Evaluating yield of DNA extraction methods across different tissues of moon jellyfish Aurelia aurita (Linnaeus, 1758)

Sümeyra Zeynep Çalıcı; Buse Bayrak; Hatice Buse Yavuz; Nida Kelel; Zeynep Aslıhan Avşaroğlu; Merve Nur Aydemir

doi:10.46309/biodicon.2025.1697734

Research Article

Ay denizanası Aurelia aurita'nın (Linnaeus, 1758) farklı dokularında DNA izolasyon yöntemlerinin verimliliklerinin değerlendirilmesi

Year 2025, Volume: 18 Issue: 3, 291 - 300

Sümeyra Zeynep Çalıcı , Buse Bayrak , Hatice Buse Yavuz , Nida Kelel , Zeynep Aslıhan Avşaroğlu , Merve Nur Aydemir

https://doi.org/10.46309/biodicon.2025.1697734

Abstract

Özet
Amaç: Bu çalışma, jelatinimsi yapısı nedeniyle DNA izolasyonu zor olan denizanası Aurelia aurita’dan elde edilecek DNA verimini optimize etmeyi; doku türü, enzimatik inkübasyon süresi ve farklı izolasyon yöntemlerinin etkilerini karşılaştırarak değerlendirmeyi amaçlamıştır.
Yöntem: Toplamda üç farklı DNA izolasyon yöntemi (salting-out, kit bazlı ve Trizol bazlı) dört farklı doku türü (gonad, tentakül, epidermis ve gastrodermis) üzerinde uygulanmış, her biri Proteinaz K ile 0, 1, 3 ve 24 saat inkübasyona tabi tutulmuştur. Böylece 48 farklı kombinasyon analiz edilmiştir.
Bulgular: En yüksek DNA konsantrasyonları gonad dokularında elde edilmiş olup bu durum, dokunun yüksek hücresel yoğunluğu ve yapısal bütünlüğü ile ilişkilendirilmiştir. Özellikle 1–3 saatlik Proteinaz K uygulamasıyla birlikte salting-out yöntemi, diğer iki yönteme kıyasla daha yüksek verim sağlamıştır. Aşırı nemli olan epidermis ve gastrodermis dokularında ise yaş ağırlık ölçümünde sapmalar oluşmuş ve bu durum biyolojik girdiye göre DNA veriminin olduğundan düşük hesaplanmasına neden olmuştur.
Sonuç: Jelatinöz denizel omurgasızlardan DNA izolasyonunda doku seçimi, enzimatik inkübasyon süresi ve kullanılan metodoloji büyük önem taşımaktadır. Aurelia aurita örneklerinde, özellikle gonad dokusuna 1–3 saatlik Proteinaz K uygulaması ile salting-out yöntemi kullanımı, verimli ve güvenilir bir DNA izolasyonu için önerilmektedir.

Keywords

DNA izolasyonu , DNA ekstraksiyonu , Aurelia aurita , tuzla çöktürme yöntemi , DNA verimi

