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Pan D, Shi Y, Huang M, Li X, Wang Z, Zhang Y, Sun H, Wang Z. Physiological indices and liver gene expression related to glucose supply in Brandt's vole (Lasiopodomys brandtii) exhibit species- and oxygen concentration-specific responses to hypoxia. Comp Biochem Physiol B Biochem Mol Biol 2024; 270:110911. [PMID: 37898361 DOI: 10.1016/j.cbpb.2023.110911] [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: 04/20/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 10/30/2023]
Abstract
Brandt's vole (Lasiopodomys brandtii) is a species with hypoxia tolerance, and glucose serves as the primary energy substrate under hypoxia. However, the glucose supply in Brandt's voles under hypoxia has not been studied. This study aimed to investigate characteristics in physiological indices and liver gene expression associated with glucose supply in Brandt's voles under hypoxia. Serum glucose of Brandt's voles remained stable under 10% O2, increased under 7.5% O2, and decreased under 5% O2. Serum lactate increased under 10% O2, decreased under 7.5% O2, increased at 6 h and decreased at 12 h under 5% O2. Liver glycogen increased under 10% O2, remained constant under 7.5% O2, and reduced under 5% O2. Pepck and G6pase expression associated with gluconeogenesis decreased under 10% O2, while Pepck expression decreased and G6pase expression increased under 7.5% and 5% O2. Regarding genes related to glycogen metabolism, Gys expression decreased at all oxygen concentrations, Phk expression increased under 5% O2, and Gp expression increased under 7.5% and 5% O2. The alterations in glucose, lactate, liver glycogen, and gene expression related to glycogenolysis in Kunming mice (Mus musculus, control species) are similar to discovery of Brandt's voles under 7.5% O2, but gene expression involved in gluconeogenesis and glycogen synthesis increased. The findings suggest that Brandt's voles are more tolerant to hypoxia than Kunming mice, and their physiological indices and liver gene expression related to glucose supply exhibit species- and oxygen concentration-specific responses to hypoxia. This research offers novel insights for studying hypoxia tolerance of Brandt's voles.
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Affiliation(s)
- Dan Pan
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan Province, PR China
| | - Yuhua Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan Province, PR China
| | - Maolin Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan Province, PR China
| | - Xiujuan Li
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan Province, PR China
| | - Zishi Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan Province, PR China
| | - Yifeng Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan Province, PR China
| | - Hong Sun
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan Province, PR China; Centre for Nutritional Ecology, Zhengzhou University, Zhengzhou, Henan Province, PR China.
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan Province, PR China.
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Kuo HC, Yao CT, Liao BY, Weng MP, Dong F, Hsu YC, Hung CM. Weak gene-gene interaction facilitates the evolution of gene expression plasticity. BMC Biol 2023; 21:57. [PMID: 36941675 PMCID: PMC10029303 DOI: 10.1186/s12915-023-01558-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/10/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Individual organisms may exhibit phenotypic plasticity when they acclimate to different conditions. Such plastic responses may facilitate or constrain the adaptation of their descendant populations to new environments, complicating their evolutionary trajectories beyond the genetic blueprint. Intriguingly, phenotypic plasticity itself can evolve in terms of its direction and magnitude during adaptation. However, we know little about what determines the evolution of phenotypic plasticity, including gene expression plasticity. Recent laboratory-based studies suggest dominance of reversing gene expression plasticity-plastic responses that move the levels of gene expression away from the new optima. Nevertheless, evidence from natural populations is still limited. RESULTS Here, we studied gene expression plasticity and its evolution in the montane and lowland populations of an elevationally widespread songbird-the Rufous-capped Babbler (Cyanoderma ruficeps)-with reciprocal transplant experiments and transcriptomic analyses; we set common gardens at altitudes close to these populations' native ranges. We confirmed the prevalence of reversing plasticity in genes associated with altitudinal adaptation. Interestingly, we found a positive relationship between magnitude and degree of evolution in gene expression plasticity, which was pertinent to not only adaptation-associated genes but also the whole transcriptomes from multiple tissues. Furthermore, we revealed that genes with weaker expressional interactions with other genes tended to exhibit stronger plasticity and higher degree of plasticity evolution, which explains the positive magnitude-evolution relationship. CONCLUSIONS Our experimental evidence demonstrates that species may initiate their adaptation to new habitats with genes exhibiting strong expression plasticity. We also highlight the role of expression interdependence among genes in regulating the magnitude and evolution of expression plasticity. This study illuminates how the evolution of phenotypic plasticity in gene expression facilitates the adaptation of species to challenging environments in nature.
