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Kumar P, Bharti VK, Kumar K. Effect of short-term exposure to high-altitude hypoxic climate on feed-intake, blood glucose level and physiological responses of native and non-native goat. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2024; 68:795-806. [PMID: 38374293 DOI: 10.1007/s00484-024-02624-6] [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: 05/27/2023] [Revised: 01/03/2024] [Accepted: 01/14/2024] [Indexed: 02/21/2024]
Abstract
The exposure to high altitude and cold stress poses challenges in maintaining normal physiological standards and body homeostasis in non-native animals. To enhance our understanding of the physiology of native and non-native goats in high-altitude environments, we conducted a comparative study to examine the impact of natural hypoxic and cold stress conditions on their feed intake (FIT) and associated changes in physiological responses, including plasma glucose concentration (PGC). The study took place at an altitude of 3505.2 m above mean sea level and involved twenty-two healthy females from two different breeds of goats. This study was conducted over a period of 56 days after the arrival of non-native Black Bengal goats (BBN) and compared with native Changthangi (CHAN) goats. Both groups were extensively reared in a natural high-altitude and cold-stress environment in Leh, India, and were subjected to defined housing and management practices. The parameters evaluated included FIT, PGC, respiration rate, heart rate, pulse rate, and rectal temperature. High altitudes had a significant (p < 0.05) impact on FIT, PGC, respiration rate, heart rate, pulse rate, and rectal temperature in BBN, whereas these parameters remained stable in CHAN throughout the study period. Additionally, the detrimental effects of high-altitude stress were more pronounced in non-native goats compared to native goats. These findings suggest that physiological responses in non-native goats tend to stabilize after an initial period of adverse effects in high-altitude environments. Based on the physiological responses and glucose concentration, it is recommended to pay special attention to the nutrition of non-native goats for up to the third week (21 days) after their arrival in high-altitude areas.
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Affiliation(s)
- Prabhat Kumar
- DRDO-Defence Institute of High-Altitude Research (DIHAR), Leh, Ladakh UT, India.
- Indira Gandhi Institute of Medical Sciences (IGIMS), Patna, Bihar, India.
| | - Vijay K Bharti
- DRDO-Defence Institute of High-Altitude Research (DIHAR), Leh, Ladakh UT, India.
| | - Krishna Kumar
- DRDO-Defence Institute of High-Altitude Research (DIHAR), Leh, Ladakh UT, India
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2
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Wu Y, Xiong Y, Ji Y, Cheng Y, Zhu Q, Jiao X, Chang Y, Zhao N, Yang J, Lei F, Song G. Metabolic and microbial changes in light-vented bulbul during recent northward range expansion. Curr Zool 2024; 70:24-33. [PMID: 38476130 PMCID: PMC10926257 DOI: 10.1093/cz/zoad005] [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: 12/08/2022] [Accepted: 02/10/2023] [Indexed: 03/14/2024] Open
Abstract
Endotherms recently expanding to cold environments generally exhibit strong physiological acclimation to sustain high body temperature. During this process, gut microbes likely play a considerable role in host physiological functions, including digestion and thermogenesis. The light-vented bulbul Pycnonotus sinensis represents one such species. It used to be restricted to the Oriental realm but expanded its distribution range north to the Palearctic areas during the past few decades. Here, we explored the seasonal dynamics of the resting metabolic rate (RMR) and microbiota for local and newly colonized populations of the species. Our results showed that the mass-adjusted RMR and body mass were positively correlated with latitude variations in both seasons. Consistently, the gut microbiota showed a corresponding variation to the northern cold environments. In the two northern populations, the alpha diversity decreased compared with those of the two southern populations. Significant differences were detected in dominant phyla, such as Firmicutes, Bacteroidetes, Proteobacteria, and Desulfobacterota in both seasons. The core microbiota showed geographic differences in the winter, including the elevated relative abundance of 5 species in northern populations. Finally, to explore the link between microbial communities and host metabolic thermogenesis, we conducted a correlation analysis between microbiota and mass-adjusted RMR. We found that more genera were significantly correlated with mass-adjusted RMR in the wintering season compared to the breeding season (71 vs. 23). These results suggest that microbiota of the lighted-vented bulbul linked with thermogenesis in diversity and abundance under northward expansion.
