta
- Dept. of Applied Biology, University of Science and Technology Meghalaya, Baridua, Meghalaya 793101, India
| | - Prashant Kaushik
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, 125004, India
| | - Jitesh Kumar
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, United States
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11
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Agamy R, Mahouda SF, Azzam AH, Gad Allah AAI, Abdel-Mageed II. Characteristics of sudanese camel-hair fibres under subtropical desert condition. Trop Anim Health Prod 2024; 56:112. [PMID: 38526648 PMCID: PMC10963578 DOI: 10.1007/s11250-024-03951-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 03/01/2024] [Indexed: 03/27/2024]
Abstract
The study assessed the quality and variability of camel hair fibres in arid regions of Egypt. Raw camel-hair samples were collected from fifteen Sudanese camels divided into seven males (414.60 ± 38.19 kg, BW) and eight females (401.67 ± 26.76 kg BW), and the study investigated the influences of animal sex on both the physical and chemical traits of camel-hair fibers. The relationships among physical properties and both mineral and amino acid content were studied. Camel's sex had no significant effect on any of the studied traits including fibre diameter (FD), prickle factor (PF), medullated fibre (MF), staple length (SL) and staple strength (SS). In the meantime, no significant differences were found between males and females in fibers' minerals contents except potassium, where fibres of females had significantly higher potassium content than those of males. For amino acids contents in camel fibres, camel sex had a significant effect only on glutamic acid, since fibres of males showed higher (P < 0.05) content than females. Fibre diameter had positive (P < 0.01) correlations with prickle factor (r = 0.83) and medullated fibres (r = 0.73). Zinc content in camel fibres was positively correlated with fibre diameter (r = 0.57; P < 0.05) and medullated fibres (r = 0.73; P < 0.01). Moreover, a significant (negative correlation coefficient P < 0.05) was found between fibre diameter and both sulfur and proline contents (r=-0.39 and - 0.56). Ammonia content in fibres was correlated negatively (P < 0.05) with prickle factor and elongation (r=-0.62 and - 0.58, respectively). The variability in the physical properties and chemical composition of Sudanese camel-hair fibers under subtropical desert conditions may shed light on the possibility of improving fiber quality.
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Affiliation(s)
- Rania Agamy
- Animal Production Department, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Sabry F Mahouda
- Animal and Poultry Division, Desert Research Center, Cairo, Egypt.
| | - Ali H Azzam
- Animal and Poultry Division, Desert Research Center, Cairo, Egypt
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12
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Bahbahani H, Alfoudari A, Al-Ateeqi A, Al Abri M, Almathen F. Positive selection footprints and haplotype distribution in the genome of dromedary camels. Animal 2024; 18:101098. [PMID: 38377812 DOI: 10.1016/j.animal.2024.101098] [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] [Received: 10/09/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
Dromedary camels are a domestic species characterized by various adaptive traits. Limited efforts have been employed toward identifying genetic regions and haplotypes under selection that might be related to such adaptations. These genetic elements are considered valuable sources that should be conserved to maintain the dromedaries' adaptability. Here, we have analyzed whole genome sequences of 40 dromedary camels from different Arabian Peninsula populations to assess their genetic relationship and define regions with signatures of selection. Genetic distinction based on geography was observed, classifying the populations into four groups: (1) North and Central, (2) West, (3) Southwest, and (4) Southeast, with substantial levels of genetic admixture. Using the de-correlated composite of multiple signal approach, which combines four intra-population analyses (Tajima's D index, nucleotide diversity, integrated haplotype score, and number of segregating sites by length), a total of 36 candidate regions harboring 87 genes were identified to be under positive selection. These regions overlapped with 185 haplotype blocks encompassing 1 340 haplotypes, of which 30 (∼2%) were found to be approaching fixation. The defined candidate genes are associated with different biological processes related to the dromedaries' adaptive physiologies, including neurological pathways, musculoskeletal development, fertility, fat distribution, immunity, visual development, and kidney physiology. The results of this study highlight opportunities for further investigations at the whole-genome level to enhance our understanding of the evolutionary pressures shaping the dromedary genome.
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Affiliation(s)
- H Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait.
| | - A Alfoudari
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait
| | - A Al-Ateeqi
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - M Al Abri
- Department of Animal and Veterinary Sciences, Sultan Qaboos University, Muscat, Oman
| | - F Almathen
- Department of Public Health, King Faisal University, 400 Al-Ahsa, Kingdom of Saudi Arabia; Camel Research Center, King Faisal University, 400 Al-Ahsa, Saudi Arabia
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13
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Xu L, Zhou K, Huang X, Chen H, Dong H, Chen Q. Whole-genome resequencing provides insights into the diversity and adaptation to desert environment in Xinjiang Mongolian cattle. BMC Genomics 2024; 25:176. [PMID: 38355434 PMCID: PMC10865613 DOI: 10.1186/s12864-024-10084-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/02/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Xinjiang Mongolian cattle is an indigenous breed that inhabits the Taklimakan Desert and is characterized by its small body size. However, the genomic diversity, origin, and genetic basis underlying the adaptation to the desert environment have been poorly studied. RESULTS We analyzed patterns of Xinjiang Mongolian cattle genetic variation by sequencing 20 genomes together with seven previously sequenced genomes and comparing them to the 134 genomes of nine representative breeds worldwide. Among the breeds of Bos taurus, we found the highest nucleotide diversity (0.0024) associated with the lower inbreeding coefficient (2.0110-6), the lowest linkage disequilibrium (r2 = 0.3889 at distance of 10 kb), and the highest effective population size (181 at 20 generations ago) in Xinjiang Mongolian cattle. The genomic diversity pattern could be explained by a limited introgression of Bos indicus genes. More importantly, similarly to desert-adapted camel and same-habitat sheep, we also identified signatures of selection including genes, GO terms, and/or KEGG pathways controlling water reabsorption and osmoregulation, metabolic regulation and energy balance, as well as small body size in Xinjiang Mongolian cattle. CONCLUSIONS Our results imply that Xinjiang Mongolian cattle might have acquired distinct genomic diversity by virtue of the introgression of Bos indicus, which helps understand the demographic history. The identification of selection signatures can provide novel insights into the genomic basis underlying the adaptation of Xinjiang Mongolian cattle to the desert environment.
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Affiliation(s)
- Lei Xu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Kaiqing Zhou
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Hong Chen
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Hong Dong
- Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China.
| | - Qiuming Chen
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China.
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Blumstein DM, MacManes MD. When the tap runs dry: The multi-tissue gene expression and physiological responses of water deprived Peromyscus eremicus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576658. [PMID: 38328088 PMCID: PMC10849551 DOI: 10.1101/2024.01.22.576658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The harsh and dry conditions of desert environments have resulted in genomic adaptations, allowing for desert organisms to withstand prolonged drought, extreme temperatures, and limited food resources. Here, we present a comprehensive exploration of gene expression across five tissues (kidney, liver, lung, gastrointestinal tract, and hypothalamus) and 19 phenotypic measurements to explore the whole-organism physiological and genomic response to water deprivation in the desert-adapted cactus mouse (Peromyscus eremicus). The findings encompass the identification of differentially expressed genes and correlative analysis between phenotypes and gene expression patterns across multiple tissues. Specifically, we found robust activation of the vasopressin renin-angiotensin-aldosterone system (RAAS) pathways, whose primary function is to manage water and solute balance. Animals reduce food intake during water deprivation, and upregulation of PCK1 highlights the adaptive response to reduced oral intake via its actions aimed at maintained serum glucose levels. Even with such responses to maintain water balance, hemoconcentration still occurred, prompting a protective downregulation of genes responsible for the production of clotting factors while simultaneously enhancing angiogenesis which is thought to maintains tissue perfusion. In this study, we elucidate the complex mechanisms involved in water balance in the desert-adapted cactus mouse, P. eremicus. By prioritizing a comprehensive analysis of whole-organism physiology and multi-tissue gene expression in a simulated desert environment, we describe the complex and successful response of regulatory processes.
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Affiliation(s)
- Danielle M Blumstein
- University of New Hampshire, Molecular, Cellular, and Biomedical Sciences Department, Durham, NH 03824
| | - Matthew D MacManes
- University of New Hampshire, Molecular, Cellular, and Biomedical Sciences Department, Durham, NH 03824
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15
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Zhang CL, Zhang J, Tuersuntuoheti M, Zhou W, Han Z, Li X, Yang R, Zhang L, Zheng L, Liu S. Landscape genomics reveals adaptive divergence of indigenous sheep in different ecological environments of Xinjiang, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166698. [PMID: 37683864 DOI: 10.1016/j.scitotenv.2023.166698] [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: 04/22/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
Sheep are important livestock animals that have evolved under various ecological pressures. Xinjiang is a region with diverse and harsh environments that have shaped many local sheep breeds with unique characteristics and environmental adaptability. However, these breeds are losing ecological flexibility due to the promotion of intensive farming practices. Here we sequenced 14 local sheep breeds from Xinjiang and analyzed their genetic structure and gene flow with other sheep breeds from neighboring regions. The Tibetan Plateau was the geographic origin of Xinjiang native sheep evolution. We performed genome-environment association analysis and identified Bio9: Mean Temperature of Driest Quarter and Bio15: Precipitation Seasonality as the key environmental factors affecting Xinjiang local sheep and the key genes involved in their survival and adaptation. We classified Xinjiang native sheep breeds into six groups based on their differential genes by pairwise selective sweep analysis and Community Network Analysis. We analyzed transcriptome expression data of 832 sheep tissues and detected tissue-specific enrichment of six group-specific genes in different biological systems. Our results revealed the genetic basis of year-round estrus, drought tolerance, hypoxia resistance, and cold tolerance traits of Xinjiang sheep breeds. Moreover, we proposed conservation strategies for Xinjiang local sheep breeds and provided theoretical guidance for breeding new sheep breeds under global extreme environments.
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Affiliation(s)
- Cheng-Long Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Jihu Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Mirenisa Tuersuntuoheti
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Wen Zhou
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Zhipeng Han
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Xiaopeng Li
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Ruizhi Yang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Lulu Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Langman Zheng
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Shudong Liu
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China.