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Affiliation(s)
- Hao-Chih Kuo
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Cheng-Te Yao
- Division of Zoology, Endemic Species Research Institute, Nantou, 55244, Taiwan
| | - Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Meng-Pin Weng
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Feng Dong
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Yu-Cheng Hsu
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, 97401, Taiwan
| | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
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3
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Dymskaya MM, Volodin IA, Smorkatcheva AV, Vasilieva NA, Volodina EV. Audible, but not ultrasonic, calls reflect surface-dwelling or subterranean specialization in pup and adult Brandt’s and mandarin voles. Behav Ecol Sociobiol 2022. [DOI: 10.1007/s00265-022-03213-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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4
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Li M, Pan D, Sun H, Zhang L, Cheng H, Shao T, Wang Z. The hypoxia adaptation of small mammals to plateau and underground burrow conditions. Animal Model Exp Med 2021; 4:319-328. [PMID: 34977483 PMCID: PMC8690988 DOI: 10.1002/ame2.12183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/08/2021] [Indexed: 12/19/2022] Open
Abstract
Oxygen is one of the important substances for the survival of most life systems on the earth, and plateau and underground burrow systems are two typical hypoxic environments. Small mammals living in hypoxic environments have evolved different adaptation strategies, which include increased oxygen delivery, metabolic regulation of physiological responses and other physiological responses that change tissue oxygen utilization. Multi-omics predictions have also shown that these animals have evolved different adaptations to extreme environments. In particular, vascular endothelial growth factor (VEGF) and erythropoietin (EPO), which have specific functions in the control of O2 delivery, have evolved adaptively in small mammals in hypoxic environments. Naked mole-rats and blind mole-rats are typical hypoxic model animals as they have some resistance to cancer. This review primarily summarizes the main living environment of hypoxia tolerant small mammals, as well as the changes of phenotype, physiochemical characteristics and gene expression mode of their long-term living in hypoxia environment.
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Affiliation(s)
- Mengke Li
- School of Life SciencesZhengzhou UniversityZhengzhouP.R. China
| | - Dan Pan
- School of Life SciencesZhengzhou UniversityZhengzhouP.R. China
| | - Hong Sun
- School of Life SciencesZhengzhou UniversityZhengzhouP.R. China
- Centre for Nutritional EcologyZhengzhou UniversityZhengzhouP.R. China
| | - Lei Zhang
- School of Life SciencesZhengzhou UniversityZhengzhouP.R. China
| | - Han Cheng
- School of Life SciencesZhengzhou UniversityZhengzhouP.R. China
| | - Tian Shao
- School of Life SciencesZhengzhou UniversityZhengzhouP.R. China
| | - Zhenlong Wang
- School of Life SciencesZhengzhou UniversityZhengzhouP.R. China
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5
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Shi L, Chen B, Wang X, Huang M, Qiao C, Wang J, Wang Z. Antioxidant response to severe hypoxia in Brandt's vole Lasiopodomys brandtii. Integr Zool 2021; 17:581-595. [PMID: 34713576 DOI: 10.1111/1749-4877.12602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The antioxidant defense system is essential for animals to cope with homeostasis disruption and overcome oxidative stress caused by adverse environmental conditions such as hypoxia. However, our understanding of how this system works in subterranean rodents remains limited. In this study, Brandt's vole Lasiopodomys brandtii was exposed to normoxia (21% O2 ) or hypoxia (mild or severe hypoxia: 10% or 5% O2 ) for 6 h. Changes in key enzymes of the classic enzymatic antioxidant system at both mRNA and enzyme activity levels, and tissue antioxidant levels of the low-molecular-weight antioxidant system were determined in brain, liver, and kidney. Transcript levels of the upstream regulator NF-E2-related factor 2 (Nrf2) were also measured. We found that the mRNA expression of Nrf2 and its downstream antioxidant enzyme genes in L. brandtii were relatively conserved in response to hypoxia in most tissues and genes tested, except in the liver. Hepatic Nrf2, Cu/Zn SOD, GPx1, and GPx3 levels were significantly upregulated in response to mild hypoxia, whereas Mn SOD level decreased significantly in severe hypoxia. Unmatched with changes at the RNA level, constitutively high and relatively stable antioxidant enzyme activities were maintained throughout. For the low-molecular-weight antioxidant system, an abrupt increase of cerebral ascorbic acid (AA) levels in hypoxia indicated a tissue-specific antioxidant response. Although hypoxia did not cause significant oxidative damage in most tissues tested, the significant decrease in antioxidant enzyme activities (GPX and GR) and increase in lipid peroxidation in the kidney suggest that prolonged hypoxia may pose a critical threat to this species.