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Affiliation(s)
- Yun Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Xiong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Department of Zoology, College of Life science, Sichuan Agricultural University, Ya’an 625099, Sichuan, China
| | - Yanzhu Ji
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianghui Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolu Jiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongbin Chang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Henan Engineering Research Center of Bird-Related Outage, Zhengzhou Normal University, Zhengzhou 450044, China
| | - Na Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, Anhui, China
| | - Jing Yang
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xian 710021, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Chen G, Chen J, Qi L, Yin Y, Lin Z, Wen H, Zhang S, Xiao C, Bello SF, Zhang X, Nie Q, Luo W. Bulk and single-cell alternative splicing analyses reveal roles of TRA2B in myogenic differentiation. Cell Prolif 2024; 57:e13545. [PMID: 37705195 PMCID: PMC10849790 DOI: 10.1111/cpr.13545] [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: 05/09/2023] [Revised: 08/08/2023] [Accepted: 08/28/2023] [Indexed: 09/15/2023] Open
Abstract
Alternative splicing (AS) disruption has been linked to disorders of muscle development, as well as muscular atrophy. However, the precise changes in AS patterns that occur during myogenesis are not well understood. Here, we employed isoform long-reads RNA-seq (Iso-seq) and single-cell RNA-seq (scRNA-seq) to investigate the AS landscape during myogenesis. Our Iso-seq data identified 61,146 full-length isoforms representing 11,682 expressed genes, of which over 52% were novel. We identified 38,022 AS events, with most of these events altering coding sequences and exhibiting stage-specific splicing patterns. We identified AS dynamics in different types of muscle cells through scRNA-seq analysis, revealing genes essential for the contractile muscle system and cytoskeleton that undergo differential splicing across cell types. Gene-splicing analysis demonstrated that AS acts as a regulator, independent of changes in overall gene expression. Two isoforms of splicing factor TRA2B play distinct roles in myogenic differentiation by triggering AS of TGFBR2 to regulate canonical TGF-β signalling cascades differently. Our study provides a valuable transcriptome resource for myogenesis and reveals the complexity of AS and its regulation during myogenesis.
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Affiliation(s)
- Genghua Chen
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Jiahui Chen
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Lin Qi
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Yunqian Yin
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Zetong Lin
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Huaqiang Wen
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Shuai Zhang
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Chuanyun Xiao
- Human and Animal PhysiologyWageningen UniversityWageningenThe Netherlands
| | - Semiu Folaniyi Bello
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Xiquan Zhang
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Qinghua Nie
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Wen Luo
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
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Hao Y, Song G, Zhang YE, Zhai W, Jia C, Ji Y, Tang S, Lv H, Qu Y, Lei F. Divergent contributions of coding and noncoding sequences to initial high-altitude adaptation in passerine birds endemic to the Qinghai-Tibet Plateau. Mol Ecol 2023; 32:3524-3540. [PMID: 37000417 DOI: 10.1111/mec.16942] [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: 12/12/2022] [Revised: 02/27/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023]
Abstract
Early events in the evolution of an ancestral lineage can shape the adaptive patterns of descendant species, but the evolutionary mechanisms driving initial adaptation from an ancestor remain largely unexplored. High-altitude adaptations have been extensively explored from the viewpoint of protein-coding genes; however, the contribution of noncoding regions remains relatively neglected. Here, we integrate genomic and transcriptomic data to investigate adaptive evolution in the ancestor of three high-altitude snowfinch species endemic to the Qinghai-Tibet Plateau. Our genome-wide scan for adaptation in the snowfinch ancestor identifies strong adaptation signals in functions of development and metabolism for the coding genes, but in functions of the nervous system development for noncoding regions. This pattern is exclusive to the snowfinch ancestor compared to a control ancestral lineage subject to weak selection. Changes in noncoding regions in the snowfinch ancestor, especially those nearest to coding genes, may be disproportionately associated with the differential expression of genes in the brain tissue compared to other tissues. Extensive gene expression in the brain tissue can be further altered via genetic regulatory networks of transcription factors harbouring potential accelerated regulatory regions (e.g., the development-related transcription factor YEATS4). Altogether, our study provides new evidence concerning how coding and noncoding sequences work through decoupled pathways in initial adaptation to the selective pressure of high-altitude environments. The analysis highlights the idea that noncoding sequences may be promising elements in facilitating the rapid evolution and adaptation to high altitudes.
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Affiliation(s)
- Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanzhu Ji
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shiyu Tang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Hongrui Lv
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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5
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Enlarged fins of Tibetan catfish provide new evidence of adaptation to high plateau. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2253-7. [PMID: 36802318 DOI: 10.1007/s11427-022-2253-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/30/2022] [Indexed: 02/23/2023]
Abstract
The uplift of the Tibetan Plateau significantly altered the geomorphology and climate of the Euroasia by creating large mountains and rivers. Fishes are more likely to be affected relative to other organisms, as they are largely restricted to river systems. Faced with the rapidly flowing water in the Tibetan Plateau, a group of catfish has evolved greatly enlarged pectoral fins with more numbers of fin-rays to form an adhesive apparatus. However, the genetic basis of these adaptations in Tibetan catfishes remains elusive. In this study, we performed comparative genomic analyses based on the chromosome-level genome of Glyptosternum maculatum in family Sisoridae and detected some proteins with conspicuously high evolutionary rates in particular in genes involved in skeleton development, energy metabolism, and hypoxia response. We found that the hoxd12a gene evolved faster and a loss-of-function assay of hoxd12a supports a potential role for this gene in shaping the enlarged fins of these Tibetan catfishes. Other genes with amino acid replacements and signatures of positive selection included proteins involved in low temperature (TRMU) and hypoxia (VHL) responses. Functional assays reveal that the G. maculatumTRMU allele generates more mitochondrial ATP than the ancestral allele found in low-altitude fishes. Functional assays of VHL alleles suggest that the G. maculatum allele has lower transactivation activity than the low-altitude forms. These findings provide a window into the genomic underpinnings of physiological adaptations that permit G. maculatum to survive in the harsh environment of the Tibetan Himalayas that mirror those that are convergently found in other vertebrates such as humans.
