Skip to main content

Advertisement

SpringerLink
Log in

Metabolome and Transcriptome Association Analysis Reveals the Link Between Pigmentation and Nutrition Utilization in the Juveniles of Sea Cucumber Holothuria leucospilota

  • Research
  • Published:
Marine Biotechnology Aims and scope Submit manuscript

Abstract

The sea cucumber Holothuria leucospilota is an economically and ecologically important tropical species. Following development into juveniles, H. leucospilota undergoes a color change from white to black, involving a pigmentation process for over a period of several months. In this study, a combination of liquid chromatography-tandem mass spectrometry (LC–MS/MS) and Next-Generation sequencing (NGS) were employed to investigate the changes in metabolomic and transcriptomic profiles during pigmentation in H. leucospilota juveniles. The metabolomic analysis identified a total of 341 metabolites, of which 52 were found to be differentially regulated (P < 0.05 and VIP > 1), with 27 being upregulated in white individuals and 25 in black individuals. Additionally, 632 differentially expressed genes (DEGs) were identified, with 380 genes upregulated in white samples and 252 genes upregulated in black samples. Interestingly, the melanin content and tyrosinase transcript levels did not display significant differences between the two groups. Metabolomic data suggested the involvement of the linoleic acid metabolic pathway in pigmentation. Transcriptomic analysis, coupled with realtime PCR validation, revealed a decrease in the transcript levels of digestive enzymes like α-amylase, maltase-glucoamylase, and trehalase after the juveniles changed to black. Furthermore, the mRNA expressions of major yolk proteins showed a decline, indicating a shift in the accumulation of protein nutrient sources. Overall, our findings suggest that during the pigmentation process in H. leucospilota, no significant changes were observed in the classical melanin pathway, while notable alterations were observed in their nutritional status. This study provides valuable insights into the regulatory mechanisms of pigmentation in marine organisms.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

Availability of Data and Materials

The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: BioProject, accession number: PRJNA997441.

References

  • Abdelrazig S, Safo L, Rance GA, Fay MW, Theodosiou E, Topham PD, Kim DH, Fernandez-Castane A (2020) Metabolic characterisation of Magnetospirillum gryphiswaldense MSR-1 using LC-MS-based metabolite profiling. RSC Adv 10:32548–32560

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Anderson SC, Flemming JM, Watson R, Lotze HK (2011) Serial exploitation of global sea cucumber fisheries. Fish Fish 12:317–339

    Article  Google Scholar 

  • Brooks JM, Wessel GM (2002) The major yolk protein in sea urchins is a transferrin-like, iron binding protein. Dev Biol 245:1–12

    Article  CAS  PubMed  Google Scholar 

  • Calestani C, Wessel GM (2018) These colors don’t run: regulation of pigment-biosynthesis in echinoderms. Results Probl Cell Differ 65:515–525

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen T, Ren C, Wong NK, Yan A, Sun C, Fan D, Luo P, Jiang X, Zhang L, Ruan Y, Li J, Wu X, Huo D, Huang J, Li X, Wu F, E, Z., Cheng, C., Zhang, X., Wang, Y. & Hu, C. (2023) The Holothuria leucospilota genome elucidates sacrificial organ expulsion and bioadhesive trap enriched with amyloid-patterned proteins. Proc Natl Acad Sci U S A 120:e2213512120. https://doi.org/10.1073/pnas.2213512120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eriksson H, Robinson G, Slater MJ, Troell M (2012) Sea cucumber aquaculture in the Western Indian Ocean: challenges for sustainable livelihood and stock improvement. Ambio 41:109–121

    Article  PubMed  Google Scholar 

  • Fujiwara A, Unuma T, Ohno K, Yamano K (2010) Molecular characterization of the major yolk protein of the Japanese common sea cucumber (Apostichopus japonicus) and its expression profile during ovarian development. Comp Biochem Physiol Mol Integr Physiol 155:34–40