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16
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Conca W, Saleh SM, Al-Rabiah R, Parhar RS, Abd-Elnaeim M, Al-Hindas H, Tinson A, Kroell KB, Liedl KR, Collison K, Kishore U, Al-Mohanna F. The immunoglobulin A isotype of the Arabian camel ( Camelus dromedarius) preserves the dualistic structure of unconventional single-domain and canonical heavy chains. Front Immunol 2023; 14:1289769. [PMID: 38162642 PMCID: PMC10756906 DOI: 10.3389/fimmu.2023.1289769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/30/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction The evolution of adaptive immunity in Camelidae resulted in the concurrent expression of classic heterotetrameric and unconventional homodimeric heavy chain-only IgG antibodies. Heavy chain-only IgG bears a single variable domain and lacks the constant heavy (CH) γ1 domain required for pairing with the light chain. It has not been reported whether this distinctive feature of IgG is also observed in the IgA isotype. Methods Gene-specific primers were used to generate an IgA heavy chain cDNA library derived from RNA extracted from the dromedary's third eyelid where isolated lymphoid follicles and plasma cells abound at inductive and effector sites, respectively. Results Majority of the cDNA clones revealed hallmarks of heavy chain-only antibodies, i.e. camelid-specific amino acid substitutions in framework region 1 and 2, broad length distribution of complementarity determining region 3, and the absence of the CHα1 domain. In a few clones, however, the cDNA of the canonical IgA heavy chain was amplified which included the CHα1 domain, analogous to CHγ1 domain in IgG1 subclass. Moreover, we noticed a short, proline-rich hinge, and, at the N-terminal end of the CHα3 domain, a unique, camelid-specific pentapeptide of undetermined function, designated as the inter-α region. Immunoblots using rabbit anti-camel IgA antibodies raised against CHα2 and CHα3 domains as well as the inter-α region revealed the expression of a ~52 kDa and a ~60 kDa IgA species, corresponding to unconventional and canonical IgA heavy chain, respectively, in the third eyelid, trachea, small and large intestine. In contrast, the leporine anti-CHα1 antibody detected canonical, but not unconventional IgA heavy chain, in all the examined tissues, milk, and serum, in addition to another hitherto unexplored species of ~45 kDa in milk and serum. Immunohistology using anti-CHα domain antibodies confirmed the expression of both variants of IgA heavy chains in plasma cells in the third eyelid's lacrimal gland, conjunctiva, tracheal and intestinal mucosa. Conclusion We found that in the dromedary, the IgA isotype has expanded the immunoglobulin repertoire by co-expressing unconventional and canonical IgA heavy chains, comparable to the IgG class, thus underscoring the crucial role of heavy chain-only antibodies not only in circulation but also at the mucosal frontiers.
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Affiliation(s)
- Walter Conca
- Department of Executive Health Medicine, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
- Department of Cell Biology, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Soad M. Saleh
- Department of Cell Biology, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Rana Al-Rabiah
- Department of Cell Biology, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Ranjit Singh Parhar
- Department of Cell Biology, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Mahmoud Abd-Elnaeim
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Assiut University, Assiut, Egypt
| | - Hussein Al-Hindas
- Department of Cell Biology, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Alexander Tinson
- Management of Scientific Centers and Presidential Camels, Department of President’s Affairs, Hilli ET and Cloning Centre, Al Ain, United Arab Emirates
| | | | - Klaus Roman Liedl
- Center for Chemistry and Biomedicine, University of Innsbruck, Innsbruck, Austria
| | - Kate Collison
- Department of Cell Biology, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Uday Kishore
- Department of Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Futwan Al-Mohanna
- Department of Cell Biology, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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17
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Rodon J, Te N, Ballester M, Segalés J, Vergara-Alert J, Bensaid A. Quantification of camelid cytokine mRNA expression in PBMCs by microfluidic qPCR technology. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 149:105061. [PMID: 37717710 DOI: 10.1016/j.dci.2023.105061] [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: 02/16/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
Abstract
Camelids are economically and socially important in several parts of the world and might carry pathogens with epizootic or zoonotic potential. However, biological research in these species is limited due to lack of reagents. Here, we developed RT-qPCR assays to quantify a panel of camelid innate and adaptive immune response genes, which can be monitored in a single run. The assays were validated with PHA, PMA-ionomycin, and Poly I:C-stimulated PBMCs from alpaca, dromedary camel and llama, including normalization by multiple reference genes. Further, comparative gene expression analyses for the different camelid species were performed by a unique microfluidic qPCR assay. Compared to unstimulated controls, PHA and PMA-ionomycin stimulation elicited robust Th1 and Th2 responses in PBMCs from camelid species. Additional activation of type I and type III IFN signalling pathways was described exclusively in PHA-stimulated dromedary lymphocytes, in contrast to those from alpaca and llama. We also found that PolyI:C stimulation induced robust antiviral response genes in alpaca PBMCs. The proposed methodology should be useful for the measurement of immune responses to infection or vaccination in camelid species.
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Affiliation(s)
- Jordi Rodon
- Unitat mixta d'investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Catalonia, Spain.
| | - Nigeer Te
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Catalonia, Spain.
| | - Maria Ballester
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), 08140, Caldes de Montbui, Spain.
| | - Joaquim Segalés
- Unitat mixta d'investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Catalonia, Spain; Department de Sanitat i Anatomia Animals, Facultat de Veterinaria, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, 08193, Bellaterra, Catalonia, Spain.
| | - Júlia Vergara-Alert
- Unitat mixta d'investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Catalonia, Spain.
| | - Albert Bensaid
- Unitat mixta d'investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Catalonia, Spain.
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Al Abri M, Alfoudari A, Mohammad Z, Almathen F, Al-Marzooqi W, Al-Hajri S, Al-Amri M, Bahbahani H. Assessing genetic diversity and defining signatures of positive selection on the genome of dromedary camels from the southeast of the Arabian Peninsula. Front Vet Sci 2023; 10:1296610. [PMID: 38098998 PMCID: PMC10720651 DOI: 10.3389/fvets.2023.1296610] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Dromedary camels (Camelus dromedarius) are members of the Camelini tribe within the Camelidae family. They are distributed throughout North Africa, the Arabian Peninsula and Southeast Asia. This domestic species is characterized by its superior adaptability to the harsh desert environment. In this study, whole autosomal data of 29 dromedary samples from the Southeast Arabian Peninsula in Oman; 10 from Muscat, 14 from Al-Batinah, and 5 from Al-Sharqiya, were investigated to assess their genetic relationship and to define candidate signatures of positive selection. A minimal genetic distinction that separates Muscat dromedaries from the other two populations was observed, with a degree of genetic admixture between them. Using the de-correlated composite of multiple signals (DCMS) approach, a total of 47 candidate regions within the autosomes of these dromedary populations were defined with signatures of positive selection. These candidate regions harbor a total of 154 genes that are mainly associated with functional categories related to immune response, lipid metabolism and energy expenditure, optical and auditory functions, and long-term memory. Different functional genomic variants were called on the candidate regions and respective genes that warrant further investigation to find possible association with the different favorable phenotypes in dromedaries. The output of this study paves the way for further research efforts aimed at defining markers for use in genomic breeding programs, with the goal of conserving the genetic diversity of the species and enhancing its productivity.
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Affiliation(s)
- Mohammad Al Abri
- Department of Animal and Veterinary Sciences, Sultan Qaboos University, Muscat, Oman
| | - Ahmad Alfoudari
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Zainab Mohammad
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
- Camel Research Center, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Waleed Al-Marzooqi
- Department of Animal and Veterinary Sciences, Sultan Qaboos University, Muscat, Oman
| | - Salim Al-Hajri
- Laboratories and Research Administration, Directorate General of Veterinary Services, Royal Court Affairs, Muscat, Oman
| | - Mahmood Al-Amri
- Laboratories and Research Administration, Directorate General of Veterinary Services, Royal Court Affairs, Muscat, Oman
| | - Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
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More M, Veli E, Cruz A, Gutiérrez JP, Gutiérrez G, Ponce de León FA. Genome-Wide Association Study of Fiber Diameter in Alpacas. Animals (Basel) 2023; 13:3316. [PMID: 37958071 PMCID: PMC10648856 DOI: 10.3390/ani13213316] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/13/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
The aim of this study was the identification of candidate genomic regions associated with fiber diameter in alpacas. DNA samples were collected from 1011 female Huacaya alpacas from two geographical Andean regions in Peru (Pasco and Puno), and three alpaca farms within each region. The samples were genotyped using an Affymetrix Custom Alpaca genotyping array containing 76,508 SNPs. After the quality controls, 960 samples and 51,742 SNPs were retained. Three association study methodologies were performed. The GWAS based on a linear model allowed us to identify 11 and 35 SNPs (-log10(p-values) > 4) using information on all alpacas and alpacas with extreme values of fiber diameter, respectively. The haplotype and marker analysis method allowed us to identify nine haplotypes with standardized haplotype heritability higher than six standard deviations. The selection signatures based on cross-population extended haplotype homozygosity (XP-EHH) allowed us to identify 180 SNPs with XP-EHH values greater than |3|. Four candidate regions with adjacent SNPs identified via two association methods of analysis are located on VPA6, VPA9, VPA29 and one chromosomally unassigned scaffold. This study represents the first analysis of alpaca whole genome association with fiber diameter, using a recently assembled alpaca SNP microarray.
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Affiliation(s)
- Manuel More
- Facultad de Agronomía y Zootecnia, Universidad Nacional de San Antonio Abad del Cusco, Cusco 08006, Peru;
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, Peru; (A.C.); (F.A.P.d.L.)
| | - Eudosio Veli
- Centro Experimental La Molina, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, Peru;
| | - Alan Cruz
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, Peru; (A.C.); (F.A.P.d.L.)
- Estación Científica de Pacomarca, Inca Tops S.A., Arequipa 04007, Peru
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain;
| | - Gustavo Gutiérrez
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, Peru; (A.C.); (F.A.P.d.L.)
- Instituto de Investigación de Bioquímica y Biología Molecular, Universidad Nacional Agraria La Molina, Lima 15024, Peru
| | - F. Abel Ponce de León
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, Peru; (A.C.); (F.A.P.d.L.)
- Department of Animal Science, University of Minnesota, Minneapolis, MN 55108, USA
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Cheng Y, Ren Y, Wang W, Zhang W. Similar proteome expression profiles of the aggregated lymphoid nodules area and Peyer's patches in Bactrian camel. BMC Genomics 2023; 24:608. [PMID: 37821839 PMCID: PMC10568864 DOI: 10.1186/s12864-023-09715-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND The presence of Aggregated Lymphoid Nodules Area (ALNA) is a notable anatomical characteristic observed in the abomasum of Bactrian camels. This area is comprised of two separate regions, namely the Reticular Mucosal Folds Region (RMFR) and the Longitudinal Mucosal Folds Region (LMFR). The histological properties of ALNA exhibit significant similarities to those of Peyer's patches (PPs) found in the gastrointestinal system. The functional characteristics of ALNA were examined in relation to mucosal immunity in the gastrointestinal system. RESULTS We used iTRAQ-based proteomic analysis on twelve Bactrian camels to measure the amount of proteins expressed in ALNA. In the experiment, we sampled the RMFR and LMFR separately from the ALNA and compared their proteomic quantification results with samples from the PPs. A total of 1253 proteins were identified, among which 39 differentially expressed proteins (DEPs) were found between RMFR and PPs, 33 DEPs were found between LMFR and PPs, and 22 DEPs were found between LMFR and RMFR. The proteins FLNA, MYH11, and HSPB1 were chosen for validation using the enzyme-linked immunosorbent assay (ELISA), and the observed expression profiles were found to be in agreement with the results obtained from the iTRAQ study. The InnateDB database was utilized to get data pertaining to immune-associated proteins in ALNA. It was observed that a significant proportion, specifically 76.6%, of these proteins were found to be associated with the same orthogroups as human immune-related genes. These proteins are acknowledged to be associated with a diverse range of functions, encompassing the uptake, processing and presentation of antigens, activation of lymphocytes, the signaling pathways of T-cell and B-cell receptors, and the control of actin polymerization. CONCLUSIONS The experimental results suggest that there are parallels in the immune-related proteins found in ALNA and PPs. Although there are variations in the structures of LMFR and RMFR, the proteins produced in both structures exhibit a high degree of similarity and perform comparable functions in the context of mucosal immune responses.
