RNA-seq analysis provides insight into molecular adaptations of Andrias davidianus
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.
KeywordsChinese giant salamander Transcriptome Molecular adaptation Longevity Starvation tolerance
We thank Chongqing Kui Xu Biotechnology Incorporated Company for providing us Chinese giant salamanders.
CSX and XFG designed the project. XFG, LZ, and XYZ conducted the experiments. JLG contributed the analysis tools. XFG wrote the manuscript with input from all authors. All authors worked on the final version of the manuscript.
This work was supported by grants from the National Natural Science Foundation of China (No. 31572270 and No. 81802099), and Natural Science Foundation of Henan Province (No. 162300410144).
- 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 (2017a) A reference gene set construction using RNA-seq of multiple tissues of Chinese giant salamander, Andrias davidianus. Gigascience 6:1–7. https://doi.org/10.1093/gigascience/gix006 CrossRefPubMedPubMedCentralGoogle Scholar
- Geng X, Li W, Shang H et al (2017b) Supporting data for "A reference gene set construction using RNA-seq of multiple tissues of Chinese Giant Salamander, Andrias davidianus". GigaScience Database. https://doi.org/10.5524/100277
- Itoi-Ochi S, Terao M, Murota H, Katayama I (2016) Local corticosterone activation by 11beta-hydroxysteroid dehydrogenase 1 in keratinocytes: the role in narrow-band UVB-induced dermatitis. Dermatoendocrinol 8:e1119958. https://doi.org/10.1080/19381980.2015.1119958 CrossRefPubMedPubMedCentralGoogle Scholar
- Jorgensen CB (2000) Amphibian respiration and olfaction and their relationships: from Robert Townson (1794) to the present. Biol Rev Camb Philos Soc 75:297–345. https://doi.org/10.1111/j.1469-185X.2000.tb00047.x CrossRefPubMedGoogle Scholar
- Lin XX, Sen I, Janssens GE, Zhou X, Fonslow BR, Edgar D, Stroustrup N, Swoboda P, Yates JR 3rd, Ruvkun G, Riedel CG (2018) DAF-16/FOXO and HLH-30/TFEB function as combinatorial transcription factors to promote stress resistance and longevity. Nat Commun 9:4400. https://doi.org/10.1038/s41467-018-06624-0 CrossRefPubMedPubMedCentralGoogle Scholar
- Mouchiroud L, Houtkooper RH, Moullan N, Katsyuba E, Ryu D, Cantó C, Mottis A, Jo YS, Viswanathan M, Schoonjans K, Guarente L, Auwerx J (2013) The NAD(+)/sirtuin pathway modulates longevity through activation of mitochondrial UPR and FOXO signaling. Cell 154:430–441. https://doi.org/10.1016/j.cell.2013.06.016 CrossRefPubMedPubMedCentralGoogle Scholar
- Nakamura K, Islam MR, Takayanagi M, Yasumuro H, Inami W, Kunahong A, Casco-Robles RM, Toyama F, Chiba C (2014) A transcriptome for the study of early processes of retinal regeneration in the adult newt, Cynops pyrrhogaster. PLoS One 9:e109831. https://doi.org/10.1371/journal.pone.0109831 CrossRefPubMedPubMedCentralGoogle Scholar
- Perez-Sanchez J, Estensoro I, Redondo MJ, Calduch-Giner JA, Kaushik S, Sitja-Bobadilla A (2013) Mucins as diagnostic and prognostic biomarkers in a fish-parasite model: transcriptional and functional analysis. PLoS One 8:e65457. https://doi.org/10.1371/journal.pone.0065457 CrossRefPubMedPubMedCentralGoogle Scholar
- Slominski A, Zbytek B, Nikolakis G, Manna PR, Skobowiat C, Zmijewski M, Li W, Janjetovic Z, Postlethwaite A, Zouboulis CC, Tuckey RC (2013) Steroidogenesis in the skin: implications for local immune functions. J Steroid Biochem Mol Biol 137:107–123. https://doi.org/10.1016/j.jsbmb.2013.02.006 CrossRefPubMedPubMedCentralGoogle Scholar
- Snider A, Bowler J (1992). Longevity of reptiles and amphibians in North American collections. Society for the Study of Amphibians and ReptilesGoogle Scholar
- Su S, Wang Y, Wang H, Huang W, Chen J, Xing J, Xu P, Yuan X, Huang C, Zhou Y (2018) Comparative expression analysis identifies the respiratory transition-related miRNAs and their target genes in tissues of metamorphosing Chinese giant salamander (Andrias davidianus). BMC Genomics 19:406. https://doi.org/10.1186/s12864-018-4662-5 CrossRefPubMedPubMedCentralGoogle Scholar
- Turvey ST, Chen S, Tapley B, Wei G, Xie F, Yan F, Yang J, Liang Z, Tian H, Wu M, Okada S, Wang J, Lü J, Zhou F, Papworth SK, Redbond J, Brown T, Che J, Cunningham AA (2018) Imminent extinction in the wild of the world’s largest amphibian. Curr Biol: CB 28:R592–R594. https://doi.org/10.1016/j.cub.2018.04.005 CrossRefPubMedGoogle Scholar
- Zhu B, Feng Z, Qu A, Gao H, Zhang Y, Sun D, Song W, Saura A (2002a) Brief report. The karyotype of the caudate amphibian Andrias davidianus. Hereditas 136:85–88. https://doi.org/10.1034/j.1601-5223.2002.1360112.x CrossRefPubMedGoogle Scholar
- Zhu B, Feng Z, Qu A, Gao H, Zhang Y, Sun D, Song W, Saura A (2002b) The karyotype of the caudate amphibian Andrias davidianus. Hereditas 136:85–88. https://doi.org/10.1034/j.1601-5223.2002.1360112.x CrossRefPubMedGoogle Scholar