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Guo Y, Wu W, Yang X. Coordinated microRNA/mRNA Expression Profiles Reveal Unique Skin Color Regulatory Mechanisms in Chinese Giant Salamander (Andrias davidianus). Animals (Basel) 2023; 13:ani13071181. [PMID: 37048437 PMCID: PMC10093658 DOI: 10.3390/ani13071181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/18/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
The Chinese giant salamander (Andrias davidianus) has been increasingly popular in the aquaculture market in China in recent years. In the breeding process of Andrias davidianus, we found that some albino individuals were extremely rare and could not be inherited stably, which severely limits their commercialization in the aquaculture market. In this study, we performed transcriptome and small RNA (sRNA) sequencing analyses in the skin samples of wild-type (WT) and albino (AL) Andrias davidianus. In total, among 5517 differentially expressed genes (DEGs), 2911 DEGs were down-regulated in AL, including almost all the key genes involved in melanin formation. A total of 25 miRNAs were differentially expressed in AL compared to WT, of which 17 were up-regulated. Through the integrated analysis, no intersection was found between the target genes of the differentially expressed miRNAs and the key genes for melanin formation. Gene Ontology (GO) and KEGG pathway analyses on DEGs showed that these genes involved multiple processes relevant to melanin synthesis and the key signal pathway MAPK. Interestingly, the transcription factors SOX10 and PAX3 and the Wnt signaling pathway that play a key role in other species were not included, while the other two transcription factors in the SOX family, SOX21 and SOX7, were included. After analyzing the key genes for melanin formation, it was interesting to note an alternative splicing form of the MITF in WT and a critical mutation of the SLC24A5 gene in AL, which might be the main reason for the skin color change of Andrias davidianus. The results contributed to understanding the molecular mechanism of skin pigmentation in Andrias davidianus and accelerating the acquisition process of individuals with specific body colors by genetic means.
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Geng X, Zhang L, Zang X, Guo J, Xu C. RNA-seq analysis provides insight into molecular adaptations of Andrias davidianus. Dev Genes Evol 2019; 229:197-206. [PMID: 31734771 DOI: 10.1007/s00427-019-00641-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/30/2019] [Indexed: 02/07/2023]
Abstract
The Chinese giant salamander Andrias davidianus is regarded as an ideal model for studying local adaptations, such as longevity, tolerance to starvation, and cutaneous respiration. Transcriptome analysis is useful for studying the large and complex genomes of amphibians. Based on the coding gene set of adult A. davidianus, dozens of A. davidianus-specific genes were identified and three signaling pathway (JAK-STAT, HIF-1, and FoxO) genes were expanded as compared with other amphibians. The results of the pathway analysis of A. davidianus-specific genes indicated that the molecular adaptation of A. davidianus may have required a more rapid evolution of the immune system. Additionally, for the first time, the gene expressions in different parts of the skin tissue were compared. The results of the comparison analysis demonstrated that lateral skin could be more focused on mucus secretion, dorsal skin on immunity and melanogenesis, and abdominal skin on water and salt metabolism. This study provides the first insight into studying longevity and starvation tolerance in A. davidianus, and offers a basis for further investigation of the molecular mechanisms of adaptations in amphibians.
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Affiliation(s)
- Xiaofang Geng
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Lu Zhang
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Xiayan Zang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China
| | - Jianlin Guo
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China
| | - Cunshuan Xu
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China.
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Geng X, Guo J, Zang X, Chang C, Shang H, Wei H, Xu C. Proteomic analysis of eleven tissues in the Chinese giant salamander (Andrias davidianus). Sci Rep 2019; 9:16415. [PMID: 31712686 PMCID: PMC6848178 DOI: 10.1038/s41598-019-50909-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/11/2018] [Indexed: 02/08/2023] Open
Abstract
The Chinese giant salamander (Andrias davidianus, CGS) is the largest extant amphibian species in the world. Global quantitative proteome analysis of multiple tissues would indicate tissue-specific physiological processes and clarify the function of each protein from a whole-organism perspective. This study performed proteome analysis of eleven tissues collected from adult CGSs using iTRAQ coupled with LC-MS/MS technology. Based on the predicted protein database from previously obtained CGS transcriptome data, 2153 proteins were identified for subsequent analysis. A weighted gene co-expression network analysis (WGCNA) clustered 2153 proteins into 17 co-expressed modules, which will be useful for predicting the functions of unannotated proteins. The protein levels of molecular complexes with housekeeping functions, such as ribosomes, spliceosomes and mitochondrial respiratory chain complexes, were tightly regulated in different tissues of the CGS, as they are in mammalian tissues. Transcription regulator, pathway and bio-functional analysis of tissue-specific proteins showed that highly expressed proteins largely reflected the physiological functions of specific tissues. Our data, as an initial atlas of protein expression of an amphibian species, will be useful for further molecular biology research on CGS.