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Affiliation(s)
- Yujiao Cheng
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yan Ren
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Wenhui Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China.
| | - Wangdong Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China.
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21
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Pauciullo A, Versace C, Gaspa G, Letaief N, Bedhiaf-Romdhani S, Fulgione A, Cosenza G. Sequencing and Characterization of αs2-Casein Gene ( CSN1S2) in the Old-World Camels Have Proven Genetic Variations Useful for the Understanding of Species Diversification. Animals (Basel) 2023; 13:2805. [PMID: 37685069 PMCID: PMC10487017 DOI: 10.3390/ani13172805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
The CSN1S2 gene encodes αs2-casein, the third most abundant protein in camel milk. Despite its importance in foals, human nutrition, and dairy processing, the CSN1S2 gene in camels has received little attention. This study presents the first complete characterization of the CSN1S2 gene sequence in Old-World camels (Camelus bactrianus and Camelus dromedarius). Additionally, the gene promoter, consisting of 752 bp upstream of exon 1, was analyzed. The entire gene comprises 17 exons, ranging in length from 24 bp (exons 4, 8, 11, and 13) to 280 bp (exon 17). Interesting was the identification of the exon 12 in both species. The promoter analysis revealed 24 putative binding sites in the Bactrian camel and 22 in dromedary camel. Most of these sites were typical elements associated with milk protein, such as C/EBP-α, C/EBP-β, Oct-1, and AP1. The SNP discovery showed relatively high genetic diversity compared to other camel casein genes (CSN1S1, CSN2, and CSN3), with a total of 34 polymorphic sites across the two species. Particularly noteworthy is the transition g.311G>A in the CSN1S2 promoter, creating a new putative consensus binding site for a C/EBP-β in the Bactrian camel. At the exon level, two novel variants were found. One was detected in exon 6 of the Bactrian camel (g.3639C>G), resulting in an amino acid replacement, p.36Ile>Met. The second variant was found in noncoding exon 17 of dromedary CSN1S2 (g.1511G>T). Although this mutation occurs in the 3'-UnTranslated Region, it represents the first example of exonic polymorphism in the CSN1S2 for this species. This SNP also affects the binding sites of different microRNAs, including the seed sequence of the miRNA 4662a-3p, highlighting its role as a regulatory factor for CSN1S2 gene. A PCR-RFLP was set up for genotyping a dromedary Tunisian population (n = 157), and the minor allele frequency was found to be 0.27 for the G allele, indicating a potential yield improvement margin. The interspersed elements (INEs) analysis revealed 10 INEs covering 7.34% and 8.14% of the CSN1S2 sequence in the Bactrian and dromedary camels, respectively. Furthermore, six elements (A, B, F, H, I, and L) are shared among cattle and camels and are partially found in other ruminants, suggesting a common ancestral origin of these retrotransposons. Conversely, elements C, D, E, and G are specific to camels.
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Affiliation(s)
- Alfredo Pauciullo
- Department of Agriculture, Forest and Food Sciences, University of Torino, 10095 Grugliasco, Italy
| | - Carmine Versace
- Department of Agriculture, Forest and Food Sciences, University of Torino, 10095 Grugliasco, Italy
| | - Giustino Gaspa
- Department of Agriculture, Forest and Food Sciences, University of Torino, 10095 Grugliasco, Italy
| | - Neyrouz Letaief
- Department of Agriculture, Forest and Food Sciences, University of Torino, 10095 Grugliasco, Italy
- Laboratory of Animal and Forage Production, National Agricultural Research Institute of Tunisia, University of Carthage, Ariana 1004, Tunisia
| | - Sonia Bedhiaf-Romdhani
- Laboratory of Animal and Forage Production, National Agricultural Research Institute of Tunisia, University of Carthage, Ariana 1004, Tunisia
| | - Andrea Fulgione
- Department of Agriculture, University of Napoli Federico II, 80055 Portici, Italy
| | - Gianfranco Cosenza
- Department of Agriculture, University of Napoli Federico II, 80055 Portici, Italy
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22
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Peng X, Cheng J, Li H, Feijó A, Xia L, Ge D, Wen Z, Yang Q. Whole-genome sequencing reveals adaptations of hairy-footed jerboas (Dipus, Dipodidae) to diverse desert environments. BMC Biol 2023; 21:182. [PMID: 37649052 PMCID: PMC10469962 DOI: 10.1186/s12915-023-01680-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Environmental conditions vary among deserts across the world, spanning from hyper-arid to high-elevation deserts. However, prior genomic studies on desert adaptation have focused on desert and non-desert comparisons overlooking the complexity of conditions within deserts. Focusing on the adaptation mechanisms to diverse desert environments will advance our understanding of how species adapt to extreme desert environments. The hairy-footed jerboas are well adapted to diverse desert environments, inhabiting high-altitude arid regions, hyper-arid deserts, and semi-deserts, but the genetic basis of their adaptation to different deserts remains unknown. RESULTS Here, we sequenced the whole genome of 83 hairy-footed jerboas from distinct desert zones in China to assess how they responded under contrasting conditions. Population genomics analyses reveal the existence of three species in hairy-footed jerboas distributed in China: Dipus deasyi, Dipus sagitta, and Dipus sowerbyi. Analyses of selection between high-altitude desert (elevation ≥ 3000m) and low-altitude desert (< 500m) populations identified two strongly selected genes, ATR and HIF1AN, associated with intense UV radiation and hypoxia in high-altitude environments. A number of candidate genes involved in energy and water homeostasis were detected in the comparative genomic analyses of hyper-arid desert (average annual precipitation < 70mm) and arid desert (< 200mm) populations versus semi-desert (> 360mm) populations. Hyper-arid desert animals also exhibited stronger adaptive selection in energy homeostasis, suggesting water and resource scarcity may be the main drivers of desert adaptation in hairy-footed jerboas. CONCLUSIONS Our study challenges the view of deserts as homogeneous environments and shows that distinct genomic adaptations can be found among desert animals depending on their habitats.
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Affiliation(s)
- Xingwen Peng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, 100049, China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Hong Li
- Novogene Bioinformatics Institute, Haidian District, Beijing, 100083, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China.
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Tao W, Aniwar L, ZuliPicar A, Tulafu H, Zhang R, Liu B, Wu W, Huang J. Analysis of Genetic Diversity and Population Structure of Tarim and Junggar Bactrian Camels Based on Simplified GBS Genome Sequencing. Animals (Basel) 2023; 13:2349. [PMID: 37508126 PMCID: PMC10376019 DOI: 10.3390/ani13142349] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
In view of the severe reduction in Bactrian camel germplasm resources, scientific evaluation, protection, and utilization is particularly important. Therefore, it is necessary to investigate the genetic diversity and genetic structure of this species, and identify the genes that have played important roles in its evolution. In this study, 21,971 SNPs were identified in 118 domestic Bactrian camels from the Tarim (n = 60) and Junggar (n = 58) populations using simplified GBS genome sequencing. The results show that Tarim and Junggar Bactrian camels have high nucleotide diversity. A phylogenetic tree constructed using structural analysis, principal component analysis (PCA), and the adjacency method (NJ) showed that Tarim and Junggar Bactrian camels were clustered together. The selection signals revealed that the Tarim and Junggar Bactrian camels shared 108 genes under positive selection, including WNT1, WNT10B, CD14, SEC61A2, DPAGT1, FOXO6, etc. These selected genes were widely involved in the immune system, embryonic development, lipid metabolism, and other processes. From a genomic analysis perspective, the genetic relationship between TLM and ZGE camels is close, with an average Fst of 0.048 and a relatively low average differentiation coefficient between the two populations. In addition, shared selected genes in the long-term depression pathway were significantly enriched in Tarim and Junggar. These findings will offer support and assistance for the exploration of genetic resource preservation, economically significant traits, and the mechanisms underlying biological characteristics, molecular breeding, and disease.
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Affiliation(s)
- Weikun Tao
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, China
| | - Lazat Aniwar
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, China
| | - Azat ZuliPicar
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, China
| | - Hanikzi Tulafu
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, China
| | - Rongyin Zhang
- Institute of Quality Standards, Xinjiang Academy of Animal Husbandry Sciences, Urumqi 830000, China
| | - Bo Liu
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, China
| | - Weiwei Wu
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, China
| | - Juncheng Huang
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, China
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24
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Folschweiller S, Sauer JF. Behavioral State-Dependent Modulation of Prefrontal Cortex Activity by Respiration. J Neurosci 2023; 43:4795-4807. [PMID: 37277176 PMCID: PMC10312056 DOI: 10.1523/jneurosci.2075-22.2023] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 06/07/2023] Open
Abstract
Respiration-rhythmic oscillations in the local field potential emerge in the mPFC, a cortical region with a key role in the regulation of cognitive and emotional behavior. Respiration-driven rhythms coordinate local activity by entraining fast γ oscillations as well as single-unit discharges. To what extent respiration entrainment differently engages the mPFC network in a behavioral state-dependent manner, however, is not known. Here, we compared the respiration entrainment of mouse PFC local field potential and spiking activity (23 male and 2 female mice) across distinct behavioral states: during awake immobility in the home cage (HC), during passive coping in response to inescapable stress under tail suspension (TS), and during reward consumption (Rew). Respiration-driven rhythms emerged during all three states. However, prefrontal γ oscillations were more strongly entrained by respiration during HC than TS or Rew. Moreover, neuronal spikes of putative pyramidal cells and putative interneurons showed significant respiration phase-coupling throughout behaviors with characteristic phase preferences depending on the behavioral state. Finally, while phase-coupling dominated in deep layers in HC and Rew conditions, TS resulted in the recruitment of superficial layer neurons to respiration. These results jointly suggest that respiration dynamically entrains prefrontal neuronal activity depending on the behavioral state.SIGNIFICANCE STATEMENT The mPFC, through its extensive connections (e.g., to the amygdala, the striatum, serotoninergic and dopaminergic nuclei), flexibly regulates cognitive behaviors. Impairment of prefrontal functions can lead to disease states, such as depression, addiction, or anxiety disorders. Deciphering the complex regulation of PFC activity during defined behavioral states is thus an essential challenge. Here, we investigated the role of a prefrontal slow oscillation that has recently attracted rising interest, the respiration rhythm, in modulating prefrontal neurons during distinct behavioral states. We show that prefrontal neuronal activity is differently entrained by the respiration rhythm in a cell type- and behavior-dependent manner. These results provide first insight into the complex modulation of prefrontal activity patterns by rhythmic breathing.