    Article  Google Scholar 

  • Gagnebin Y, Tonoli D, Lescuyer P, Ponte B, De Seigneux S, Martin PY, Schappler J, Boccard J, Rudaz S (2017) Metabolornic analysis of urine samples by UHPLC-QTOF-MS: impact of normalization strategies. Anal Chim Acta 955:27–35

    Article  CAS  PubMed  Google Scholar 

  • Hansson LA (2004) Plasticity in pigmentation induced by conflicting threats from predation and UV radiation. Ecology 85:1005–1016

    Article  Google Scholar 

  • Hiramatsu N, Todo T, Sullivan CV, Schilling J, Reading BJ, Matsubara T, Ryu YW, Mizuta H, Luo WS, Nishimiya O, Wu MQ, Mushirobira Y, Yilmaz O, Hara A (2015) Ovarian yolk formation in fishes: molecular mechanisms underlying formation of lipid droplets and vitellogenin-derived yolk proteins. Gen Comp Endocrinol 221:9–15

    Article  CAS  PubMed  Google Scholar 

  • Horai H, Arita M, Kanaya S, Nihei Y, Ikeda T, Suwa K, Ojima Y, Tanaka K, Tanaka S, Aoshima K, Oda Y, Kakazu Y, Kusano M, Tohge T, Matsuda F, Sawada Y, Hirai MY, Nakanishi H, Ikeda K, Akimoto N, Maoka T, Takahashi H, Ara T, Sakurai N, Suzuki H, Shibata D, Neumann S, Iida T, Tanaka K, Funatsu K, Matsuura F, Soga T, Taguchi R, Saito K, Nishioka T (2010) MassBank: a public repository for sharing mass spectral data for life sciences. J Mass Spectrom 45:703–714

    Article  CAS  PubMed  Google Scholar 

  • Huang W, Huo D, Yu ZH, Ren CH, Jiang X, Luo P, Chen T, Hu CQ (2018) Spawning, larval development and juvenile growth of the tropical sea cucumber Holothuria leucospilota. Aquaculture 488:22–29

    Article  Google Scholar 

  • Huo D, Jiang X, Wu XF, Ren CH, Yu ZH, Liu JS, Li HM, Ruan Y, Wen J, Chen T, Hu CQ (2018) First echinoderm trehalase from a tropical sea cucumber (Holothuria leucospilota): molecular cloning and mRNA expression in different tissues, embryonic and larval stages, and under a starvation challenge. Gene 665:74–81

    Article  CAS  PubMed  Google Scholar 

  • Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kang JH, Yu KH, Park JY, An CM, Jun JC, Lee SJ (2011) Allele-specific PCR genotyping of the HSP70 gene polymorphism discriminating the green and red color variants sea cucumber (Apostichopus japonicus). J Genet Genomics 38:351–355

    CAS  PubMed  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Larson SD, Hoyt ZN, Eckert GL, Gill VA (2013) Impacts of sea otter (Enhydra lutris) predation on commercially important sea cucumbers (Parastichopus californicus) in southeast Alaska. Can J Fish Aquat Sci 70:1498–1507

    Article  Google Scholar 

  • Li Z, Zhou MY, Ruan Y, Chen XL, Ren CH, Yang H, Zhang X, Liu JS, Li H, Zhang L, Hu CQ, Chen T, Wu XG (2022) Transcriptomic analysis reveals yolk accumulation mechanism from the hepatopancreas to ovary in the pacific white shrimp Litopenaeus vannamei. Front Mar Sci 9:15. https://doi.org/10.3389/fmars.2022.948105

    Article  Google Scholar 

  • Mactavish T, Stenton-Dozey J, Vopel K, Savage C (2012) Deposit-feeding sea cucumbers enhance mineralization and nutrient cycling in organically-enriched coastal sediments. PLoS ONE 7:11. https://doi.org/10.1371/journal.pone.0050031