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6
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Rougemont Q, Xuereb A, Dallaire X, Moore JS, Normandeau E, Perreault-Payette A, Bougas B, Rondeau EB, Withler RE, Van Doornik DM, Crane PA, Naish KA, Garza JC, Beacham TD, Koop BF, Bernatchez L. Long-distance migration is a major factor driving local adaptation at continental scale in Coho salmon. Mol Ecol 2023; 32:542-559. [PMID: 35000273 DOI: 10.1111/mec.16339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/19/2021] [Accepted: 12/23/2021] [Indexed: 01/25/2023]
Abstract
Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species' homing behaviour may promote the establishment of local adaptation. We genotyped 7829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. The results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidate single nucleotide polymorphisms associated with long-distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.
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Affiliation(s)
- Quentin Rougemont
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada.,CEFE, Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, CNRS, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier, Montpellier, France
| | - Amanda Xuereb
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Xavier Dallaire
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Jean-Sébastien Moore
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Alysse Perreault-Payette
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Bérénice Bougas
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Eric B Rondeau
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada.,Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Ruth E Withler
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Donald M Van Doornik
- National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Manchester Research Station, Port Orchard, Washington, USA
| | - Penelope A Crane
- Conservation Genetics Laboratory, U.S. Fish and Wildlife Service, Anchorage, Alaska, USA
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - John Carlos Garza
- Department of Ocean Sciences and Institute of Marine Sciences, University of California Santa Cruz, Santa Cruz, California, USA
| | - Terry D Beacham
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
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XIONG Y, HAO Y, CHENG Y, FAN L, SONG G, LI D, QU Y, LEI F. Comparative transcriptomic and metabolomic analysis reveals pectoralis highland adaptation across altitudinal songbirds. Integr Zool 2022; 17:1162-1178. [PMID: 34935284 PMCID: PMC9786770 DOI: 10.1111/1749-4877.12620] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Pectoralis phenotypic variation plays a fundamental role in locomotion and thermogenesis in highland birds. However, its regulatory and metabolic mechanisms remain enigmatic to date. Here, we integrated phenomic, transcriptomic, and metabolomic approaches to determine muscle variation and its underpinning mechanisms across altitudinal songbirds. Phenomics confirmed that all highland birds had considerable increases in muscle oxidative capacity, capillarity, and mitochondrial abundance in our study. Correspondingly, transcriptomic analyses found that differentially expressed genes in phenotype-associated modules enriched for blood vessel, muscle structure development, and mitochondrial organization. Despite similar traits and functional enrichments across highland birds, different mechanisms drove their occurrence in high-altitude tree sparrow and 2 snow finches. Importantly, a metabolic feature shared by all the 3 highland birds is the improvement in insulin sensitivity and glucose utilization through activating insulin signaling pathway, which is vital to increase muscle oxidative capacity and maintain metabolic homeostasis. Nevertheless, fatty acid biosynthesis and oxidation are enhanced in only 2 snow finches which had a long evolutionary history on the high plateau, also differing from ketone body metabolism in recently introduced colonizer of the tree sparrow of the high plateau. Our study represents a vital contribution to reveal the regulatory and metabolic basis of pectoralis variation across altitudinal songbirds.