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Affiliation(s)
- Shani Folschweiller
- Institute of Physiology 1, Medical Faculty, University of Freiburg, D-79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Jonas-Frederic Sauer
- Institute of Physiology 1, Medical Faculty, University of Freiburg, D-79104 Freiburg, Germany
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25
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Amandykova M, Dossybayev K, Mussayeva A, Saitou N, Zhunusbayeva Z, Bekmanov B. A Study of the Genetic Structure of Hybrid Camels in Kazakhstan. Genes (Basel) 2023; 14:1373. [PMID: 37510278 PMCID: PMC10379372 DOI: 10.3390/genes14071373] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Camel farming is gaining scientific interest due to its unique agricultural characteristics. Camels are versatile for milk and meat production, wool, racing, transport, and tourism. To use their full potential, it is essential to improve our understanding of the genetic structure of these animals. One-humped and two-humped camels have received detailed genetic descriptions, while there is no such information for their hybrids, which outperform their parent species in several agricultural characteristics. Thus, in this study, for the first time, the whole genome sequencing data (WGS) of five hybrid camels bred in the Almaty region of Kazakhstan are presented in comparison with the WGS data of one-humped, two-humped, and wild camels. A total of 43,552,164 single-nucleotide polymorphisms were found across the studied groups. Further comparison of these SNPs showed the following number of private SNPs among the populations: hybrid camels (3,271,083), wild camels (2,515,591), Bactrians (1,244,694), and dromedaries (531,224). The genetic structure of the studied animals was described, and a phylogenetic tree was built to assess their genetic distance. It was found that the studied hybrids are genetically closer to dromedaries since they were on the close branch of the phylogenetic tree.
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Affiliation(s)
- Makpal Amandykova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050040, Kazakhstan
- Laboratory of Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan
| | - Kairat Dossybayev
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050040, Kazakhstan
- Laboratory of Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan
| | - Aizhan Mussayeva
- Laboratory of Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan
| | - Naruya Saitou
- Saitou Naruya Laboratory, National Institute of Genetics, 1111 Yata, Mishima 411-8540, Shizuoka, Japan
| | - Zhazira Zhunusbayeva
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050040, Kazakhstan
| | - Bakytzhan Bekmanov
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050040, Kazakhstan
- Laboratory of Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan
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26
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Liu W, Shrestha R, Lowe A, Zhang X, Spaeth L. Self-formation of concentric zones of telencephalic and ocular tissues and directional retinal ganglion cell axons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.22.533827. [PMID: 36993285 PMCID: PMC10055356 DOI: 10.1101/2023.03.22.533827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The telencephalon and eye in mammals are originated from adjacent fields at the anterior neural plate. Morphogenesis of these fields generates telencephalon, optic-stalk, optic-disc, and neuroretina along a spatial axis. How these telencephalic and ocular tissues are specified coordinately to ensure directional retinal ganglion cell (RGC) axon growth is unclear. Here, we report the self-formation of human telencephalon-eye organoids comprising concentric zones of telencephalic, optic-stalk, optic-disc, and neuroretinal tissues along the center-periphery axis. Initially-differentiated RGCs grew axons towards and then along a path defined by adjacent PAX2+ optic-disc cells. Single-cell RNA sequencing of CONCEPT organoids not only confirmed telencephalic and ocular identities but also identified expression signatures of early optic-disc, optic-stalk, and RGCs. These signatures were similar to those in human fetal retinas. Optic-disc cells in CONCEPT organoids differentially expressed FGF8 and FGF9 ; FGFR inhibitions drastically decreased RGC differentiation and directional axon growth. Through the identified RGC-specific cell-surface marker CNTN2, electrophysiologically-excitable RGCs were isolated under a native condition. Our findings provide insight into the coordinated specification of early telencephalic and ocular tissues in humans and establish resources for studying RGC-related diseases such as glaucoma. Impact statement A human telencephalon-eye organoid model that exhibited axon growth and pathfinding from retinal ganglion cell (RGC) axons is reported; via cell surface marker CNTN2 identified using scRNA-seq, early RGCs were isolated under a native condition.
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Affiliation(s)
- Wei Liu
- Department of Ophthalmology and Visual Sciences
- Department of Genetics
- The Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine
| | - Rupendra Shrestha
- Department of Ophthalmology and Visual Sciences
- Department of Genetics
- The Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine
| | - Albert Lowe
- Department of Ophthalmology and Visual Sciences
- Department of Genetics
| | | | - Ludovic Spaeth
- Dominick P. Purpura Department of Neuroscience Albert Einstein College of Medicine, Bronx, NY 10461
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27
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Zhang Z, Xia T, Zhou S, Yang X, Lyu T, Wang L, Fang J, Wang Q, Dou H, Zhang H. High-Quality Chromosome-Level Genome Assembly of the Corsac Fox ( Vulpes corsac) Reveals Adaptation to Semiarid and Harsh Environments. Int J Mol Sci 2023; 24:ijms24119599. [PMID: 37298549 DOI: 10.3390/ijms24119599] [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: 04/24/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
The Corsac fox (Vulpes corsac) is a species of fox distributed in the arid prairie regions of Central and Northern Asia, with distinct adaptations to dry environments. Here, we applied Oxford-Nanopore sequencing and a chromosome structure capture technique to assemble the first Corsac fox genome, which was then assembled into chromosome fragments. The genome assembly has a total length of 2.2 Gb with a contig N50 of 41.62 Mb and a scaffold N50 of 132.2 Mb over 18 pseudo-chromosomal scaffolds. The genome contained approximately 32.67% of repeat sequences. A total of 20,511 protein-coding genes were predicted, of which 88.9% were functionally annotated. Phylogenetic analyses indicated a close relation to the Red fox (Vulpes vulpes) with an estimated divergence time of ~3.7 million years ago (MYA). We performed separate enrichment analyses of species-unique genes, the expanded and contracted gene families, and positively selected genes. The results suggest an enrichment of pathways related to protein synthesis and response and an evolutionary mechanism by which cells respond to protein denaturation in response to heat stress. The enrichment of pathways related to lipid and glucose metabolism, potentially preventing stress from dehydration, and positive selection of genes related to vision, as well as stress responses in harsh environments, may reveal adaptive evolutionary mechanisms in the Corsac fox under harsh drought conditions. Additional detection of positive selection for genes associated with gustatory receptors may reveal a unique desert diet strategy for the species. This high-quality genome provides a valuable resource for studying mammalian drought adaptation and evolution in the genus Vulpes.
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Affiliation(s)
- Zhihao Zhang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Tian Xia
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Shengyang Zhou
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Xiufeng Yang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Tianshu Lyu
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Lidong Wang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Jiaohui Fang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Qi Wang
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir 021000, China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir 021000, China
| | - Honghai Zhang
- School of Life Science, Qufu Normal University, Qufu 273165, China
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28
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Maiti S, Nazmeen A, Banerjee A. Significant impact of redox regulation of estrogen-metabolizing proteins on cellular stress responses. Cell Biochem Funct 2023. [PMID: 37139830 DOI: 10.1002/cbf.3796] [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: 01/02/2023] [Revised: 04/07/2023] [Accepted: 04/17/2023] [Indexed: 05/05/2023]
Abstract
The ultimate driving force, stress, promotes adaptability/evolution in proliferating organisms, transforming tumorigenic growth. Estradiol (E2) regulates both phenomena. In this study, bioinformatics-tools, site-directed-mutagenesis (human estrogen-sulfotransferase/hSULT1E1), HepG2 cells tested with N-acetyl-cysteine (NAC/thiol-inducer) or buthionine-sulfoxamine (BSO/thiol-depletory) were evaluated for hSULT1E1 (estradiol-sulphating/inactivating) functions. Reciprocal redox regulation of steroid sulfatase (STS, E2-desulfating/activating) results in the Cys-formylglycine transition by the formylglycine-forming enzyme (FGE). The enzyme sequences and structures were examined across the phylogeny. Motif/domain and the catalytic conserve sequences and protein-surface-topography (CASTp) were investigated. The E2 binding to SULT1E1 suggests that the conserved-catalytic-domain in this enzyme has critical Cysteine 83 at position. This is strongly supported by site-directed mutagenesis/HepG2-cell research. Molecular-docking and superimposition studies of E2 with the SULT1E1 of representative species and to STS reinforce this hypothesis. SULT1E1-STS are reciprocally activated in response to the cellular-redox-environment by the critical Cys of these two enzymes. The importance of E2 in organism/species proliferation and tissue tumorigenesis is highlighted.
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Affiliation(s)
- Smarajit Maiti
- Department of Biochemistry, Cell & Molecular Therapeutics Lab, Oriental Institute of Science & Technology, Midnapore, India
| | - Aarifa Nazmeen
- Department of Biochemistry, Cell & Molecular Therapeutics Lab, Oriental Institute of Science & Technology, Midnapore, India
| | - Amrita Banerjee
- Department of Biochemistry, Cell & Molecular Therapeutics Lab, Oriental Institute of Science & Technology, Midnapore, India
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29
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Yahyaoui MH. Characterization and genetic diversity of MHC class II DRB genes in the Arabian camel (Camelus dromedarius). Immunogenetics 2023:10.1007/s00251-023-01303-x. [PMID: 37014380 PMCID: PMC10072047 DOI: 10.1007/s00251-023-01303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 03/08/2023] [Indexed: 04/05/2023]
Abstract
This study investigated the MHC DRB genes in the Arabian camel (Camelus dromedarius). The results revealed the presence of - at least - two transcribed DRB-like genes in chromosome 20, designated MhcCadr-DRB1 and MhcCadr-DRB2. These genes are 155 Kb apart, have similar gene structure, and are transcribed in opposite directions. Compared to DRB1, the DRB2 locus contains a deletion of 12 nucleotides in the second exon (270 bp), exhibits lower transcript abundance, and is expressed as two splice variants differing by exon 2 skipping. This gene seems to be of minor functional relevance in the dromedary camel. Conversely, the DRB1 is thought to be the main gene in this species showing higher transcript abundance and polymorphism levels. A total of seven DRB1 exon 2 alleles were identified in the Tunisian dromedary camel resulting from 18 amino acid substitutions. Six full length alleles were characterized at the mRNA level. Although there is no clear evidence for balancing selection (i.e., heterozygote advantage), signals of weak historical positive selection acting on the DRB1 gene were detected, as indicated by the limited number of the sites being positively selected. This trend might be related to the low exposure to pathogens and to the demographic history of the species. Comparative analysis with Bactrian and wild camel genomes suggested occurrence of trans species polymorphism (TSP) in the Camelus genus. The results lay the foundation for the MHC DRB1 genetic diversity analysis in this genus since the developed genotyping protocols are fully applicable in the three Camelus species.