    Article  CAS  Google Scholar 

  • Marrugo-Negrete J, Pinedo-Hernandez J, Marrugo-Madrid S, Navarro-Frometa E, Diez S (2021) Sea cucumber as bioindicator of trace metal pollution in coastal sediments. Biol Trace Elem Res 199:2022–2030

    Article  CAS  PubMed  Google Scholar 

  • Navarro-Reig M, Jaumot J, Garcia-Reiriz A, Tauler R (2015) Evaluation of changes induced in rice metabolome by Cd and Cu exposure using LC-MS with XCMS and MCR-ALS data analysis strategies. Anal Bioanal Chem 407:8835–8847

    Article  CAS  PubMed  Google Scholar 

  • Ni JB, Zeng Z, Kong DZ, Hou L, Huang HQ, Ke CH (2014) Vitellogenin of Fujian oyster, Crassostrea angulata: synthesized in the ovary and controlled by estradiol-17 beta. Gen Comp Endocrinol 202:35–43

    Article  CAS  PubMed  Google Scholar 

  • Nicholson JK, Connelly J, Lindon JC, Holmes E (2002) Metabonomics: a platform for studying drug toxicity and gene function. Nat Rev Drug Discov 1:153–161

    Article  CAS  PubMed  Google Scholar 

  • Oskouian B, Saba JD (2004) Death and taxis: what non-mammalian models tell us about sphingosine-1-phosphate. Semin Cell Dev Biol 15:529–540

    Article  CAS  PubMed  Google Scholar 

  • Parveen F, Bender D, Law SH, Mishra VK, Chen CC, Ke LY (2019) Role of ceramidases in sphingolipid metabolism and human diseases. Cells 8:19. https://doi.org/10.3390/cells8121573

    Article  CAS  Google Scholar 

  • Purcell SW, Eriksson H (2015) Echinoderms piggybacking on sea cucumbers: benign effects on sediment turnover and movement of hosts. Mar Biol Res 11:666–670

    Article  Google Scholar 

  • Purcell SW, Conand C, Uthicke S and Byrne M (2016) Ecological roles of exploited sea cucumbers. IN Hughes, R.N., Hughes, D.J., Smith, I.P. & Dale, A.C. (Eds.) Oceanography and marine biology: an annual review, Vol 54. Boca Raton: Crc Press-Taylor & Francis Group

  • Purcell SW (2014) Value, market preferences and trade of Beche-De-Mer from Pacific Island sea cucumbers. PLoS One 9. https://doi.org/10.1371/journal.pone.0095075

  • Quinville BM, Deschenes NM, Ryckman AE, Walia JS (2021) A comprehensive review: sphingolipid metabolism and implications of disruption in sphingolipid homeostasis. Int J Mol Sci 22:37. https://doi.org/10.3390/ijms22115793

    Article  CAS  Google Scholar 

  • Ruan Y, Wong NK, Zhang X, Zhu CH, Wu XF, Ren CH, Luo P, Jiang X, Ji JT, Wu XG, Hu CQ and Chen T (2020) Vitellogenin receptor (VgR) mediates oocyte maturation and ovarian development in the pacific white shrimp (Litopenaeus vannamei). Front Physiol 11. https://doi.org/10.3389/fphys.2020.00485

  • Shaw J, Costa-Pinheiro P, Patterson L, Drews K, Spiegel S and Kester M (2018) Novel sphingolipid-based cancer therapeutics in the personalized medicine era. IN Chalfant CE and Fisher PB (Eds) Sphingolipids in Cancer. San Diego: Elsevier Academic Press Inc

  • Shyu AB, Raff RA, Blumenthal T (1986) Expression of the vitellogenin gene in female and male sea-urchin. Proc Natl Acad Sci USA 83:3865–3869

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Slominski A, Tobin DJ, Shibahara S, Wortsman J (2004) Melanin pigmentation in mammalian skin and its hormonal regulation. Physiol Rev 84:1155–1228

    Article  CAS  PubMed  Google Scholar 

  • Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, Merrill AH, Murphy RC, Raetz CRH, Russell DW, Subramaniam S (2007) LMSD: LIPID MAPS structure database. Nucleic Acids Res 35:D527–D532