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Affiliation(s)
- Ying XIONG
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Yan HAO
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Yalin CHENG
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Liqing FAN
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina,Key Laboratory of Forest Ecology in Tibet Plateau of Ministry of EducationInstitute of Tibet Plateau EcologyTibet Agriculture & Animal Husbandry UniversityNyingchiChina
| | - Gang SONG
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
| | - Dongming LI
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life SciencesHebei Normal UniversityShijiazhuangChina
| | - Yanhua QU
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
| | - Fumin LEI
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina,Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
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8
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Zhang Z, Sui Z, Zhang J, Li Q, Zhang Y, Wang C, Li X, Xing F. Identification of Signatures of Selection for Litter Size and Pubertal Initiation in Two Sheep Populations. Animals (Basel) 2022; 12:ani12192520. [PMID: 36230262 PMCID: PMC9559472 DOI: 10.3390/ani12192520] [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: 08/09/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 11/23/2022] Open
Abstract
Fecundity is an important economic trait in sheep that directly affects their economic and productive efficiency. Our study aimed to identify SNP loci associated with sheep puberty or litter size which could be used in future breeding programs to improve fertility. Genomic DNA was obtained from Hetian and Cele Black sheep breeds and used for reduced-representation genome sequencing to identify SNP loci associated with pubertal initiation and litter size. Selective signatures analysis was performed based on the fixation index and nucleotide diversity, followed by pathway analysis of the genes contained in the selected regions. The selected SNP loci in the genes associated with pubertal initiation and litter size were validated using both sheep breeds. In total, 384,718 high quality SNPs were obtained and 376 genes were selected. Functional annotation of genes and enrichment analysis identified 12 genes associated with pubertal initiation and 11 genes associated with litter size. SNP locus validation showed that two SNP on PAK1 and four on ADCY1 may be associated with pubertal initiation, and one SNP on GNAQ gene (NC_040253.1: g.62677376G > A) was associated with litter size in Cele Black sheep. Our results provide new theoretical support for sheep breeding.
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9
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Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation. iScience 2022; 25:103899. [PMID: 35243257 PMCID: PMC8873613 DOI: 10.1016/j.isci.2022.103899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/12/2021] [Accepted: 02/07/2022] [Indexed: 11/20/2022] Open
Abstract
The phenotypic plasticity in responses to short-term stress can provide clues for understanding the adaptive fixation mechanism of genetic variation during long-term exposure to extreme environments. However, few studies have compared short-term stress responses with long-term evolutionary patterns; in particular, no interactions between the two processes have been evaluated in high-altitude environment. We performed RNA sequencing in embryo fibroblasts derived from great tits and mice to explore transcriptional responses after exposure to simulated high-altitude environmental stresses. Transcriptional changes of genes associated with metabolic pathways were identified in both bird and mice cells after short-term stress responses. Genomic comparisons among long-term highland tits and mammals and their lowland relatives revealed similar pathways (e.g., metabolic pathways) with that initiated under short-term stress transcriptional responses in vitro. These findings highlight the indicative roles of short-term stress in the long-term adaptation, and adopt common paths to molecular adaptation in mouse and bird cells. Short-term stress and long-term adaptations share the common metabolic pathways Phenotypic plasticity can promote adaptive evolution Adopt common paths to molecular adaptation in mouse and bird cells
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Feng P, Zeng T, Yang H, Chen G, Du J, Chen L, Shen J, Tao Z, Wang P, Yang L, Lu L. Whole-genome resequencing provides insights into the population structure and domestication signatures of ducks in eastern China. BMC Genomics 2021; 22:401. [PMID: 34058976 PMCID: PMC8165772 DOI: 10.1186/s12864-021-07710-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 05/12/2021] [Indexed: 01/03/2023] Open
Abstract
Background Duck is an ancient domesticated animal with high economic value, used for its meat, eggs, and feathers. However, the origin of indigenous Chinese ducks remains elusive. To address this question, we performed whole-genome resequencing to first explore the genetic relationship among variants of these domestic ducks with their potential wild ancestors in eastern China, as well as understand how the their genomes were shaped by different natural and artificial selective pressures. Results Here, we report the resequencing of 60 ducks from Chinese spot-billed ducks (Anas zonorhyncha), mallards (Anas platyrhnchos), Fenghua ducks, Shaoxing ducks, Shanma ducks and Cherry Valley Pekin ducks of eastern China (ten from each population) at an average effective sequencing depth of ~ 6× per individual. The results of population and demographic analysis revealed a deep phylogenetic split between wild (Chinese spot-billed ducks and mallards) and domestic ducks. By applying selective sweep analysis, we identified that several candidate genes, important pathways and GO categories associated with artificial selection were functionally related to cellular adhesion, type 2 diabetes, lipid metabolism, the cell cycle, liver cell proliferation, and muscle functioning in domestic ducks. Conclusion Genetic structure analysis showed a close genetic relationship of Chinese spot-billed ducks and mallards, which supported that Chinese spot-billed ducks contributed to the breeding of domestic ducks. During the long history of artificial selection, domestic ducks have developed a complex biological adaptation to captivity. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07710-2.
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Affiliation(s)
- Peishi Feng
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China.,Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Tao Zeng
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hua Yang
- Institute of Quality and Standards for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jinping Du
- Institute of Animal Husbandry and Veterinary Science, Hubei Academy of Agricultural Science, Wuhan, China
| | - Li Chen
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Junda Shen
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhenrong Tao
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ping Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China.
| | - Lin Yang
- College of Animal Science, South China Agricultural University, Guangzhou, China.
| | - Lizhi Lu
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
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