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Affiliation(s)
- Mohamed Habib Yahyaoui
- Livestock and Wildlife Laboratory LR16IRA04, Arid Lands Institute, Medenine, Tunisia.
- Department of Life Sciences, Faculty of Sciences, University of Gabès, Gabès, Tunisia.
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El-Hady E, Behairy A, Goda NA, Abdelbaset-Ismail A, Ahmed AE, Al-Doaiss AA, Abd El-Rahim I, Alshehri MA, Aref M. Comparative physiological, morphological, histological, and AQP2 immunohistochemical analysis of the Arabian camels (Camelus dromedarius) and oxen kidney: Effects of adaptation to arid environments. FRONTIERS IN ANIMAL SCIENCE 2023. [DOI: 10.3389/fanim.2023.1078159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023] Open
Abstract
Compared to other mammals, Arabian camels are ideal models for exploring the structural adaptations that enable camels to survive in arid environments. Thus, this study aimed to explore how evolutionary adaptation to arid conditions modifies the characteristics of the kidneys in Arabian camels (Camelus dromedarius) compared to oxen. Urine samples were physically and chemically analyzed. Harvested kidneys were subjected to topographical and fast spin echo magnetic resonance (FSE-MR) imaging. Histology, histomorphometry, and Aquaporin-2 (AQP2) expression by immunohistochemistry were also performed. Here, in dromedaries, sodium and potassium values in the urine were much higher (p=0.001, for both), whereas chloride was much lower (p=0.004) than the values of oxen. Compared with oxen, the level of the hormone aldosterone in serum was significantly lower (p=0.002), whereas creatinine and urea were significantly higher (p=0.005 and p=0.001, respectively). Uric acid in dromedaries and oxen did not differ significantly (p=0.349). Like sodium levels (p=0.001) in dromedary serum, chloride was also much higher (p=0.002) than in oxen. The average value of potassium was much lower (p=0.009) than that of oxen. Morphologically, anatomical and FSE MRI studies revealed that minor and major calyces were not found in dromedary kidneys. The renal pelvis was not found in oxen, and the major calyx was directly connected to the ureter. The dromedary kidney contained a wider medullary portion as well as increased diameters for renal corpuscles (RCs), proximal convoluted tubules (PCTs), and collecting tubules (CTs, p<0.05) compared with the oxen. We also noted that AQP2 was significantly expressed in dromedary nephron components, except for RCs, compared with oxen as shown by immunohistochemistry. Overall, these data strongly suggest that the dromedary has a greater ability to adapt to harsh desert conditions in terms of producing highly concentrated urine than oxen.
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Bahbahani H, Al-Zoubi S, Ali F, Afana A, Dashti M, Al-Ateeqi A, Wragg D, Al-Bustan S, Almathen F. Signatures of purifying selection and site-specific positive selection on the mitochondrial DNA of dromedary camels (Camelus dromedarius). Mitochondrion 2023; 69:36-42. [PMID: 36690316 DOI: 10.1016/j.mito.2023.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
The two species of the Old World Camelini tribe, dromedary and Bactrian camels, show superior adaptability to the different environmental conditions they populate, e.g. desert, mountains and coastal areas, which might be associated with adaptive variations on their mitochondrial DNA. Here, we investigate signatures of natural selection in the 13-mitochondrial protein-coding genes of different dromedary camel populations from the Arabian Peninsula, Africa and southwest Asia. The full mitogenome sequences of 42 dromedaries, 38 domestic Bactrian, 29 wild Bactrian camels and 31 samples representing the New World Lamini tribe reveal species-wise genetic distinction among Camelidae family species, with no evidence of geographic distinction among dromedary camels. We observe gene-wide signals of adaptive divergence between the Old World and New World camels, with evidence of purifying selection among Old World camel species. Upon comparing the different Camelidae tribes, 27 amino acid substitutions across ten mtDNA protein-coding genes were found to be under positive selection, in which, 24 codons were defined to be under positive adaptive divergence between Old World and New World camels. Seven codons belonging to three genes demonstrated positive selection in dromedary lineage. A total of 89 codons were found to be under positive selection in Camelidae family based on investigating the impact of amino acid replacement on the physiochemical properties of proteins, including equilibrium constant and surrounding hydrophobicity. These mtDNA variants under positive selection in the Camelidae family might be associated with their adaptation to their contrasting environments.
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Affiliation(s)
- Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait.
| | - Sanaa Al-Zoubi
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait
| | - Fatima Ali
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait
| | - Arwa Afana
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait
| | - Mohammed Dashti
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Abdulaziz Al-Ateeqi
- Environment and Life Sciences research center, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - David Wragg
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Suzanne Al-Bustan
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, 400 Al-Ahsa, Saudi Arabia; Camel Research Center, King Faisal University, 400 Al-Ahsa, Saudi Arabia
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El-Gendy SAA, Alsafy MAM, Rutland CS, Ez Elarab SM, Abd-Elhafeez HH, Kamal BM. Ossa cordis and os aorta in the one-humped camel: Computed tomography, light microscopy and morphometric analysis. Microsc Res Tech 2023; 86:53-62. [PMID: 36354738 PMCID: PMC10100463 DOI: 10.1002/jemt.24256] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 09/12/2022] [Accepted: 10/29/2022] [Indexed: 11/12/2022]
Abstract
The present study describes the morphological characteristics of the camel heart Ossa cordis, and os aorta using computed tomography soft tissue window (CT) alongside 3D render volume reconstructions and light microscopy. The current study techniques demonstrated the Ossa cordis and os aorta in the cardiac window with more precision than the black and white (ghost), and angiography images. Transverse and sagittal CT images additionally demonstrated the presence of Ossa cordis and os aorta. This study is the first to record two small Ossa cordis sinistrum and one os aorta in the camel heart, in addition to the more commonly observed singular, large, os cordis dextrum. The os cordis dextrum was always located in the upper part of the interventricular septum, near to its junction with the atrium, forming an elongated rectangular shape when observed transversally. The wider cranial part was composed from bone, whereas the caudal aspect was narrow and contained both bone and cartilage. Light microscopy identified that the os cordis dextrum consisted of trabecular bone, marrow spaces, and hyaline cartilage. Two Ossa cordis sinistrum were detected on the left side of the heart, one in the right fibrous ring and another in the interventricular septum, microscopy showed that both contained only trabecular bone with osteocytes, osteoblasts, and osteoclasts. At the level of ascending aorta, there was also trabecular bone containing osteocytes, an os aorta.
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Affiliation(s)
- Samir A A El-Gendy
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Alexandria University, Alexandria, Egypt
| | - Mohamed A M Alsafy
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Alexandria University, Alexandria, Egypt
| | - Catrin S Rutland
- School of Veterinary Medicine and Science, Faculty of Medicine, University of Nottingham, Nottingham, UK
| | - Samar M Ez Elarab
- Department of Histology and Cytology, Faculty of Veterinary Medicine, Alexandria University, Alexandria, Egypt
| | - Hanan H Abd-Elhafeez
- Department of Cell and Tissues, Faculty of Veterinary Medicine, Assiut University, Asyut, Egypt
| | - Basma M Kamal
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, University of Sadat City, Sadat, Egypt
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The Flourishing Camel Milk Market and Concerns about Animal Welfare and Legislation. Animals (Basel) 2022; 13:ani13010047. [PMID: 36611656 PMCID: PMC9817819 DOI: 10.3390/ani13010047] [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: 11/17/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
The worldwide dromedary milk production has increased sharply since the beginning of this century due to prolonged shelf life, improved food-safety and perceived health benefits. Scientific confirmation of health claims will expand the market of dromedary milk further. As a result, more and more dromedaries will be bred for one purpose only: the highest possible milk production. However, intensive dromedary farming systems have consequences for animal welfare and may lead to genetic changes. Tighter regulations will be implemented to restrict commercialization of raw milk. Protocols controlling welfare of dromedaries and gene databases of milk-dromedaries will prevent negative consequences of intensive farming. In countries where dromedaries have only recently been introduced as production animal, legislators have limited expertise on this species. This is exemplified by an assessment on behalf of the Dutch government, recommending prohibiting keeping this species from 2024 onwards because the dromedary was deemed to be insufficiently domesticated. Implementation of this recommendation in Dutch law would have devastating effects on existing dromedary farms and could also pave the way for adopting similar measures in other European countries. In this paper it is shown that the Dutch assessment lacks scientific rigor. Awareness of breeders and legislators for the increasing knowledge about dromedaries and their products would strengthen the position of dromedaries as one of the most adapted and sustainable animals.
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Yakubu A, Okpeku M, Shoyombo AJ, Onasanya GO, Dahloum L, Çelik S, Oladepo A. Exploiting morphobiometric and genomic variability of African indigenous camel populations-A review. Front Genet 2022; 13:1021685. [PMID: 36579332 PMCID: PMC9791103 DOI: 10.3389/fgene.2022.1021685] [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: 08/17/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Camels (Camelus dromedarius) in Africa are adapted to arid and the semi-arid environmental conditions, and are valuable for meat, milk and fiber production. On account of the growing demand for camels in this continent, there is a need for knowledge on their phenotypic and genetic diversity. This is fundamental to sustainable herd management and utilization including the design of appropriate breeding and conservation strategies. We reviewed studies on the phenotypic and genetic characterization, breeding objectives, systems of production, productive and reproductive performances, and pathways for the sustainable rearing and use of camels in Africa. The morphological and genetic diversity, productive and reproductive abilities of African camels suggest the existence of genetic variations that can be utilized for breeds/ecotypes' genetic improvement and conservation. Possible areas of intervention include the establishment of open nucleus and community-based breeding schemes and utilization of modern reproductive technologies for the genetic improvement of milk and meat yields, sustainable management of rangelands, capacity building of the pastoralists and agro-pastoralists, institutional supports, formation of centralized conservation centres and efficient and effective marketing systems.
