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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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Gazolla CB, Ludwig A, de Moura Gama J, Bruschi DP. Evolutionary dynamics of DIRS-like and Ngaro-like retrotransposons in Xenopus laevis and Xenopus tropicalis genomes. G3 GENES|GENOMES|GENETICS 2022; 12:6430978. [PMID: 34792579 PMCID: PMC9210276 DOI: 10.1093/g3journal/jkab391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/01/2021] [Indexed: 12/02/2022]
Abstract
Anuran genomes have a large number and diversity of transposable elements, but are little explored, mainly in relation to their molecular structure and evolutionary dynamics. Here, we investigated the retrotransposons containing tyrosine recombinase (YR) (order DIRS) in the genome of Xenopus tropicalis and Xenopus laevis. These anurans show 2n = 20 and the 2n = 36 karyotypes, respectively. They diverged about 48 million years ago (mya) and X. laevis had an allotetraploid origin (around 17–18 mya). Our investigation is based on the analysis of the molecular structure and the phylogenetic relationships of 95 DIRS families of Xenopus belonging to DIRS-like and Ngaro-like superfamilies. We were able to identify molecular signatures in the 5' and 3' noncoding terminal regions, preserved open reading frames, and conserved domains that are specific to distinguish each superfamily. We recognize two ancient amplification waves of DIRS-like elements that occurred in the ancestor of both species and a higher density of the old/degenerate copies detected in both subgenomes of X. laevis. More recent amplification waves are seen in X. tropicalis (less than 3.2 mya) and X. laevis (around 10 mya) corroborating with transcriptional activity evidence. All DIRS-like families were found in both X. laevis subgenomes, while a few were most represented in the L subgenome. Ngaro-like elements presented less diversity and quantity in X. tropicalis and X. laevis genomes, although potentially active copies were found in both species and this is consistent with a recent amplification wave seen in the evolutionary landscape. Our findings highlight a differential diversity-level and evolutionary dynamics of the YR retrotransposons in X. tropicalis and X. laevis species expanding our comprehension of the behavior of these elements in both genomes during the diversification process.
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Affiliation(s)
- Camilla Borges Gazolla
- Departamento de Genética, Laboratório de Citogenética Evolutiva e Conservação Animal (LabCECA), Universidade Federal do Paraná, Curitiba, PR 80060-000, Brazil
- Departamento de Genética, Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, PR 80060-000, Brazil
| | - Adriana Ludwig
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde (LaCTAS), Instituto Carlos Chagas—Fiocruz-PR, Curitiba, PR 81350-010, Brazil
| | - Joana de Moura Gama
- Departamento de Genética, Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, PR 80060-000, Brazil
| | - Daniel Pacheco Bruschi
- Departamento de Genética, Laboratório de Citogenética Evolutiva e Conservação Animal (LabCECA), Universidade Federal do Paraná, Curitiba, PR 80060-000, Brazil
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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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Tang M, Liao J, Peng L, Jiang L, You Z, Chen W. The complete mitochondrial genome sequences of Nanorana chayuensis. Mitochondrial DNA B Resour 2020; 5:772-773. [PMID: 33366744 PMCID: PMC7748707 DOI: 10.1080/23802359.2020.1715871] [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] [Indexed: 11/05/2022] Open
Abstract
In this study, we obtained the complete mitochondrial genome sequence of Nanorana chayuensis. The mitogenome length is 17,882 bp, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 1 non-coding control region (CR). Present data will contribute to further analysis of phylogenetic relationship and population genetics of this species.
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Affiliation(s)
- Min Tang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Jiahong Liao
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Liqing Peng
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Lichun Jiang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Zhangqiang You
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
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Liao J, Tang M, Peng L, Jiang L, You Z, Chen W. The complete mitochondrial genome sequence of Himalayan toad Duttaphrynus himalayanus (Anura: Bufonidae). Mitochondrial DNA B Resour 2020; 5:740-741. [PMID: 33366728 PMCID: PMC7748800 DOI: 10.1080/23802359.2020.1715287] [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] [Indexed: 12/02/2022] Open
Abstract
In this study, the complete mitochondrial genome of Duttaphrynus himalayanus was sequenced adopting Illumina high-throughput sequencing method. The complete mitogenome of the species was 17,172 bp in length, including 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and a non-coding control region (CR). The overall base composition of mitogenome was 29.7% A, 29.6% T, 26.0% C, and 14.7% G. Most mitochondrial genes are encoded on the heavy strand, only ND6 and eight tRNA genes on the light strand. The complete mitogenome of D. himalayanus can provide an important data for future studies on phylogenetic relationship and population genetics of this species.
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Affiliation(s)
- Jiahong Liao
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Min Tang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Liqing Peng
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Lichun Jiang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Zhangqiang You
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, 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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Cheng JX, Cai YT, Zheng YJ, Zhang JY, Storey KB, Bao YX, Yu DN. The complete mitochondrial genome of Fejervarya kawamurai (Anura: Dicroglossidae) and its phylogeny. Mitochondrial DNA B Resour 2018; 3:551-553. [PMID: 33474236 PMCID: PMC7800800 DOI: 10.1080/23802359.2018.1467219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 04/16/2018] [Indexed: 12/03/2022] Open
Abstract
The mitochondrial genome of Fejervarya kawamurai is a circular molecule of 17,650 bp in length, containing 13 protein-coding genes, two rRNA genes, 23 tRNA genes (including an extra tRNA-Met), and the control region. The AT content of the whole genome is 56.9%. In Bayesian inference (BI) and Maximum likelihood (ML) analyses, we found that F. kawamurai is a sister clade to F. multistriata and F. limnocharis. The monophyly of Fejervarya, Quasipaa, Nanorana was well supported (1.00 in BI and 100% in ML).
