Identification of Genes Regulated by 20-Hydroxyecdysone in Macrobrachium Nipponense Using Comparative Transcriptomic Analysis

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2024 Jan 5

PMID 38183039

Authors

Huwei Yuan

Pengfei Cai

Wenyi Zhang

Shubo Jin

Sufei Jiang

Yiwei Xiong

Yongsheng Gong

Hui Qiao

Hongtuo Fu

Affiliations

Soon will be listed here.

Abstract

Background: Macrobrachium nipponense is a freshwater prawn of economic importance in China. Its reproductive molt is crucial for seedling rearing and directly impacts the industry's economic efficiency. 20-hydroxyecdysone (20E) controls various physiological behaviors in crustaceans, among which is the initiation of molt. Previous studies have shown that 20E plays a vital role in regulating molt and oviposition in M. nipponense. However, research on the molecular mechanisms underlying the reproductive molt and role of 20E in M. nipponense is still limited.

Results: A total of 240.24 Gb of data was obtained from 18 tissue samples by transcriptome sequencing, with > 6 Gb of clean reads per sample. The efficiency of comparison with the reference transcriptome ranged from 87.05 to 92.48%. A total of 2532 differentially expressed genes (DEGs) were identified. Eighty-seven DEGs associated with molt or 20E were screened in the transcriptomes of the different tissues sampled in both the experimental and control groups. The reliability of the RNA sequencing data was confirmed using Quantitative Real-Time PCR. The expression levels of the eight strong candidate genes showed significant variation at the different stages of molt.

Conclusion: This study established the first transcriptome library for the different tissues of M. nipponense in response to 20E and demonstrated the dominant role of 20E in the molting process of this species. The discovery of a large number of 20E-regulated strong candidate DEGs further confirms the extensive regulatory role of 20E and provides a foundation for the deeper understanding of its molecular regulatory mechanisms.

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References

Petryk A, Warren J, Marques G, Jarcho M, Gilbert L, Kahler J . Shade is the Drosophila P450 enzyme that mediates the hydroxylation of ecdysone to the steroid insect molting hormone 20-hydroxyecdysone. Proc Natl Acad Sci U S A. 2003; 100(24):13773-8. PMC: 283497. DOI: 10.1073/pnas.2336088100. View

Liu S, Li K, Gao Y, Liu X, Chen W, Ge W . Antagonistic actions of juvenile hormone and 20-hydroxyecdysone within the ring gland determine developmental transitions in . Proc Natl Acad Sci U S A. 2017; 115(1):139-144. PMC: 5776822. DOI: 10.1073/pnas.1716897115. View

Baldini F, Gabrieli P, South A, Valim C, Mancini F, Catteruccia F . The interaction between a sexually transferred steroid hormone and a female protein regulates oogenesis in the malaria mosquito Anopheles gambiae. PLoS Biol. 2013; 11(10):e1001695. PMC: 3812110. DOI: 10.1371/journal.pbio.1001695. View

Gabrieli P, Kakani E, Mitchell S, Mameli E, Want E, Mariezcurrena Anton A . Sexual transfer of the steroid hormone 20E induces the postmating switch in Anopheles gambiae. Proc Natl Acad Sci U S A. 2014; 111(46):16353-8. PMC: 4246312. DOI: 10.1073/pnas.1410488111. View

Knapp E, Sun J . Steroid signaling in mature follicles is important for Drosophila ovulation. Proc Natl Acad Sci U S A. 2017; 114(4):699-704. PMC: 5278441. DOI: 10.1073/pnas.1614383114. View

Zhou L, Li S, Wang Z, Li F, Xiang J . An eclosion hormone-like gene participates in the molting process of Palaemonid shrimp Exopalaemon carinicauda. Dev Genes Evol. 2017; 227(3):189-199. DOI: 10.1007/s00427-017-0580-9. View

Martin-Creuzburg D, Westerlund S, Hoffmann K . Ecdysteroid levels in Daphnia magna during a molt cycle: determination by radioimmunoassay (RIA) and liquid chromatography-mass spectrometry (LC-MS). Gen Comp Endocrinol. 2007; 151(1):66-71. DOI: 10.1016/j.ygcen.2006.11.015. View

Yuan H, Qiao H, Fu Y, Fu H, Zhang W, Jin S . RNA interference shows that Spook, the precursor gene of 20-hydroxyecdysone (20E), regulates the molting of Macrobrachium nipponense. J Steroid Biochem Mol Biol. 2021; 213:105976. DOI: 10.1016/j.jsbmb.2021.105976. View

Zheng Y, Zhang W, Xiong Y, Wang J, Jin S, Qiao H . Dual roles of CYP302A1 in regulating ovarian maturation and molting in Macrobrachium nipponense. J Steroid Biochem Mol Biol. 2023; 232:106336. DOI: 10.1016/j.jsbmb.2023.106336. View

10.

Guo H, Liang Z, Zheng P, Li L, Xian J, Zhu X . Effects of nonylphenol exposure on histological changes, apoptosis and time-course transcriptome in gills of white shrimp Litopenaeus vannamei. Sci Total Environ. 2021; 781:146731. DOI: 10.1016/j.scitotenv.2021.146731. View

11.

Yuan H, Zhang W, Jin S, Jiang S, Xiong Y, Chen T . Transcriptome analysis provides novel insights into the immune mechanisms of Macrobrachium nipponense during molting. Fish Shellfish Immunol. 2022; 131:454-469. DOI: 10.1016/j.fsi.2022.10.021. View

12.

Kim D, Paggi J, Park C, Bennett C, Salzberg S . Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019; 37(8):907-915. PMC: 7605509. DOI: 10.1038/s41587-019-0201-4. View

13.

Trapnell C, Williams B, Pertea G, Mortazavi A, Kwan G, van Baren M . Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010; 28(5):511-5. PMC: 3146043. DOI: 10.1038/nbt.1621. View

14.

Anders S, Huber W . Differential expression analysis for sequence count data. Genome Biol. 2010; 11(10):R106. PMC: 3218662. DOI: 10.1186/gb-2010-11-10-r106. View

15.

Kanehisa M, Furumichi M, Sato Y, Kawashima M, Ishiguro-Watanabe M . KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Res. 2022; 51(D1):D587-D592. PMC: 9825424. DOI: 10.1093/nar/gkac963. View

16.

Hu Y, Fu H, Qiao H, Sun S, Zhang W, Jin S . Validation and Evaluation of Reference Genes for Quantitative Real-Time PCR in . Int J Mol Sci. 2018; 19(8). PMC: 6121487. DOI: 10.3390/ijms19082258. View

17.

Livak K, Schmittgen T . Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2002; 25(4):402-8. DOI: 10.1006/meth.2001.1262. View

18.

Moshtaghi A, Rahi M, Nguyen V, Mather P, Hurwood D . A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (). PeerJ. 2016; 4:e2520. PMC: 5068373. DOI: 10.7717/peerj.2520. View

19.

Rahi M, Amin S, Mather P, Hurwood D . Candidate genes that have facilitated freshwater adaptation by palaemonid prawns in the genus : identification and expression validation in a model species (). PeerJ. 2017; 5:e2977. PMC: 5301973. DOI: 10.7717/peerj.2977. View

20.

Chang E, Mykles D . Regulation of crustacean molting: a review and our perspectives. Gen Comp Endocrinol. 2011; 172(3):323-30. DOI: 10.1016/j.ygcen.2011.04.003. View