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Affiliation(s)
- Abdulmojeed Yakubu
- Department of Animal Science, Faculty of Agriculture, Centre for Sustainable Agriculture and Rural Development, Shabu-Lafia Campus, Nasarawa State University, Keffi, Nigeria
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of Kwa-Zulu Natal, Durban, South Africa
| | | | - Gbolabo O. Onasanya
- Department of Animal Science, Federal University Dutse, Dutse, Nigeria
- Deparment of Animal Genetics and Breeding, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Lahouari Dahloum
- Départment of Agronomy, Faculty of Natural Science and Life, Abdelhamid Ibn Badis, University, Mostaganem, Algeria
| | - Senol Çelik
- Department of Animal Science, Faculty of Agriculture, Bingöl University, Bingöl, Turkey
| | - Abolade Oladepo
- Discipline of Genetics, School of Life Sciences, University of Kwa-Zulu Natal, Durban, South Africa
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Bittner NKJ, Mack KL, Nachman MW. Shared Patterns of Gene Expression and Protein Evolution Associated with Adaptation to Desert Environments in Rodents. Genome Biol Evol 2022; 14:evac155. [PMID: 36268582 PMCID: PMC9648513 DOI: 10.1093/gbe/evac155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2022] [Indexed: 01/18/2023] Open
Abstract
Desert specialization has arisen multiple times across rodents and is often associated with a suite of convergent phenotypes, including modification of the kidneys to mitigate water loss. However, the extent to which phenotypic convergence in desert rodents is mirrored at the molecular level is unknown. Here, we sequenced kidney mRNA and assembled transcriptomes for three pairs of rodent species to search for shared differences in gene expression and amino acid sequence associated with adaptation to deserts. We conducted phylogenetically independent comparisons between a desert specialist and a non-desert relative in three families representing ∼70 million years of evolution. Overall, patterns of gene expression faithfully recapitulated the phylogeny of these six taxa providing a strong evolutionary signal in levels of mRNA abundance. We also found that 8.6% of all genes showed shared patterns of expression divergence between desert and non-desert taxa, much of which likely reflects convergent evolution, and representing more than expected by chance under a model of independent gene evolution. In addition to these shared changes, we observed many species-pair-specific changes in gene expression indicating that instances of adaptation to deserts include a combination of unique and shared changes. Patterns of protein evolution revealed a small number of genes showing evidence of positive selection, the majority of which did not show shared changes in gene expression. Overall, our results suggest that convergent changes in gene regulation play an important role in the complex trait of desert adaptation in rodents.
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Affiliation(s)
- Noëlle K J Bittner
- Department of Integrative Biology and Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California Berkeley, California 94720
| | - Katya L Mack
- Department of Integrative Biology and Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California Berkeley, California 94720
| | - Michael W Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California Berkeley, California 94720
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Wang G, Wang F, Pei H, Li M, Bai F, Lei C, Dang R. Genome-wide analysis reveals selection signatures for body size and drought adaptation in Liangzhou donkey. Genomics 2022; 114:110476. [PMID: 36057425 DOI: 10.1016/j.ygeno.2022.110476] [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: 12/28/2021] [Revised: 07/21/2022] [Accepted: 08/12/2022] [Indexed: 01/14/2023]
Abstract
Liangzhou donkey is a domestic animal breed distributed on the edge of the Tengger Desert in Gansu Province of China. It has small body size and strong adaptability to dry environments. Here, we sequenced 10 Liangzhou donkey genomes and compared them to the 55 genomes of 8 representative donkey breeds worldwide. The population structure analysis revealed that Liangzhou donkey harboured the ancestry with the Asian domestic donkeys (0.863) and European domestic donkeys (0.137). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the genetic diversity in Liangzhou donkey. In addition, we analyzed the genetic basis of the small body size and drought adaptation of Liangzhou donkey by using Fst, θπ-ratio, XP-EHH, CLR and θπ methods. We found that the NCAPG-LCORL on chromosome 3 may be a candidate region for small body size trait of Liangzhou donkey. The CYP4A11 gene located on chromosome 5 showed strong sign of selection sweep. CYP4A11 can convert arachidonic acid into 19(S)-HETE, which can promote water reabsorption in renal tubule and enhance the ability of Liangzhou donkey to adapt to dry environment. These results contribute to a better understanding of the underlying population structure of Liangzhou donkeys and provides a valuable resource for future research on donkey breeding in response to climate change.
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Affiliation(s)
- Gang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Fuwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Haoyu Pei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Mei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China
| | - Fuxia Bai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
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Zhao X, Zhang J, Wang H, Li H, Qu C, Wen J, Zhang X, Zhu T, Nie C, Li X, Muhatai G, Wang L, Lv X, Yang W, Zhao C, Bao H, Li J, Zhu B, Cao G, Xiong W, Ning Z, Qu L. Genomic and transcriptomic analyses reveal genetic adaptation to cold conditions in the chickens. Genomics 2022; 114:110485. [PMID: 36126832 DOI: 10.1016/j.ygeno.2022.110485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/27/2022] [Accepted: 09/16/2022] [Indexed: 01/14/2023]
Abstract
Under the pressure of natural and artificial selection, domestic animals, including chickens, have evolved unique mechanisms of genetic adaptations such as high-altitude adaptation, hot and arid climate adaptation, and desert adaptation. Here, we investigated the genetic basis of cold tolerance in chicken by integrating whole-genome and transcriptome sequencing technologies. Genome-wide comparative analyses of 118 chickens living in different latitudes showed 46 genes and several pathways that may be involved in cold adaptation. The results of the functional enrichment analysis of differentially expressed genes proved the important role of metabolic pathways and immune-related pathways in cold tolerance in chickens. The subsequent integration of whole genome and transcriptome sequencing technology further identified six genes - dnah5 (dynein axonemal heavy chain 5), ptgs2 (prostaglandin-endoperoxide synthase 2), inhba (inhibin beta A subunit), irx2 (iroquois homeobox 2), ensgalg00000054917, and ensgalg00000046652 - requiring more detailed studies. In addition, we also discovered different allele frequency distributions of five SNPs (single nucleotide polymorphisms) within ptgs2 and nine SNPs within dnah5 in chickens in different latitudes, suggesting strong selective pressure of these two genes in chickens. We provide a novel insight into the genetic adaptation in chickens to cold environments, and provide a reference for evaluating and developing adaptive chicken breeds in cold environments.
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Affiliation(s)
- Xiurong Zhao
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Jinxin Zhang
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Huie Wang
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar, Xinjiang 843300, China.
| | - Haiying Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830000, China.
| | - Changqing Qu
- Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine of Anhui Province, Fuyang Normal University, Fuyang, Anhui 236037, China.
| | - Junhui Wen
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Xinye Zhang
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Tao Zhu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Changsheng Nie
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Xinghua Li
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Gemingguli Muhatai
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar, Xinjiang 843300, China.
| | - Liang Wang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China.
| | - XueZe Lv
- Beijing Municipal General Station of Animal Science, Beijing 100107, China.
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China.
| | - Chunjiang Zhao
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Haigang Bao
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Junying Li
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Bo Zhu
- Animal Health Supervision Institute of Zhuozhou, Hebei Province 072750, China.
| | - Guomin Cao
- Animal husbandry station of Fangchenggang, Guangxi Province 538001, China.
| | - Wenjie Xiong
- Animal Disease Prevention and Control Center of Fangchenggang, Guangxi Province 538001, China.
| | - Zhonghua Ning
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Lujiang Qu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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Knoll A, Wijacki J, Plasil M, Burger PA, Horin P. Microsatellite markers of the major histocompatibility complex genomic region of domestic camels. Front Genet 2022; 13:1015288. [PMID: 36353100 PMCID: PMC9638106 DOI: 10.3389/fgene.2022.1015288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/03/2022] [Indexed: 11/29/2022] Open
Abstract
We identified and characterized 11 polymorphic microsatellite markers suitable for routine testing (three in the MHC class I sub-region, four in MHC class II and four in the MHC class III sub-region) of dromedaries and Bactrian camels. In total, 38 dromedaries and 33 Bactrian camels were genotyped, and interspecific differences were observed in the numbers of alleles and in allelic frequencies, as well as in the observed heterozygosity. These loci may be used as markers to study the adaptive genetic diversity of the MHC region in Old World camels.
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Affiliation(s)
- Ales Knoll
- Department of Animal Morphology, Physiology and Genetics, Faculty of Agronomy, Mendel University in Brno, Brno, Czechia
| | - Jan Wijacki
- Department of Animal Morphology, Physiology and Genetics, Faculty of Agronomy, Mendel University in Brno, Brno, Czechia
| | - Martin Plasil
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czechia
- CEITEC-VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Pamela A. Burger
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Petr Horin
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czechia
- CEITEC-VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
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Extracellular Vesicles in Veterinary Medicine. Animals (Basel) 2022; 12:ani12192716. [PMID: 36230457 PMCID: PMC9559303 DOI: 10.3390/ani12192716] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/23/2022] [Accepted: 10/03/2022] [Indexed: 11/16/2022] Open
Abstract
Extracellular vesicles (EVs) are cell-derived membrane-bound vesicles involved in many physiological and pathological processes not only in humans but also in all the organisms of the eukaryotic and prokaryotic kingdoms. EV shedding constitutes a fundamental universal mechanism of intra-kingdom and inter-kingdom intercellular communication. A tremendous increase of interest in EVs has therefore grown in the last decades, mainly in humans, but progressively also in animals, parasites, and bacteria. With the present review, we aim to summarize the current status of the EV research on domestic and wild animals, analyzing the content of scientific literature, including approximately 220 papers published between 1984 and 2021. Critical aspects evidenced through the veterinarian EV literature are discussed. Then, specific subsections describe details regarding EVs in physiology and pathophysiology, as biomarkers, and in therapy and vaccines. Further, the wide area of research related to animal milk-derived EVs is also presented in brief. The numerous studies on EVs related to parasites and parasitic diseases are excluded, deserving further specific attention. The literature shows that EVs are becoming increasingly addressed in veterinary studies and standardization in protocols and procedures is mandatory, as in human research, to maximize the knowledge and the possibility to exploit these naturally produced nanoparticles.
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Chafik A, Essamadi A, Çelik SY, Mavi A. Purification and biochemical characterization of catalase that confers protection against hydrogen peroxide induced by stressful desert environment: the Camelus Dromedarius kidney catalase. Prep Biochem Biotechnol 2022:1-12. [PMID: 36074915 DOI: 10.1080/10826068.2022.2119576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Camel is continually exposed to stressful desert environment that enhances generation of reactive oxygen species, including hydrogen peroxide (H2O2). Catalase plays an important role in detoxification of H2O2. A highly active catalase from camel kidney was purified to homogeneity, with a specific activity of 1,774,392 U/mg protein, using ion exchange and metal chelate affinity chromatography. The molecular weight of the enzyme was 268 kDa consisting of four identical subunits of 63 kDa. The enzyme showed higher optimum temperature (45 °C) and higher activation energy (4.37 kJ mol-1). The thermodynamic parameters, ΔH, ΔG and ΔS, were determined. The effect of various metal ions and chemicals on enzyme activity was investigated. Km, Vmax, kcat and kcat/Km values for H2O2 were found to be 46 mM, 10,715,045 U/mg, 48,265,968 s-1 and 2,966,562 s-1 mM-1, respectively. Camel kidney catalase displayed higher affinity efficiency for H2O2 and can protect reduced glutathione (GSH) from oxidation by H2O2. Sodium azide was found to be a noncompetitive inhibitor of enzyme with Ki and IC50 of 17.88 µM and 20.94 µM, respectively. Camel catalase showed unique biochemical properties. Interestingly, camel catalase can protect molecules (GSH) and organ functions (kidney) from the toxic effects of H2O2 induced by stressful desert environment.