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Affiliation(s)
- Xiaofang Geng
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China.,Henan Key Laboratory of immunology and targeted therapy, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Jianlin Guo
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China
| | - Xiayan Zang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China
| | - Cuifang Chang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China
| | - Haitao Shang
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Hong Wei
- The Engineering Technology Research Center for Germ-free and Genome-editing animal, Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China.
| | - Cunshuan Xu
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China.
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Genomic Data Reveal Conserved Female Heterogamety in Giant Salamanders with Gigantic Nuclear Genomes. G3-GENES GENOMES GENETICS 2019; 9:3467-3476. [PMID: 31439718 PMCID: PMC6778777 DOI: 10.1534/g3.119.400556] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Systems of genetic sex determination and the homology of sex chromosomes in different taxa vary greatly across vertebrates. Much progress remains to be made in understanding systems of genetic sex determination in non-model organisms, especially those with homomorphic sex chromosomes and/or large genomes. We used reduced representation genome sequencing to investigate genetic sex determination systems in the salamander family Cryptobranchidae (genera Cryptobranchus and Andrias), which typifies both of these inherent difficulties. We tested hypotheses of male- or female-heterogamety by sequencing hundreds of thousands of anonymous genomic regions in a panel of known-sex cryptobranchids and characterized patterns of presence/absence, inferred zygosity, and depth of coverage to identify sex-linked regions of these 56 gigabase genomes. Our results strongly support the hypothesis that all cryptobranchid species possess homologous systems of female heterogamety, despite maintenance of homomorphic sex chromosomes over nearly 60 million years. Additionally, we report a robust, non-invasive genetic assay for sex diagnosis in Cryptobranchus and Andrias which may have great utility for conservation efforts with these endangered salamanders. Co-amplification of these W-linked markers in both cryptobranchid genera provides evidence for long-term sex chromosome stasis in one of the most divergent salamander lineages. These findings inform hypotheses about the ancestral mode of sex determination in salamanders, but suggest that comparative data from other salamander families are needed. Our results further demonstrate that massive genomes are not necessarily a barrier to effective genome-wide sequencing and that the resulting data can be highly informative about sex determination systems in taxa with homomorphic sex chromosomes.
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Genome-wide RAD sequencing to identify a sex-specific marker in Chinese giant salamander Andrias davidianus. BMC Genomics 2019; 20:415. [PMID: 31122206 PMCID: PMC6533744 DOI: 10.1186/s12864-019-5771-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 05/03/2019] [Indexed: 11/15/2022] Open
Abstract
Background Chinese giant salamander Andrias davidianus is an endangered species. The success of artificial breeding provides a useful way to protect this species. However, the method to identify the sex and mechanism of sex determination were unclear which hinder the improvement of the artificial breeding. Detection of a sex specific marker provides an effective approach to identify genetic sex and investigate the sex determination mechanism. Results We used restriction-site-associated DNA (RAD) sequencing to isolate a sex-specific genetic marker in A. davidianus to expand knowledge of the sex determination mechanism. Four male and four female specimens were subjected to RAD sequencing, which generated 934,072,989 reads containing approximately 134.4 Gb of sequences. The first round of comparison of the assembled sequence against the opposite sex raw reads revealed 19,097 female and 17,994 male unmatched sequences. Subsequently, 19,097 female sequences were subjected to a BLAST search against male genomic data, which revealed 308 sequences unmapped to the male genome. One hundred of these were randomly selected and validated by PCR in five male and five female specimens, and four putative sex-specific sequences were produced. Further validation was performed by PCR in another 24 females and 24 males, and all female individuals exhibited the expected specific bands, while the males did not. To apply the sex-specific marker, three specimens reversed from genetic female to physiological male were found in a group exposed to elevated temperature, and 13 individuals reversed from genetic male to physiological female were obtained in a 17β-estradiol exposed group. Conclusion This is the first report of a sex-specific marker in A. davidianus and may have potential for elucidation of its sex determination mechanism and, hence, its conservation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5771-5) contains supplementary material, which is available to authorized users.
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Identification of critical sex-biased genes in Andrias davidianus by de novo transcriptome. Mol Genet Genomics 2018; 294:287-299. [PMID: 30377773 DOI: 10.1007/s00438-018-1508-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 10/22/2018] [Indexed: 02/06/2023]
Abstract
The Chinese giant salamander Andrias davidianus is a protected amphibian with high nutritional and economic value. Understanding its sex determination mechanism is important for improving culture techniques and sex control in breeding. However, little information on the characterization of critical genes involved in sex is available. Herein, sequencing of ovary and test produced 40,783,222 and 46,128,902 raw reads, respectively, which were jointly assembled into 80,497 unigenes. Of these, 36,609 unigenes were annotated, of which 8907 were female-biased and 10,385 were male-biased. Several sex-related pathways were observed, including the Wnt signaling pathway. After elevated temperature and estrogen exposure, neomale and neofemale specimens were identified by a female-specific marker for the first time. RT-qPCR analysis showed the expression profile of ten selected sex-biased genes to be exhibited consistently in male and neomale and in female and neofemale, with the exception of the Amh and TfIIIa genes. Results suggested that these genes may play important roles in A. davidianus sex determination and gonad development. This provides a basis for further investigation of the molecular mechanisms of sex determination in amphibians.
