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Wang JY, Zhang LH, Hong YH, Cai LN, Storey KB, Zhang JY, Zhang SS, Yu DN. How Does Mitochondrial Protein-Coding Gene Expression in Fejervarya kawamurai (Anura: Dicroglossidae) Respond to Extreme Temperatures? Animals (Basel) 2023; 13:3015. [PMID: 37835622 PMCID: PMC10571990 DOI: 10.3390/ani13193015] [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: 07/25/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Unusual climates can lead to extreme temperatures. Fejervarya kawamurai, one of the most prevalent anurans in the paddy fields of tropical and subtropical regions in Asia, is sensitive to climate change. The present study focuses primarily on a single question: how do the 13 mitochondrial protein-coding genes (PCGs) respond to extreme temperature change compared with 25 °C controls? Thirty-eight genes including an extra tRNA-Met gene were identified and sequenced from the mitochondrial genome of F. kawamurai. Evolutionary relationships were assessed within the Dicroglossidae and showed that Dicroglossinae is monophyletic and F. kawamurai is a sister group to the clade of (F. multistriata + F. limnocharis). Transcript levels of mitochondrial genes in liver were also evaluated to assess responses to 24 h exposure to low (2 °C and 4 °C) or high (40 °C) temperatures. Under 2 °C, seven genes showed significant changes in liver transcript levels, among which transcript levels of ATP8, ND1, ND2, ND3, ND4, and Cytb increased, respectively, and ND5 decreased. However, exposure to 4 °C for 24 h was very different in that the expressions of ten mitochondrial protein-coding genes, except ND1, ND3, and Cytb, were significantly downregulated. Among them, the transcript level of ND5 was most significantly downregulated, decreasing by 0.28-fold. Exposure to a hot environment at 40 °C for 24 h resulted in a marked difference in transcript responses with strong upregulation of eight genes, ranging from a 1.52-fold increase in ND4L to a 2.18-fold rise in Cytb transcript levels, although COI and ND5 were reduced to 0.56 and 0.67, respectively, compared with the controls. Overall, these results suggest that at 4 °C, F. kawamurai appears to have entered a hypometabolic state of hibernation, whereas its mitochondrial oxidative phosphorylation was affected at both 2 °C and 40 °C. The majority of mitochondrial PCGs exhibited substantial changes at all three temperatures, indicating that frogs such as F. kawamurai that inhabit tropical or subtropical regions are susceptible to ambient temperature changes and can quickly employ compensating adjustments to proteins involved in the mitochondrial electron transport chain.
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Affiliation(s)
- Jing-Yan Wang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Li-Hua Zhang
- Taishun County Forestry Bureau, Wenzhou 325000, China
| | - Yue-Huan Hong
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ling-Na Cai
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Jia-Yong Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Shu-Sheng Zhang
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Wuyanling National Nature Reserve, Wenzhou 325500, China
| | - Dan-Na Yu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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The mitochondrial genome and phylogenetic analysis of Rhacophorus rhodopus. Sci Rep 2022; 12:13693. [PMID: 35953583 PMCID: PMC9372073 DOI: 10.1038/s41598-022-17814-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/01/2022] [Indexed: 11/08/2022] Open
Abstract
Classification of the genus Rhacophorus has been problematic. In particular there has been considerable controversy surrounding the phylogenetic relationships among Rhacophorus rhodopus, R. bipunctatus, and R. reinwardtii. To examine the relationship among these Rhacophorus species, we assembled the complete mitochondrial genome sequence of R. rhodopus. The R. rhodopus genome is 15,789 bp in length with 12 protein-coding genes (PCGs) (losing ND5), two ribosomal genes, 22 transfer RNA genes, and a control region (D-loop). Base composition of the overall sequence was 60.86% for A + T content and 39.14% for C + G content. Most of the PCGs used ATG as a start codon, except for the COX I gene, which used the ATA start codon. COX I and ND6 used AGG and ATP8 stop codons respectively, while ND3 and ND4L used the TAA stop codon. For the remaining seven genes, the stop codons was incomplete. In addition, both 5' and 3' of the control areas had distinct repeating regions. Based on three datasets and two methods (Bayesian inference (BI) and maximum likelihood (ML)), we reconstructed three phylogenetic trees to explore the taxonomic status of the species and the phylogenetic relationship among R. rhodopus, R. bipunctatus and R. reinwardtii. Our results indicated that these three species are non-monophyletic; thus, the phylogenetic relationship among them is complex and difficult to determine. Further, R. rhodopus is divided into three lineages from different parts of China. The two Rhacophorus samples showed very close phylogenetic relationship with R. rhodopus. Our results add to the mitochondrial genome database of amphibians and will help to disentangle the phylogenetic relationships within the Rhacophoridae.