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Affiliation(s)
- Abdelbasset Chafik
- Ecole Supérieure de Technologie d'El Kelâa des Sraghna, Université Cadi Ayyad, El Kelâa des Sraghna, Morocco.,Faculté des Sciences et Techniques, Laboratoire Bioressources et Sécurité Sanitaire des Aliments, Université Cadi Ayyad, Marrakech, Morocco
| | - Abdelkhalid Essamadi
- Faculty of Sciences and Technologies, Laboratory of Biochemistry, Neurosciences, Natural Resources and Environment, Hassan First University, Settat, Morocco
| | - Safinur Yildirim Çelik
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Atatürk University, Erzurum, Turkey
| | - Ahmet Mavi
- Department of Nanoscience and Nanoengineering, Institute of Science, Atatürk University, Erzurum, Turkey.,Department of Mathematics and Science Education, Education Faculty of Kazim Karabekir, Atatürk University, Erzurum, Turkey
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Camels' biological fluids contained nanobodies: promising avenue in cancer therapy. Cancer Cell Int 2022; 22:279. [PMID: 36071488 PMCID: PMC9449263 DOI: 10.1186/s12935-022-02696-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer is a major health concern and accounts for one of the main causes of death worldwide. Innovative strategies are needed to aid in the diagnosis and treatment of different types of cancers. Recently, there has been an evolving interest in utilizing nanobodies of camel origin as therapeutic tools against cancer. Nanotechnology uses nanobodies an emerging attractive field that provides promises to researchers in advancing different scientific sectors including medicine and oncology. Nanobodies are characteristically small-sized biologics featured with the ability for deep tissue penetration and dissemination and harbour high stability at high pH and temperatures. The current review highlights the potential use of nanobodies that are naturally secreted in camels’ biological fluids, both milk and urine, in the development of nanotechnology-based therapy for treating different typesQuery of cancers and other diseases. Moreover, the role of nano proteomics in the invention of novel therapeutic agents specifically used for cancer intervention is also illustrated.
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Inaba Y, Iwamoto S, Nakayama K. Genome-wide DNA methylation status of Mongolians exhibits signs of cellular stress response related to their nomadic lifestyle. J Physiol Anthropol 2022; 41:30. [PMID: 35986394 PMCID: PMC9388360 DOI: 10.1186/s40101-022-00305-0] [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: 03/29/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022] Open
Abstract
Background Epigenetics is crucial for connecting environmental stresses with physiological responses in humans. Mongolia, where nomadic livestock pastoralism has been the primal livelihood, has a higher prevalence of various chronic diseases than the surrounding East Asian regions, which are more suitable for crop farming. The genes related to dietary stress and pathogenesis of related disorders may have varying epigenetic statuses among the human populations with diverse dietary cultures. Hence, to understand such epigenetic differences, we conducted a comparative analysis of genome-wide DNA methylation of Mongolians and crop-farming East Asians. Methods Genome-wide DNA methylation status of peripheral blood cells (PBCs) from 23 Mongolian adults and 24 Thai adults was determined using the Infinium Human Methylation 450K arrays and analyzed in combination with previously published 450K data of 20 Japanese and 8 Chinese adults. CpG sites/regions differentially methylated between Mongolians and crop-farming East Asians were detected using a linear model adjusted for sex, age, ethnicity, and immune cell heterogeneity on RnBeads software. Results Of the quality-controlled 389,454 autosomal CpG sites, 223 CpG sites were significantly differentially methylated among Mongolians and the four crop farming East Asian populations (false discovery rate < 0.05). Analyses focused on gene promoter regions revealed that PM20D1 (peptidase M20 domain containing 1), which is involved in mitochondrial uncoupling and various processes, including cellular protection from reactive oxygen species (ROS) and thermogenesis, was the top differentially methylated gene. Moreover, gene ontology enrichment analysis revealed that biological processes related to ROS metabolism were overrepresented among the top 1% differentially methylated genes. The promoter regions of these genes were generally hypermethylated in Mongolians, suggesting that the metabolic pathway detoxifying ROS might be globally suppressed in Mongolians, resulting in the high susceptibility of this population to various chronic diseases. Conclusions This study showed a significantly diverse DNA methylation status among Mongolians and crop-farming East Asians. Further, we found an association between the differentially methylated genes and various metabolic and neurodegenerative diseases. Knowledge of the epigenetic regulators might help in proper understanding, treatment, and control of such disorders, and physiological adaptation in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s40101-022-00305-0.
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Bruno S, Landi V, Senczuk G, Brooks SA, Almathen F, Faye B, Gaouar SSB, Piro M, Kim KS, David X, Eggen A, Burger P, Ciani E. Refining the Camelus dromedarius Myostatin Gene Polymorphism through Worldwide Whole-Genome Sequencing. Animals (Basel) 2022; 12:2068. [PMID: 36009658 PMCID: PMC9404819 DOI: 10.3390/ani12162068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/07/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
Myostatin (MSTN) is a highly conserved negative regulator of skeletal muscle in mammals. Inactivating mutations results in a hyper-muscularity phenotype known as "double muscling" in several livestock and model species. In Camelus dromedarius, the gene structure organization and the sequence polymorphisms have been previously investigated, using Sanger and Next-Generation Sequencing technologies on a limited number of animals. Here, we carried out a follow-up study with the aim to further expand our knowledge about the sequence polymorphisms at the myostatin locus, through the whole-genome sequencing data of 183 samples representative of the geographical distribution range for this species. We focused our polymorphism analysis on the ±5 kb upstream and downstream region of the MSTN gene. A total of 99 variants (77 Single Nucleotide Polymorphisms and 22 indels) were observed. These were mainly located in intergenic and intronic regions, with only six synonymous Single Nucleotide Polymorphisms in exons. A sequence comparative analysis among the three species within the Camelus genus confirmed the expected higher genetic distance of C. dromedarius from the wild and domestic two-humped camels compared to the genetic distance between C. bactrianus and C. ferus. In silico functional prediction highlighted: (i) 213 differential putative transcription factor-binding sites, out of which 41 relative to transcription factors, with known literature evidence supporting their involvement in muscle metabolism and/or muscle development; and (ii) a number of variants potentially disrupting the canonical MSTN splicing elements, out of which two are discussed here for their potential ability to generate a prematurely truncated (inactive) form of the protein. The distribution of the considered variants in the studied cohort is discussed in light of the peculiar evolutionary history of this species and the hypothesis that extremely high muscularity, associated with a homozygous condition for mutated (inactivating) alleles at the myostatin locus, may represent, in arid desert conditions, a clear metabolic disadvantage, emphasizing the thermoregulatory and water availability challenges typical of these habitats.
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Affiliation(s)
- Silvia Bruno
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, 70126 Bari, Italy
| | - Vincenzo Landi
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, Valenzano, 70010 Bari, Italy
| | - Gabriele Senczuk
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, Italy
| | - Samantha Ann Brooks
- Department of Animal Sciences, University of Florida, Gainesville, FL 32610, USA
| | - Faisal Almathen
- Department of Public Health, College of Veterinary Medicine, King Faisal University, Al-Ahsa 31982, Saudi Arabia
- Camel Research Center, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | | | | | - Mohammed Piro
- Department of Medicine, Surgery and Reproduction, Institut Agronomique et Vétérinaire Hassan II, Rabat BP 6202, Morocco
| | - Kwan Suk Kim
- Department of Animal Sciences, Chungbuk National University, Chungbuk 28644, Korea
| | | | | | - Pamela Burger
- Research Institute of Wildlife Ecology, Vetmeduni, 1160 Vienna, Austria
| | - Elena Ciani
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, 70126 Bari, Italy
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Ming L, Siren D, Hasi S, Jambl T, Ji R. Review of genetic diversity in Bactrian camel ( Camelus bactrianus). Anim Front 2022; 12:20-29. [PMID: 35974787 PMCID: PMC9374477 DOI: 10.1093/af/vfac027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Liang Ming
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, 010018, Hohhot, China
| | - Dalai Siren
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, 010018, Hohhot, China
| | - Surong Hasi
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture, College of Veterinary Medicine, Inner Mongolia Agricultural University, 010018, Hohhot, China
| | - Tuyatsetseg Jambl
- China-Mongolia Joint Laboratory for Biomacromolecule Research, Ulaanbaatar, Mongolia
| | - Rimutu Ji
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, 010018, Hohhot, China
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Letaief N, Bedhiaf-Romdhani S, Ben Salem W, Mohammed AAS, Gaspa G, Pauciullo A. Tunisian camel casein gene characterization reveals similarities and differences with Sudanese and Nigerian populations. J Dairy Sci 2022; 105:6783-6794. [PMID: 35840403 DOI: 10.3168/jds.2022-22081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/27/2022] [Indexed: 11/19/2022]
Abstract
Milk is a primary protein source that has always played a role in mammalian health. Despite the intensification of research projects on dromedary and the knowledge of the genetic diversity at the casein loci, the genetic structure of the Tunisian camel population still needs exploration. This study sought to determine the genetic diversity of 3 casein gene variants in 5 Tunisian camel ecotypes: c.150G>T at CSN1S1 (αS1-casein), g.2126A>G at CSN2 (β-casein), and g.1029T>C at CSN3 (κ-casein). The obtained results were compared with data published on Sudanese and Nigerian camels to establish the level of differentiation within and between populations. A total of 159 blood samples were collected from 5 Tunisian camel ecotypes and the extracted DNA was genotyped by PCR-RFLP. A streamlined genotyping protocol was also developed for CSN3. Results indicated that allele T was quite rare (0.06) at CSN1S1 for all ecotypes. Minor allele frequency was found for G (0.462) in CSN2 except for Ardhaoui Medenine ecotype who deviated from the average CSN2 allele frequency of the total population. Allele C showed minor allele frequency of 0.384 in CSN3. Among the Tunisian population, GAT (0.343) was the most represented haplotype in all ecotypes except for Ardhaoui Medenine, where GGC (0.322) was the most frequent one. Significant differences in heterozygosity and local inbreeding were observed across the Tunisian, Sudanese, and Nigerian populations, although the global fixation index indicated that only 2.2% of the genetic variance is related to ecotype differences. Instead, phylogenetic analysis revealed a closer link between the Tunisian and Sudanese populations through a clade subdivision with 3 main branches among the ecotypes. This study represents the first attempt to understand casein gene variability in Tunisian camels; with further study, milk traits and genetic differentiation among populations can be associated with the history of camel domestication.