    Article  CAS  PubMed  Google Scholar 

  • Sun JN, Yu YS, Zhao ZH, Tian RH, Li X, Chang YQ, Zhao C (2022) Macroalgae and interspecific alarm cues regulate behavioral interactions between sea urchins and sea cucumbers. Sci Rep 12:9. https://doi.org/10.1038/s41598-022-07889-8

    Article  CAS  Google Scholar 

  • Taquet C, Setiawan F, Yasuda N, Suharsono & Nadaoka, K. (2010) First observation of a large group of Holothuria leucospilota sea cucumber juveniles at a nursery in Manado (north Sulawesi, Indonesia). Beche-De-Mer Information Bulletin 31:30–34

    Google Scholar 

  • Thevenot EA, Roux A, Xu Y, Ezan E, Junot C (2015) Analysis of the human adult urinary metabolome variations with age, body mass index, and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. J Proteome Res 14:3322–3335

    Article  CAS  PubMed  Google Scholar 

  • Tian X, Gautron J, Monget P, Pascal G (2010) What makes an egg unique? Clues from evolutionary scenarios of egg-specific genes. Biol Reprod 83:893–900

    Article  CAS  PubMed  Google Scholar 

  • Tufail M, Takeda M (2008) Molecular characteristics of insect vitellogenins. J Insect Physiol 54:1447–1458

    Article  CAS  PubMed  Google Scholar 

  • Unuma T, Konishi K, Kiyomoto M, Matranga V, Yamano K, Ohta H, Yokota Y (2009) The major yolk protein is synthesized in the digestive tract and secreted into the body cavities in sea urchin larvae. Mol Reprod Dev 76:142–150

    Article  CAS  PubMed  Google Scholar 

  • Wade NM, Gabaudan J, Glencross BD (2017) A review of carotenoid utilisation and function in crustacean aquaculture. Rev Aquac 9:141–156

    Article  Google Scholar 

  • Wagele B, Witting M, Schmitt-Kopplin P, Suhre K (2012) MassTRIX reloaded: combined analysis and visualization of transcriptome and metabolome data. PLoS ONE 7:5. https://doi.org/10.1371/journal.pone.0039860

    Article  CAS  Google Scholar 

  • Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S, Fung C, Nikolai L, Lewis M, Coutouly MA, Forsythe I, Tang P, Shrivastava S, Jeroncic K, Stothard P, Amegbey G, Block D, Hau DD, Wagner J, Miniaci J, Clements M, Gebremedhin M, Guo N, Zhang Y, Duggan GE, Macinnis GD, Weljie AM, Dowlatabadi R, Bamforth F, Clive D, Greiner R, Li L, Marrie T, Sykes BD, Vogel HJ, Querengesser L (2007) HMDB: the human metabolome database. Nucleic Acids Res 35:D521–D526

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu X, Ruan Y, Chen T, Yu Z, Huo D, Li X, Wu F, Jiang X and Ren C (2020) First echinoderm alpha-amylase from a tropical sea cucumber (Holothuria leucospilota): molecular cloning, tissue distribution, cellular localization and functional production in a heterogenous E.coli system with codon optimization. PLoS One 15:e0239044. https://doi.org/10.1371/journal.pone.0239044

  • Xia JG, Wishart DS (2011) Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst. Nat Protoc 6:743–760

    Article  CAS  PubMed  Google Scholar 

  • Xing LL, Sun LN, Liu SL, Li XN, Miao T, Zhang LB, Yang HS (2017) Comparison of pigment composition and melanin content among white, light-green, dark-green, and purple morphs of sea cucumber, Apostichopus japonicus. Acta Oceanol Sin 36:45–51