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Niu Y, Zhang X, Zhang H, Xu T, Zhu L, Storey KB, Chen Q. Metabolic responses of plasma to extreme environments in overwintering Tibetan frogs Nanorana parkeri: a metabolome integrated analysis. Front Zool 2021; 18:41. [PMID: 34454525 PMCID: PMC8403389 DOI: 10.1186/s12983-021-00428-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022] Open
Abstract
Many animals lower their metabolic rate in response to low temperatures and scarcity of food in the winter in phenomena called hibernation or overwintering. Living at high altitude on the Tibetan Plateau where winters are very cold, the frog Nanorana parkeri, survives in one of the most hostile environments on Earth but, to date, relatively little is known about the biochemical and physiological adjustments for overwintering by this species. The present study profiled changes in plasma metabolites of N. parkeri between winter and summer using UHPLC-QE-MS non-target metabolomics in order to explore metabolic adaptations that support winter survival. The analysis showed that, in total, 11 metabolites accumulated and 95 were reduced in overwintering frogs compared with summer-active animals. Metabolites that increased included some that may have antioxidant functions (canthaxanthin, galactinol), act as a metabolic inhibitor (mono-ethylhexylphthalate), or accumulate as a product of anaerobic metabolism (lactate). Most other metabolites in plasma showed reduced levels in winter and were generally involved in energy metabolism including 11 amino acids (proline, isoleucine, leucine, valine, phenylalanine, tyrosine, arginine, tryptophan, methionine, threonine and histidine) and 4 carbohydrates (glucose, citrate, succinate, and malate). Pathway analysis indicated that aminoacyl-tRNA biosynthesis, phenylalanine, tyrosine and tryptophan biosynthesis, and nitrogen metabolism were potentially the most prominently altered pathways in overwintering frogs. Changes to these pathways are likely due to fasting and global metabolic depression in overwintering frogs. Concentrations of glucose and urea, commonly used as cryoprotectants by amphibians that winter on land, were significantly reduced during underwater hibernation in N. parkeri. In conclusion, winter survival of the high-altitude frog, N. parkeri was accompanied by substantial changes in metabolomic profiles and this study provides valuable information towards understanding the special adaptive mechanisms of N. parkeri to winter stresses.
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Affiliation(s)
- Yonggang Niu
- School of Life Sciences, Dezhou University, Dezhou, 253023, Shandong, China. .,School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China.
| | - Xuejing Zhang
- School of Life Sciences, Dezhou University, Dezhou, 253023, Shandong, China
| | - Haiying Zhang
- School of Life Sciences, Dezhou University, Dezhou, 253023, Shandong, China
| | - Tisen Xu
- School of Life Sciences, Dezhou University, Dezhou, 253023, Shandong, China
| | - Lifeng Zhu
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Kenneth B Storey
- Department of Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Qiang Chen
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China.