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Affiliation(s)
- N Letaief
- National Agronomic Institute of Tunisia 1082, Tunis, Tunisia; Laboratory of Animal and Forage Production, National Agricultural Research Institute of Tunisia, University of Carthage, Ariana 1004, Tunisia
| | - S Bedhiaf-Romdhani
- Laboratory of Animal and Forage Production, National Agricultural Research Institute of Tunisia, University of Carthage, Ariana 1004, Tunisia
| | - W Ben Salem
- Animal and Pasture Agency, Tunis 1002, Tunisia
| | - A A S Mohammed
- Department of Agriculture, Forest and Food Sciences, University of Torino, 10095 Grugliasco (TO), Italy
| | - G Gaspa
- Department of Agriculture, Forest and Food Sciences, University of Torino, 10095 Grugliasco (TO), Italy
| | - A Pauciullo
- Department of Agriculture, Forest and Food Sciences, University of Torino, 10095 Grugliasco (TO), Italy.
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Burger PA, Ciani E. Structural and functional genomics in Old World camels-where do we stand and where to go. Anim Front 2022; 12:30-34. [PMID: 35974786 PMCID: PMC9374506 DOI: 10.1093/af/vfac047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Pamela A Burger
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, University of Veterinary Medicine, 1160 Vienna, Austria
| | - Elena Ciani
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Bari, Italy
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Kandeel M, Al-Taher A, Venugopala KN, Marzok M, Morsy M, Nagaraja S. Camel Proteins and Enzymes: A Growing Resource for Functional Evolution and Environmental Adaptation. Front Vet Sci 2022; 9:911511. [PMID: 35903143 PMCID: PMC9315206 DOI: 10.3389/fvets.2022.911511] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/23/2022] [Indexed: 11/15/2022] Open
Abstract
In less agroecological parts of the Asian, Arabian, and African deserts, Camelus dromedarius play an important role in human survival. For many years, camels have been employed as a source of food, a tool of transportation, and a means of defense. They are becoming increasingly important as viable livestock animals in many desert climates. With the help of camel genetics, genomics and proteomics known so far, this review article will summarize camel enzymes and proteins, which allow them to thrive under varied harsh environmental situations. An in-depth study of the dromedary genome revealed the existence of protein-coding and fast-developing genes that govern a variety of metabolic responses including lipid and protein metabolism, glucoamylase, flavin-containing monooxygenase and guanidinoacetate methyltransferase are other metabolic enzymes found in the small intestine, liver, pancreas, and spleen. In addition, we will discuss the handling of common medications by camel liver cytochrome p 450, which are different from human enzymes. Moreover, camels developed several paths to get optimum levels of trace elements like copper, zinc, selenium, etc., which have key importance in their body for normal regulation of metabolic events. Insulin tolerance, carbohydrate and energy metabolism, xenobiotics metabolizing enzymes, vimentin functions, behavior during the rutting season, resistance to starvation and changes in blood composition and resistance to water loss were among the attractive aspects of camel enzymes and proteins peculiarities in the camels. Resolving the enigma of the method of adaptation and the molecular processes linked with camel life is still a developing repository full of mysteries that need additional exploration.
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Affiliation(s)
- Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafr El Sheikh University, Kafr El Sheikh, Egypt
| | - Abdulla Al-Taher
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Katharigatta N. Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Mohamed Marzok
- Department of Clinical Sciences, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
- Department of Surgery, Faculty of Veterinary Medicine, Kafr El Sheikh University, Kafr El Sheikh, Egypt
| | - Mohamed Morsy
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
- Department of Pharmacology, Faculty of Medicine, Minia University, Minya, Egypt
| | - Sreeharsha Nagaraja
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
- Department of Pharmaceutics, Vidya Siri College of Pharmacy, Bengaluru, India
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Tijjani A, Salim B, da Silva MVB, Eltahir HA, Musa TH, Marshall K, Hanotte O, Musa HH. Genomic signatures for drylands adaptation at gene-rich regions in African zebu cattle. Genomics 2022; 114:110423. [PMID: 35803449 PMCID: PMC9388378 DOI: 10.1016/j.ygeno.2022.110423] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/20/2022] [Accepted: 06/30/2022] [Indexed: 11/25/2022]
Abstract
Background Indigenous Sudanese cattle are mainly indicine/zebu (humped) type. They thrive in the harshest dryland environments characterised by high temperatures, long seasonal dry periods, nutritional shortages, and vector disease challenges. Here, we sequenced 60 indigenous Sudanese cattle from six indigenous breeds and analysed the data using three genomic scan approaches to unravel cattle adaptation to the African dryland region. Results We identified a set of gene-rich selective sweep regions, detected mostly on chromosomes 5, 7 and 19, shared across African and Gir zebu. These include genes involved in immune response, body size and conformation, and heat stress response. We also identified selective sweep regions unique to Sudanese zebu. Of these, a 250 kb selective sweep on chromosome 16 spans seven genes, including PLCH2, PEX10, PRKCZ, and SKI, which are involved in alternative adaptive metabolic strategies of insulin signalling, glucose homeostasis, and fat metabolism. Conclusions Our results suggest that environmental adaptation may involve recent and ancient selection at gene-rich regions, which might be under a common regulatory genetic control, in zebu cattle. Sudanese cattle thrive in the harshest environments of the African drylands. Bos indicus shared selected genes are involved in immune response, conformation, and heat stress response. Sudanese zebu-specific sweep includes genes involved in alternative adaptive metabolic strategies of insulin signalling, glucose homeostasis, and fat metabolism. Environmental adaptation in zebu cattle may involve recent and ancient selection at gene-rich regions, which might be under a common regulatory genetic control.
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Affiliation(s)
- Abdulfatai Tijjani
- International Livestock Research Institute (ILRI), PO 5689, Addis Ababa, Ethiopia; Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Ethiopia, PO Box 5689, Addis Ababa, Ethiopia; Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, United Kingdom.
| | - Bashir Salim
- Faculty of Veterinary Medicine, University of Khartoum, Sudan
| | | | | | - Taha H Musa
- Biomedical Research Institute, Darfur College, Sudan
| | - Karen Marshall
- International Livestock Research Institute (ILRI), PO Box 30709, Nairobi 00100, Kenya; Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, P.O. Box 30709, Nairobi 00100, Kenya
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), PO 5689, Addis Ababa, Ethiopia; Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Ethiopia, PO Box 5689, Addis Ababa, Ethiopia; Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, United Kingdom.
| | - Hassan H Musa
- Institute of Molecular Biology, University of Nyala, Sudan; Faculty of Medical Laboratory Sciences, University of Khartoum, Sudan.
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What's in a name? Common name misuse potentially confounds the conservation of the wild camel Camelus ferus. ORYX 2022. [DOI: 10.1017/s0030605322000114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Abstract
Common names allow species diversity to be acknowledged by experts and non-specialists alike; they are descriptors with both scientific and cultural implications. However, a lack of clarity when using a common name could risk altering perceptions of threatened species. This is the case for the Critically Endangered wild camel Camelus ferus, which, despite extensive evidence of its species status, is frequently referred to in English as wild Bactrian camel. However, the wild camel (Mongolian: хавтгай, khavtgai; Chinese: 野骆驼, ye luo tuo) is not a wild version of the domestic Bactrian camel Camelus bactrianus but a separate species near extinction, with an estimated population of c. 950. Failure to clearly separate Bactrian and wild camels in name risks masking the plight of the few remaining wild camels with the visible abundance of the domesticated species. Here we advocate the use of the accurate English common name wild camel for C. ferus ideally alongside its Indigenous names to correctly represent its cultural and conservation importance.
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Luo S, Li Y, Li S, Jiang R, Deng F, Liu G, Zhang J. Expression Regulation of Water Reabsorption Genes and Transcription Factors in the Kidneys of Lepus yarkandensis. Front Physiol 2022; 13:856427. [PMID: 35721542 PMCID: PMC9204326 DOI: 10.3389/fphys.2022.856427] [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: 01/18/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
Lepus yarkandensis is a desert-dwelling animal that has various adaptations to cope with drought. The kidney maintains water and acid-base balance mainly through the vasopressin-regulated water reabsorption pathway and proximal tubular bicarbonate reabsorption pathway. In this study, we compared the differentially expressed genes (DEGs) and transcription factors in the kidneys of L. yarkandensis and Oryctolagus cuniculus to explore the relationship between the DEGs in kidneys and the animals’ adaptations. Transcriptome sequencing data were used to predict the differentially-expressed water reabsorption genes and their transcription factors. Quantitative real-time PCR, immunohistochemistry, and western blotting were used to detect and verify the expression of DEGs in the kidney at mRNA and protein levels. Transcriptome analysis of the kidney of L. yarkandensis and O. cuniculus showed that 6,610 genes were up-regulated and 5,727 genes down-regulated in data shared by both species. According to the data, 232 transcription factors and their corresponding target genes were predicted, from which genes and transcription factors related to renal water reabsorption were screened. Quantitative RT-PCR results showed AQP1, AQP2, ADCY3, HIF1A, CREB3, and NFATc1 had higher expression in the L. yarkandensis kidney; in comparison, FXYD2 mRNA expression levels were lower. In western blotting, transcription factors HIF1A, NFATc1, NF-κB1, and critical genes ADCY3, ATPA1, and SLC4A4, were highly expressed in the kidneys of L. yarkandensis. Immunohistochemical results showed that the ADCY3 protein was in the basolateral membrane of the collecting duct, the ATP1A1 protein was in the basolateral membrane and medulla of proximal tubules, and the SLC4A4 protein was in the basolateral membrane of proximal tubules. According to these results can be inferred that HIF1A, NFATc1, and NF-κB1 play a certain role in regulating the expression of genes related to water reabsorption in the kidney of L. yarkandensis, thus improving the water reclamation efficiency of L. yarkandensis, so as to adapt to the arid desert environment.
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Affiliation(s)
- Shengjie Luo
- College of Life Sciences and Technology, Tarim University, Alar, China
| | - Yongle Li
- College of Life Sciences and Technology, Tarim University, Alar, China
| | - Shuwei Li
- College of Life Sciences and Technology, Tarim University, Alar, China.,Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources, Tarim University, Alar, China
| | - Renjun Jiang
- College of Life Sciences and Technology, Tarim University, Alar, China
| | - Fang Deng
- College of Life Sciences and Technology, Tarim University, Alar, China
| | - Guoquan Liu
- Anhui Province Key Laboratory of Translational Cancer Research and Department of Biochemistry, College of Laboratory Medicine, Bengbu Medical College, Bengbu, China.,College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Jianping Zhang
- College of Life Sciences and Technology, Tarim University, Alar, China.,Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources, Tarim University, Alar, China
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