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Affiliation(s)
- Luye Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Bojian Chen
- College of Environmental Science and Engineering, Tongji University, Shanghai, China.,Jiaxing-Tongji Environmental Research Institute, Jiaxing, China
| | - Xinrui Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Maolin Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Congcong Qiao
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Jingou Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China.,Centre for Nutritional Ecology, Zhengzhou University, Zhengzhou, China
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6
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Li M, Tian X, Li X, Huang M, Huang S, Wu Y, Jiang M, Shi Y, Shi L, Wang Z. Diverse energy metabolism patterns in females in Neodon fuscus, Lasiopodomys brandtii, and Mus musculus revealed by comparative transcriptomics under hypoxic conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 783:147130. [PMID: 34088150 DOI: 10.1016/j.scitotenv.2021.147130] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 03/28/2021] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
The effects of global warming and anthropogenic disturbance force animals to migrate from lower to higher elevations to find suitable new habitats. As such migrations increase hypoxic stress on the animals, it is important to understand how plateau- and plain-dwelling animals respond to low-oxygen environments. We used comparative transcriptomics to explore the response of Neodon fuscus, Lasiopodomys brandtii, and Mus musculus skeletal muscle tissues to hypoxic conditions. Results indicate that these species have adopted different oxygen transport and energy metabolism strategies for dealing with a hypoxic environment. N. fuscus promotes oxygen transport by increasing hemoglobin synthesis and reduces the risk of thrombosis through cooperative regulation of genes, including Fga, Fgb, Alb, and Ttr; genes such as Acs16, Gpat4, and Ndufb7 are involved in regulating lipid synthesis, fatty acid β-oxidation, hemoglobin synthesis, and electron-linked transmission, thereby maintaining a normal energy supply in hypoxic conditions. In contrast, the oxygen-carrying capacity and angiogenesis of red blood cells in L. brandtii are promoted by genes in the CYP and COL families; this species maintains its bodily energy supply by enhancing the pentose phosphate pathway and mitochondrial fatty acid synthesis pathway. However, under hypoxia, M. musculus cannot effectively transport additional oxygen; thus, its cell cycle, proliferation, and migration are somewhat affected. Given its lack of hypoxic tolerance experience, M. musculus also shows significantly reduced oxidative phosphorylation levels under hypoxic conditions. Our results suggest that the glucose capacity of M. musculus skeletal muscle does not provide sufficient energy during hypoxia; thus, we hypothesize that it supplements its bodily energy by synthesizing ketone bodies. For the first time, we describe the energy metabolism pathways of N. fuscus and L. brandtii skeletal muscle tissues under hypoxic conditions. Our findings, therefore, improve our understanding of how vertebrates thrive in high altitude and plain habitats when faced with hypoxic conditions.
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Affiliation(s)
- Mengyang Li
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Xiangyu Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Xiujuan Li
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Maolin Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Shuang Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yue Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Mengwan Jiang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yuhua Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Luye Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China.
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; School of Physical Education (Main campus), Zhengzhou University, Zhengzhou 450001, Henan, China.