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Jiang L, Zhang M, Deng L, Xu Z, Shi H, Jia X, Lai Z, Ruan Q, Chen W. Characteristics of the mitochondrial genome of Rana omeimontis and related species in Ranidae: Gene rearrangements and phylogenetic relationships. Ecol Evol 2020; 10:12817-12837. [PMID: 33304496 PMCID: PMC7713938 DOI: 10.1002/ece3.6824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/16/2020] [Accepted: 08/20/2020] [Indexed: 12/01/2022] Open
Abstract
The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. In this study, we achieved detail knowledge about the mitogenome of the species. The length of the genome is 20,120 bp, including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a noncoding control region. Similar to other amphibians, we found that only nine genes (ND6 and eight tRNA genes) are encoded on the light strand (L) and other genes on the heavy strand (H). Totally, The base composition of the mitochondrial genome included 27.29% A, 28.85% T, 28.87% C, and 15.00% G, respectively. The control regions among the Rana species were found to exhibit rich genetic variability and A + T content. R. omeimontis was clustered together with R. chaochiaoensis in phylogenetic tree. Compared to R. amurensis and R. kunyuensi, it was more closely related to R. chaochiaoensis, and a new way of gene rearrangement (ND6-trnE-Cytb-D-loop-trnL2 (CUN)-ND5-D-loop) was also found in the mitogenome of R. amurensis and R. kunyuensi. Our results about the mitochondrial genome of R. omeimontis will contribute to the future studies on phylogenetic relationship and the taxonomic status of Rana and related Ranidae species.
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Affiliation(s)
- Lichun Jiang
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangChina
| | - Min Zhang
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Lu Deng
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Zhongwen Xu
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Hongyan Shi
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Xiaodong Jia
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Zhenli Lai
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangChina
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Jiang LC, Lv GH, Jia XD, Ruan QP, Chen W. Mitogenome, Gene Rearrangement and Phylogeny of Dicroglossidae Revisited. ANN ZOOL FENN 2020. [DOI: 10.5735/086.057.0117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Li-Chun Jiang
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, CN-621000 Mianyang, Sichuan, P.R. China
| | - Gui-Hua Lv
- Dongyang Institute of Maize Research, Zhejiang Academy of Agricultural Sciences, CN-322100 Dongyang, Zhejiang, P.R. China
| | - Xiao-Dong Jia
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, CN-621000 Mianyang, Sichuan, P.R. China
| | - Qi-Ping Ruan
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, CN-621000 Mianyang, Sichuan, P.R. China
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, CN-621000 Mianyang, Sichuan, P.R. China
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Niu Y, Cao W, Storey KB, He J, Wang J, Zhang T, Tang X, Chen Q. Metabolic characteristics of overwintering by the high-altitude dwelling Xizang plateau frog, Nanorana parkeri. J Comp Physiol B 2020; 190:433-444. [PMID: 32274534 DOI: 10.1007/s00360-020-01275-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 03/20/2020] [Accepted: 03/27/2020] [Indexed: 12/12/2022]
Abstract
The Xizang plateau frog, Nanorana parkeri, has the highest altitudinal distribution of all frogs in the world and survives the cold of winter without feeding by entering into a hibernating state. However, little attention has been paid to its physiological and biochemical characteristics that support overwintering underwater in small ponds. Here, we measured metabolic rate and heart rate, and collected liver and muscle samples from N. parkeri in summer and winter for analysis of mitochondrial respiration rate, and activities and relative mRNA transcript expression of metabolic enzymes. Compared with summer-collected frogs, both resting metabolic rate and heart rate were significantly reduced in winter-collected frogs. Both state 3 and state 4 respiration of liver mitochondria were also significantly reduced in winter but muscle mitochondria showed a decline only in state 3 respiration in winter. The activities and corresponding mRNA expression of cytochrome c oxidase showed a marked decline in winter, whereas the activities and corresponding mRNA expression of lactate dehydrogenase increased in winter-collected frogs, compared to summer. The thermal sensitivity (Q10 values) for state 3 respiration rate by liver mitochondria, and activities of lactate dehydrogenase, and cytochrome c oxidase all increased in winter-collected frogs, compared with summer frogs, suggesting that overwintering frogs were more sensitive to changes in external temperature. Enzyme changes mainly result from lower overall quantities of these enzymes as well as post-translational modifications. We conclude that overwintering N. parkeri exhibit a seasonal, temperature-independent suppression of metabolism that is mediated at multiple levels: physiological, mitochondrial, gene expression and enzyme activity levels.