    Article  CAS  Google Scholar 

  • Xing LL, Sun LN, Liu SL, Wan ZX, Li XN, Miao T, Zhang LB, Bai YC, Yang HS (2018) Growth, histology, ultrastructure and expression of MITF and astacin in the pigmentation stages of green, white and purple morphs of the sea cucumber, Apostichopus japonicus. Aquac Res 49:177–187

    Article  CAS  Google Scholar 

  • Xing LL, Sun LN, Liu SL, Zhang LB and Yang HS (2021) Comparative metabolomic analysis of the body wall from four varieties of the sea cucumber Apostichopus japonicus. Food Chem 352. https://doi.org/10.1016/j.foodchem.2021.129339

  • Yao LL, Zhao B, Wang Q, Jiang XY, Han S, Hu W and Li CL (2023) Contribution of the TGF beta signaling pathway to pigmentation in sea cucumber (Apostichopus japonicus). Front Marine Sci 10:1101725. https://doi.org/10.3389/fmars.2023.1101725

  • Yu ZH, Wu H, Tu YK, Hong ZS, Luo JW (2022) Effects of diet on larval survival, growth, and development of the sea cucumber Holothuria leucospilota. Aquac Nutr 2022:10. https://doi.org/10.1155/2022/8947997

    Article  CAS  Google Scholar 

  • Zhao Y, Wang H, Wang H, Pi Y and Chen M (2022) Metabolic response of the sea cucumber Apostichopus japonicus during the estivation-arousal cycles. Front Marine Sci 9. https://doi.org/10.3389/fmars.2022.980221

Download references

Funding

This work was supported by the National Natural Science Foundation of China (42176132, 41906101), the National Key R & D Program of China (2022YFD2401301, 2018YFD0901605), and the Key Deployment Project of Centre for Ocean Mega-Research of Science, Chinese Academy of Sciences (COMS2020Q03).

Author information

Authors and Affiliations

  1. CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People’s Republic of China

    Jiasheng Huang, Zixuan E, Wenjie Pan, Chunhua Ren, Peng Luo, Bo Ma, Yang Liu, Chaoqun Hu, Xiao Jiang & Ting Chen

  2. Shanghai Collaborative Innovation Centre for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, People’s Republic of China

    Zhi Li & Xugan Wu

  3. Guangdong Institute for Drug Control, Guangzhou, 5106630, People’s Republic of China

    Tiehao Lin

  4. University of Chinese Academy of Sciences, Beijing, 100049, People’s Republic of China

    Jiasheng Huang, Zixuan E, Wenjie Pan, Bo Ma & Yang Liu

  5. Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, People’s Republic of China

    Chunhua Ren, Peng Luo, Xiao Jiang & Ting Chen

  6. Guangxi Key Laboratory of Marine Environmental Science, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, 530007, People’s Republic of China

    Chaoqun Hu

Authors
  1. Jiasheng Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zixuan E
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wenjie Pan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Zhi Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Tiehao Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Chunhua Ren
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Peng Luo
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Bo Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Yang Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Xugan Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Chaoqun Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Xiao Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Ting Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Conceptualization: XJ and TC; investigation: JH, ZE, WP, BM, and YL; methodology: JH, ZL, TL, and CR; formal analysis: JH, ZE and ZL; writing—original draft preparation: JH and TC; writing—review and editing: XJ and TC; funding acquisition: CH, XJ, and TC; resources: TL, CR, PL, XW, and CH; supervision: XW, CH, and TC.

Corresponding authors

Correspondence to Xiao Jiang or Ting Chen.

Ethics declarations

Ethics Approval

Not applicable.

Consent to Participate

Not applicable.

Consent for Publication

Not applicable.

Competing Interest

The authors declare no competing interests.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 29 KB)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Huang, J., E, Z., Pan, W. et al. Metabolome and Transcriptome Association Analysis Reveals the Link Between Pigmentation and Nutrition Utilization in the Juveniles of Sea Cucumber Holothuria leucospilota. Mar Biotechnol 25, 1110–1122 (2023). https://doi.org/10.1007/s10126-023-10263-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10126-023-10263-y

Keywords

Search

Navigation