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7
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Shi L, Liu L, Li X, Wu Y, Tian X, Shi Y, Wang Z. Phylogeny and evolution of Lasiopodomys in subfamily Arvivolinae based on mitochondrial genomics. PeerJ 2021; 9:e10850. [PMID: 33777513 PMCID: PMC7977381 DOI: 10.7717/peerj.10850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/06/2021] [Indexed: 01/02/2023] Open
Abstract
The species of Lasiopodomys Lataste 1887 with their related genera remains undetermined owing to inconsistent morphological characteristics and molecular phylogeny. To investigate the phylogenetic relationship and speciation among species of the genus Lasiopodomys, we sequenced and annotated the whole mitochondrial genomes of three individual species, namely Lasiopodomys brandtii Radde 1861, L. mandarinus Milne-Edwards 1871, and Neodon (Lasiopodomys) fuscus Büchner 1889. The nucleotide sequences of the circular mitogenomes were identical for each individual species of L. brandtii, L. mandarinus, and N. fuscus. Each species contained 13 protein-coding genes (PCGs), 22 transfer RNAs, and 2 ribosomal RNAs, with mitochondrial genome lengths of 16,557 bp, 16,562 bp, and 16,324 bp, respectively. The mitogenomes and PCGs showed positive AT skew and negative GC skew. Mitogenomic phylogenetic analyses suggested that L. brandtii, L. mandarinus, and L. gregalis Pallas 1779 belong to the genus Lasiopodomys, whereas N. fuscus belongs to the genus Neodon grouped with N. irene. Lasiopodomys showed the closest relationship with Microtus fortis Büchner 1889 and M. kikuchii Kuroda 1920, which are considered as the paraphyletic species of genera Microtus. TMRCA and niche model analysis revealed that Lasiopodomys may have first appeared during the early Pleistocene epoch. Further, L. gregalis separated from others over 1.53 million years ago (Ma) and then diverged into L. brandtii and L. mandarinus 0.76 Ma. The relative contribution of climatic fluctuations to speciation and selection in this group requires further research.
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Affiliation(s)
- Luye Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Likuan Liu
- School of Life Sciences, Qinghai Normal University, Xining, Qinghai, China
| | - Xiujuan Li
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yue Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiangyu Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yuhua Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
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8
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Shi L, Jiang M, Li M, Shang X, Li X, Huang M, Wu Y, Qiao C, Wang X, Tian X, Shi Y, Wang Z. Regulation of HIF-1α and p53 in stress responses in the subterranean rodents Lasiopodomys mandarinus and Lasiopodomys brandtii (Rodentia: Cricetidae). ZOOLOGIA 2021. [DOI: 10.3897/zoologia.38.e58607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The response mechanism and interaction patterns of HIF-1α and p53 in animals in an hypoxic environment are crucial for their hypoxic tolerance and adaptation. Many studies have shown that underground rodents have better hypoxic adaptation characteristics. However, the mechanism by which HIF-1α and p53 in underground rodents respond to hypoxic environments compared with in ground rodents remains unclear. Further, whether a synergy between HIF-1α and p53 enables animals tolerate extremely hypoxic environments is unclear. We studied HIF-1α and p53 expression in the brain tissue and cell apoptosis in the hippocampal CA1 region during 6 hours of acute hypoxia (5% oxygen) in Lasiopodomys mandarinus (Milne-Edwards, 1871) and Lasiopodomys brandtii (Radde, 1861), two closely related small rodents with different life characteristics (underground and aboveground, respectively), using a comparative biology method to determine the mechanisms underlying their adaptation to this environment. Our results indicate that HIF-1α and p53 expression is more rapid in L. mandarinus than in L. brandtii under acute hypoxic environments, resulting in a significant synergistic effect in L. mandarinus. Correlation analysis revealed that HIF-1α expression and the apoptotic index of the hippocampal CA1 regions of the brain tissues of L. mandarinus and L. brandtii, both under hypoxia, were significantly negatively and positively correlated, respectively. Long-term existence in underground burrow systems could enable better adaptation to hypoxia in L. mandarinus than in L. brandtii. We speculate that L. mandarinus can quickly eliminate resulting damage via the synergistic effect of p53 and HIF-1α in response to acute hypoxic environments, helping the organism quickly return to a normal state after the stress.