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Affiliation(s)
- Yonggang Niu
- School of Life Sciences, Dezhou University, Dezhou, China.,Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China.,State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Wangjie Cao
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Kenneth B Storey
- Department of Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Jie He
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Jinzhou Wang
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Tao Zhang
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Xiaolong Tang
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Qiang Chen
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China. .,State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China.
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Zhang JY, Luu BE, Yu DN, Zhang LP, Al-attar R, Storey KB. The complete mitochondrial genome of Dryophytes versicolor: Phylogenetic relationship among Hylidae and mitochondrial protein-coding gene expression in response to freezing and anoxia. Int J Biol Macromol 2019; 132:461-469. [DOI: 10.1016/j.ijbiomac.2019.03.220] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/28/2019] [Accepted: 03/28/2019] [Indexed: 11/17/2022]
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Jiang L, You Z, Yu P, Ruan Q, Chen W. The first complete mitochondrial genome sequence of Nanorana parkeri and Nanorana ventripunctata (Amphibia: Anura: Dicroglossidae), with related phylogenetic analyses. Ecol Evol 2018; 8:6972-6987. [PMID: 30073060 PMCID: PMC6065340 DOI: 10.1002/ece3.4214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 11/24/2022] Open
Abstract
Members of the Nanorana genus (family Dicroglossidae) are often referred to as excellent model species with which to study amphibian adaptations to extreme environments and also as excellent keystone taxa for providing insights into the evolution of the Dicroglossidae. However, a complete mitochondrial genome is currently only available for Nanorana pleskei. Thus, we analyzed the complete mitochondrial genomes of Nanorana parkeri and Nanorana ventripunctata to investigate their evolutionary relationships within Nanorana and their phylogenetic position in the family Dicroglossidae. Our results showed that the genomes of N. parkeri (17,837 bp) and N. ventripunctata (18,373 bp) encode 13 protein‐coding genes (PCGs), two ribosomal RNA genes, 23 transfer RNA (tRNA) genes, and a noncoding control region. Overall sequences and genome structure of the two species showed high degree of similarity with N. pleskei, although the motif structures and repeat sequences of the putative control region showed clear differences among these three Nanorana species. In addition, a tandem repeat of the tRNA‐Met gene was found located between the tRNA‐Gln and ND2 genes. On both the 5′ and 3′‐sides, the control region possessed distinct repeat regions; however, the CSB‐2 motif was not found in N. pleskei. Based on the nucleotide sequences of 13 PCGs, our phylogenetic analyses, using Bayesian inference and maximum‐likelihood methods, illustrate the taxonomic status of Nanorana with robust support showing that N. ventripunctata and N. pleskei are more closely related than they are to N. parkeri. In conclusion, our analyses provide a more robust and reliable perspective on the evolutionary history of Dicroglossidae than earlier analyses, which used only a single species (N. pleskei).
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Affiliation(s)
- Lichun Jiang
- Ecological Security and Protection Key Laboratory of Sichuan Province Mianyang Normal University Mianyang Sichuan China.,Key Laboratory for Molecular Biology and Biopharmaceutics School of Life Science and Technology Mianyang Normal University Mianyang Sichuan China
| | - Zhangqiang You
- Ecological Security and Protection Key Laboratory of Sichuan Province Mianyang Normal University Mianyang Sichuan China
| | - Peng Yu
- Key Laboratory for Molecular Biology and Biopharmaceutics School of Life Science and Technology Mianyang Normal University Mianyang Sichuan China
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and Biopharmaceutics School of Life Science and Technology Mianyang Normal University Mianyang Sichuan China
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province Mianyang Normal University Mianyang Sichuan China
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