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Affiliation(s)
- Jian-Xiang Cheng
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China
| | - Yu-Ting Cai
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China
| | - Yu-Jie Zheng
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China
| | - Jia-Yong Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, China
| | | | - Yi-Xin Bao
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, China
| | - Dan-Na Yu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, China
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Cai YT, Ma L, Xu CJ, Li P, Zhang JY, Storey KB, Yu DN. The complete mitochondrial genome of the hybrid of Hoplobatrachus chinensis (♀)× H. rugulosus (♂) and its phylogeny. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:344-345. [PMID: 33474164 PMCID: PMC7799566 DOI: 10.1080/23802359.2018.1450661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The complete mitochondrial genome sequence of the hybrid of Hoplobatrachus chinensis (♀) × H. rugulosus (♂) was obtained in this study. The circular mitochondrial genome was 20,282 bp in length (including extra ND5 genes). Compared with the complete mitogenome of the parents, the results indicated that the mitochondria of the hybrid tiger frog was consistent with a maternal inheritance. Phylogenetic analyses using concatenated nucleotide sequences of the 11 protein-coding genes with two different methods (maximum likelihood and MrBayes analysis) both highly supported a close relationship of the hybrid frogs with the Chinese tiger frog (=H. chinensis).
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Affiliation(s)
- Yu-Ting Cai
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Lin Ma
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Chen-Jie Xu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Peng Li
- College of Life Science, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Jia-Yong Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China.,Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | | | - Dan-Na Yu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China.,Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, China
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Zhang JY, Zhang LP, Yu DN, Storey KB, Zheng RQ. Complete mitochondrial genomes of Nanorana taihangnica and N. yunnanensis (Anura: Dicroglossidae) with novel gene arrangements and phylogenetic relationship of Dicroglossidae. BMC Evol Biol 2018; 18:26. [PMID: 29486721 PMCID: PMC6389187 DOI: 10.1186/s12862-018-1140-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 02/15/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Complete mitochondrial (mt) genomes have been used extensively to test hypotheses about microevolution and to study population structure, phylogeography, and phylogenetic relationships of Anura at various taxonomic levels. Large-scale mt genomic reorganizations have been observed among many fork-tongued frogs (family Dicroglossidae). The relationships among Dicroglossidae and validation of the genus Feirana are still problematic. Hence, we sequenced the complete mt genomes of Nanorana taihangnica (=F. taihangnica) and N. yunnanensis as well as partial mt genomes of six Quasipaa species (dicroglossid taxa), two Odorrana and two Amolops species (Ranidae), and one Rhacophorus species (Rhacophoridae) in order to identify unknown mt gene rearrangements, to investigate the validity of the genus Feirana, and to test the phylogenetic relationship of Dicroglossidae. RESULTS In the mt genome of N. taihangnica two trnM genes, two trnP genes and two control regions were found. In addition, the trnA, trnN, trnC, and trnQ genes were translocated from their typical positions. In the mt genome of N. yunnanensis, three control regions were found and eight genes (ND6, trnP, trnQ, trnA, trnN, trnC, trnY and trnS genes) in the L-stand were translocated from their typical position and grouped together. We also found intraspecific rearrangement of the mitochondrial genomes in N. taihangnica and Quasipaa boulengeri. In phylogenetic trees, the genus Feirana nested deeply within the clade of genus Nanorana, indicating that the genus Feirana may be a synonym to Nanorana. Ranidae as a sister clade to Dicroglossidae and the clade of (Ranidae + Dicroglossidae) as a sister clade to (Mantellidae + Rhacophoridae) were well supported in BI analysis but low bootstrap in ML analysis. CONCLUSIONS We found that the gene arrangements of N. taihangnica and N. yunnanensis differed from other published dicroglossid mt genomes. The gene arrangements in N. taihangnica and N. yunnanensis could be explained by the Tandem Duplication and Random Loss (TDRL) and the Dimer-Mitogenome and Non-Random Loss (DMNR) models, respectively. The invalidation of the genus Feirana is supported in this study.
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Affiliation(s)
- Jia-Yong Zhang
- Key lab of wildlife biotechnology, conservation and utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Le-Ping Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China
| | - Dan-Na Yu
- Key lab of wildlife biotechnology, conservation and utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China.
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China.
| | - Kenneth B Storey
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Rong-Quan Zheng
- Xingzhi College, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China
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Chang L, He S, Zhang J, Zhang Q, Li S. The complete mitochondrial genome sequence of Eudocimus ruber (Pelecaniformes:Threskiornithidae). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:2941-2. [DOI: 10.3109/19401736.2015.1060451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Liao Chang
- College of Medicine and Forensics, Xi’an Jiaotong University, Xi’an, China and
| | - Shiyang He
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jianbo Zhang
- College of Medicine and Forensics, Xi’an Jiaotong University, Xi’an, China and
| | - Qian Zhang
- College of Medicine and Forensics, Xi’an Jiaotong University, Xi’an, China and
| | - Shengbin Li
- College of Medicine and Forensics, Xi’an Jiaotong University, Xi’an, China and
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