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9
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Pejo M, Tomasco IH. Adaptive evolution of β-globin gene in subterranean in South America octodontid rodents. Gene 2020; 772:145352. [PMID: 33359035 DOI: 10.1016/j.gene.2020.145352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/15/2020] [Accepted: 12/01/2020] [Indexed: 11/17/2022]
Abstract
The convergent evolution of subterranean rodents is an excellent model to study how natural selection operates and the genetic bases of these adaptations, but the study on the different taxa has been very uneven and still insufficient. In the octodontoid caviomorph rodent superfamily there are two independent lineages where they have recently evolved into totally underground lifestyles: the genera Ctenomys (tuco-tucos) and Spalacopus (coruro). The underground habitat is characterized by an hypoxic and hypercapnic atmosphere, thus gas exchange is one of the most important challenges for these animals. The invasion of the underground niche could have modified the selective regimes of proteins involved in the respiration and transport of O2 of these rodents, positively selecting mutations of higher affinity for O2. Here we examine the sequence variation in the beta globin gene in these two lineages, within a robust phylogenetic context. Using different approaches (classical and Bayesian maximum likelihood (PAML/Datamonkey) and alternatives methods (TreeSAAP)) we found at least three sites with evidence of positive selection in underground lineages, especially the basal branch that leads to the Octodontidae family and the branch that leads to the coruro, suggesting some adaptive changes to the underground life. We also found a convergence with another underground rodent, which cannot be identified by the above methods.
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Affiliation(s)
- Mariana Pejo
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ivanna H Tomasco
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
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10
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Jiang M, Shi L, Li X, Dong Q, Sun H, Du Y, Zhang Y, Shao T, Cheng H, Chen W, Wang Z. Genome-wide adaptive evolution to underground stresses in subterranean mammals: Hypoxia adaption, immunity promotion, and sensory specialization. Ecol Evol 2020; 10:7377-7388. [PMID: 32760535 PMCID: PMC7391338 DOI: 10.1002/ece3.6462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 12/18/2022] Open
Abstract
Life underground has provided remarkable examples of adaptive evolution in subterranean mammals; however, genome-wide adaptive evolution to underground stresses still needs further research. There are approximately 250 species of subterranean mammals across three suborders and six families. These species not only inhabit hypoxic and dark burrows but also exhibit evolved adaptation to hypoxia, cancer resistance, and specialized sensory systems, making them an excellent model of evolution. The adaptive evolution of subterranean mammals has attracted great attention and needs further study. In the present study, phylogenetic analysis of 5,853 single-copy orthologous gene families of five subterranean mammals (Nannospalax galili, Heterocephalus glaber, Fukomys damarensis, Condylura cristata, and Chrysochloris asiatica) showed that they formed fou distinct clusters. This result is consistent with the traditional systematics of these species. Furthermore, comparison of the high-quality genomes of these five subterranean mammalian species led to the identification of the genomic signatures of adaptive evolution. Our results show that the five subterranean mammalian did not share positively selected genes but had similar functional enrichment categories, including hypoxia tolerance, immunity promotion, and sensory specialization, which adapted to the environment of underground stresses. Moreover, variations in soil hardness, climate, and lifestyles have resulted in different molecular mechanisms of adaptation to the hypoxic environment and different degrees of visual degradation. These results provide insights into the genome-wide adaptive evolution to underground stresses in subterranean mammals, with special focus on the characteristics of hypoxia adaption, immunity promotion, and sensory specialization response to the life underground.
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Affiliation(s)
- Mengwan Jiang
- School of Life SciencesZhengzhou UniversityZhengzhouChina
| | - Luye Shi
- School of Life SciencesZhengzhou UniversityZhengzhouChina
| | - Xiujuan Li
- School of Life SciencesZhengzhou UniversityZhengzhouChina
| | - Qianqian Dong
- School of Life SciencesZhengzhou UniversityZhengzhouChina
| | - Hong Sun
- School of Life SciencesZhengzhou UniversityZhengzhouChina
| | - Yimeng Du
- School of Life SciencesZhengzhou UniversityZhengzhouChina
| | - Yifeng Zhang
- School of Life SciencesZhengzhou UniversityZhengzhouChina
| | - Tian Shao
- School of Life SciencesZhengzhou UniversityZhengzhouChina
| | - Han Cheng
- School of Life SciencesZhengzhou UniversityZhengzhouChina
| | - Weihua Chen
- College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Zhenlong Wang
- School of Life SciencesZhengzhou UniversityZhengzhouChina
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11