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Huang Y, Xiong JL, Gao XC, Sun XH. Transcriptome analysis of the Chinese giant salamander ( Andrias davidianus) using RNA-sequencing. GENOMICS DATA 2017; 14:126-131. [PMID: 29159068 PMCID: PMC5675895 DOI: 10.1016/j.gdata.2017.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/21/2017] [Accepted: 10/21/2017] [Indexed: 12/21/2022]
Abstract
The Chinese giant salamander (Andrias davidianus) is an economically important animal on academic value. However, the genomic information of this species has been less studied. In our study, the transcripts of A. davidianus were obtained by RNA-seq to conduct a transcriptomic analysis. In total 132,912 unigenes were generated with an average length of 690 bp and N50 of 1263 bp by de novo assembly using Trinity software. Using a sequence similarity search against the nine public databases (CDD, KOG, NR, NT, PFAM, Swiss-prot, TrEMBL, GO and KEGG databases), a total of 24,049, 18,406, 36,711, 15,858, 20,500, 27,515, 36,705, 28,879 and 10,958 unigenes were annotated in databases, respectively. Of these, 6323 unigenes were annotated in all database and 39,672 unigenes were annotated in at least one database. Blasted with KEGG pathway, 10,958 unigenes were annotated, and it was divided into 343 categories according to different pathways. In addition, we also identified 29,790 SSRs. This study provided a valuable resource for understanding transcriptomic information of A. davidianus and laid a foundation for further research on functional gene cloning, genomics, genetic diversity analysis and molecular marker exploitation in A. davidianus.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Jian Li Xiong
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Xiao Chan Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Xi Hong Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
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Geng X, Li W, Shang H, Gou Q, Zhang F, Zang X, Zeng B, Li J, Wang Y, Ma J, Guo J, Jian J, Chen B, Qiao Z, Zhou M, Wei H, Fang X, Xu C. A reference gene set construction using RNA-seq of multiple tissues of Chinese giant salamander, Andrias davidianus. Gigascience 2017; 6:1-7. [PMID: 28204480 PMCID: PMC5467019 DOI: 10.1093/gigascience/gix006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/07/2017] [Indexed: 01/11/2023] Open
Abstract
Background Chinese giant salamander (CGS) is the largest extant amphibian species in the world. Owing to its evolutionary position and four peculiar phenomenon of life (longevity, starvation tolerance, regenerative ability, and hatch without sunshine), it is an invaluable model species for research. However, lack of genomic resources leads to fewer study progresses in these fields, due to its huge genome of ∼50 GB making it extremely difficult to be assembled. Results We reported the sequenced transcriptome of more than 20 tissues from adult CGS using Illumina Hiseq 2000 technology, and a total of 93 366 no-redundancy transcripts with a mean length of 1326 bp were obtained. We developed for the first time an efficient pipeline to construct a high-quality reference gene set of CGS and obtained 26 135 coding genes. BUSCO and homologous assessment showed that our assembly captured 70.6% of vertebrate universal single-copy orthologs, and this coding gene set had a higher proportion of completeness CDS with comparable quality of the protein sets of Tibetan frog. Conclusions These highest quality data will provide a valuable reference gene set to the subsequent research of CGS. In addition, our strategy of de novo transcriptome assembly and protein identification is applicable to similar studies.
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Affiliation(s)
- Xiaofang Geng
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China.,Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
| | | | - Haitao Shang
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Qiang Gou
- Chongqing Kui Xu Biotechnology Incorporated Company, Kaixian Country, Chongqing 405423, China
| | - Fuchun Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
| | - Xiayan Zang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Benhua Zeng
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Jiang Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Ying Wang
- Chongqing Kui Xu Biotechnology Incorporated Company, Kaixian Country, Chongqing 405423, China
| | - Ji Ma
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
| | - Jianlin Guo
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | | | - Bing Chen
- Chongqing Kui Xu Biotechnology Incorporated Company, Kaixian Country, Chongqing 405423, China
| | - Zhigang Qiao
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Minghui Zhou
- Chongqing Kui Xu Biotechnology Incorporated Company, Kaixian Country, Chongqing 405423, China
| | - Hong Wei
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | | | - Cunshuan Xu
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
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Geng X, Wei H, Shang H, Zhou M, Chen B, Zhang F, Zang X, Li P, Sun J, Che J, Zhang Y, Xu C. Proteomic analysis of the skin of Chinese giant salamander (Andrias davidianus). J Proteomics 2015; 119:196-208. [DOI: 10.1016/j.jprot.2015.02.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/07/2015] [Accepted: 02/11/2015] [Indexed: 12/18/2022]
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