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Dong Q, Wang Z, Jiang M, Sun H, Wang X, Li Y, Zhang Y, Cheng H, Chai Y, Shao T, Shi L, Wang Z. Transcriptome analysis of the response provided by Lasiopodomys mandarinus to severe hypoxia includes enhancing DNA repair and damage prevention. Front Zool 2020; 17:9. [PMID: 32256671 PMCID: PMC7106638 DOI: 10.1186/s12983-020-00356-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/16/2020] [Indexed: 02/08/2023] Open
Abstract
Background Severe hypoxia induces a series of stress responses in mammals; however, subterranean rodents have evolved several adaptation mechanisms of energy metabolisms and O2 utilization for hypoxia. Mammalian brains show extreme aerobic metabolism. Following hypoxia exposure, mammals usually experience irreversible brain damage and can even develop serious diseases, such as hypoxic ischemic encephalopathy and brain edema. To investigate mechanisms underlying the responses of subterranean rodents to severe hypoxia, we performed a cross-species brain transcriptomic analysis using RNA sequencing and identified differentially expressed genes (DEGs) between the subterranean rodent Lasiopodomys mandarinus and its closely related aboveground species L. brandtii under severe hypoxia (5.0% O2, 6 h) and normoxia (20.9% O2, 6 h). Results We obtained 361 million clean reads, including 69,611 unigenes in L. mandarinus and 69,360 in L. brandtii. We identified 359 and 515 DEGs by comparing the hypoxic and normoxia groups of L. mandarinus and L. brandtii, respectively. Gene Ontology (GO) analysis showed that upregulated DEGs in both species displayed similar terms in response to severe hypoxia; the main difference is that GO terms of L. brandtii were enriched in the immune system. However, in the downregulated DEGs, GO terms of L. mandarinus were enriched in cell proliferation and protein transport and those of L. brandtii were enriched in nuclease and hydrolase activities, particularly in terms of developmental functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that upregulated DEGs in L. mandarinus were associated with DNA repair and damage prevention as well as angiogenesis and metastasis inhibition, whereas downregulated DEGs were associated with neuronal synaptic transmission and tumor-associated metabolic pathways. In L. brandtii, upregulated KEGG pathways were enriched in the immune, endocrine, and cardiovascular systems and particularly in cancer-related pathways, whereas downregulated DEGs were associated with environmental information processing and misregulation in cancers. Conclusions L. mandarinus has evolved hypoxia adaptation by enhancing DNA repair, damage prevention, and augmenting sensing, whereas L. brandtii showed a higher risk of tumorigenesis and promoted innate immunity toward severe hypoxia. These results reveal the hypoxic mechanisms of L. mandarinus to severe hypoxia, which may provide research clues for hypoxic diseases.
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Affiliation(s)
- Qianqian Dong
- 1School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan Province China
| | - Zishi Wang
- 1School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan Province China
| | - Mengwan Jiang
- 1School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan Province China
| | - Hong Sun
- 2College of Physical Education (main campus), Zhengzhou University, Zhengzhou, Henan Province China
| | - Xuqin Wang
- 1School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan Province China
| | - Yangwei Li
- 1School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan Province China.,3Central Laboratory, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008 Henan Province China
| | - Yifeng Zhang
- 1School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan Province China
| | - Han Cheng
- 1School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan Province China
| | - Yurong Chai
- 4School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan Province China
| | - Tian Shao
- 1School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan Province China
| | - Luye Shi
- 1School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan Province China
| | - Zhenlong Wang
- 1School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan Province China
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Tian X, Gu S, Pan D, Shi L, Wang Z. The complete mitochondrial genome of Lasiopodomys brandtii. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:364-365. [PMID: 33366558 PMCID: PMC7748823 DOI: 10.1080/23802359.2019.1703567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, the complete mitochondrial (mt) genome sequence of Lasiopodomys brandtii was determined using Illumina NovaSeq platform. The assembled genome was 16,557 bp in length and included 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. The total nucleotide composition frequencies present clearly the A-T skew (59.5%), which mostly in D-loop and PCGs regions. Whole mt genome phylogenetic analysis revealed a closely related among Lasiopodomys, Proedromys, and Microtus with high support. It would provide further evolutionary research for the subfamily Arvicolinae.
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Affiliation(s)
- Xiangyu Tian
- School of Life Sciences, Zhengzhou University, Henan, Zhengzhou, P. R. China
| | - Shiming Gu
- School of Life Sciences, Zhengzhou University, Henan, Zhengzhou, P. R. China
| | - Dan Pan
- School of Life Sciences, Zhengzhou University, Henan, Zhengzhou, P. R. China
| | - Luye Shi
- School of Life Sciences, Zhengzhou University, Henan, Zhengzhou, P. R. China
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Henan, Zhengzhou, P. R. China
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