Project Number

FLO-2024-40848

References

[1] Putnam, N., Srivastava, M., Hellsten, U., Dirks, B., Chapman, J., … & Salamov, A. (2007). Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science, 317. https://doi.org/10.1126/science.1139158
[2] Park, E., Hwang, D.S., Lee, J.-S., Song, J.-I., Seo, T.-K., & Won, Y.-J. (2012). Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record. Molecular Phylogenetics and Evolution, 62(1), 329–345. https://doi.org/10.1016/j.ympev.2011.10.008
[3] Purcell, J. E., Uye, S., & Lo, W. (2007). Anthropogenic causes of jellyfish blooms and their direct consequences for humans: A review. Marine Ecology Progress Series, 350, 153–174. https://doi.org/10.3354/meps07093
[4] Condon, R. H., Steinberg, D. K., del Giorgio, P. A., Bouvier, T. C., Bronk, D. A., … & Graham, W. M. (2011). Jellyfish blooms result in a major microbial respiratory sink of carbon in marine systems. Proceedings of the National Academy of Sciences, 108(25), 10225–10230. https://doi.org/10.1073/pnas.1015782108
[5] Brekhman, V., Malik, A., Haas, B., (2015). Transcriptome profiling of the dynamic life cycle of the scyphozoan jellyfish Aurelia aurita. BMC Genomics, 16(74). https://doi.org/10.1186/s12864-015-1320-z
[6] Purcell, J. E. (2007). Environmental effects on asexual reproduction rates of the scyphozoan Aurelia labiata. Marine Ecology Progress Series, 348, 183–196. https://doi.org/10.3354/meps07056
[7] Miller, M.-E. C., & Graham, W. M. (2012). Environmental evidence that seasonal hypoxia enhances survival and success of jellyfish polyps in the northern Gulf of Mexico. Journal of Experimental Marine Biology and Ecology, 432–433, 113–120. https://doi.org/10.1016/j.jembe.2012.07.015
[8] Fuchs, B., Wang, W., Graspeuntner, S., Li, Y., Insua, S., Herbst, E., ... & Khalturin, K. (2014). Regulation of polyp-to-jellyfish transition in Aurelia aurita. Current Biology, 24(3), 263–268. https://doi.org/10.1016/j.cub.2013.12.003
[9] Lucas, C. H., & Dawson, M. N. (2014). What are jellyfishes and thaliaceans and why do they bloom? In Jellyfish Blooms (pp. 9–44). Springer. https://doi.org/10.1007/978-94-007-7015-7_2
[10] Brotz, L., Cheung, W. W. L., Kleisner, K., Pakhomov, E., … & Pauly, D. (2012). Increasing jellyfish populations: Trends in large marine ecosystems. Hydrobiologia, 690(1), 3–20. https://doi.org/10.1007/s10750-012-1039-7
[11] Goldstein, J., & Steiner, U. K. (2019). Ecological drivers of jellyfish blooms: The complex life history of a ‘well‐known’ medusa (Aurelia aurita). Journal of Animal Ecology, 89(3), 697–707. https://doi.org/10.1111/1365-2656.13147
[12] Purcell, J. E. (2011). Jellyfish and ctenophore blooms coincide with human proliferations and environmental perturbations. Annual Review of Marine Science, 4(1), 209–235. https://doi.org/10.1146/annurev-marine-120709-142751
[13] Richardson, A. J., Bakun, A., Hays, G. C., & Gibbons, M. J. (2009). The jellyfish joyride: Causes, consequences and management responses to a more gelatinous future. Trends in Ecology & Evolution, 24(6), 312–322. https://doi.org/10.1016/j.tree.2009.01.010
[14] Brown, D. D., & Cai, L. (2007). Amphibian metamorphosis. Developmental Biology, 306(1), 20–33. https://doi.org/10.1016/j.ydbio.2007.03.021
[15] McBrayer, Z., Ono, H., Shimell, M., Parvy, J., Beckstead, R. B., Warren, J. T., ... & O’Connor, M. B. (2007). Prothoracicotropic hormone regulates developmental timing and body size in Drosophila. Developmental Cell, 13(6), 857–871. https://doi.org/10.1016/j.devcel.2007.11.003
[16] Laudet, V. (2011). The origins and evolution of vertebrate metamorphosis. Current Biology, 21(18), R726–R737. https://doi.org/10.1016/j.cub.2011.07.030
[17] Miglioli, A., Canesi, L., Gomes, I. D. L., Schubert, M., & Dumollard, R. (2021). Nuclear receptors and development of marine invertebrates. Genes, 12(1), 52. https://doi.org/10.3390/genes12010083
[18] Fujita, S., Kuranaga, & E., Nakajima, Y. (2021). Regeneration potential of jellyfish: Cellular mechanisms and molecular insights. Genes, 12(5), 758. https://doi.org/10.3390/genes12050758
[19] Cunningham, K., Anderson, D. J., & Weissbourd, B. (2024). Jellyfish for the study of nervous system evolution and function. Current Opinion in Neurobiology, 88, 102903. https://doi.org/10.1016/j.conb.2024.102903
[20] Kurchaba, N., Cassone, B. J., Northam, C., Ardelli, B. F., & LeMoine, C. M. R. (2020). Effects of MP polyethylene microparticles on microbiome and inflammatory response of larval zebrafish. Toxics, 8(3), 55. https://doi.org/10.3390/toxics8030055
[21] Yang, B., Liu, B., & Chen, Z. (2020). DNA Extraction with TRIzol Reagent Using a Silica Column. Analytical Sciences, 37(7), 1033–1037. https://doi.org/10.2116/analsci.20p361
[22] Sugrue, V. J., Prescott, M., Glendining, K. A., Bond, D. M., Horvath, S., Anderson, G. M., ... & Hore, T. A. (2025). The androgen clock is an epigenetic predictor of long-term male hormone exposure. Proceedings of the National Academy of Sciences, 122(3), e2420087121. https://doi.org/10.1073/pnas.2420087121
[23] Martínez, G., Shaw, E. M., Carrillo, M., & Zanuy, S. (1998). Protein Salting-Out Method Applied to Genomic DNA Isolation from Fish Whole Blood. BioTechniques, 24(2), 238–239. https://doi.org/10.2144/98242bm14
[24] Desjardins, P., & Conklin, D. (2010). NanoDrop Microvolume Quantitation of nucleic acids. Journal of Visualized Experiments, 1. https://doi.org/10.3791/2565
[25] Sthle, L., & Wold, S. (1989). Analysis of variance (ANOVA). Chemometrics and Intelligent Laboratory Systems, 6(4), 259–272. https://doi.org/10.1016/0169-7439(89)80095-4
[26] Sevindik, E., Coşkun, F., Selvi, S., & Alkaç, S. A. (2013). Comparative analysis of the genomic DNA isolation methods on some Silene L. (Caryophyllaceae). Biological Diversity and Conservation, 6(3), 67-71.
[27] Dawson, M. N., & Jacobs, D. K. (2001). Molecular evidence for cryptic species of Aurelia aurita (Cnidaria, Scyphozoa). Biological Bulletin, 200(1), 92–96. https://doi.org/10.2307/1543089
[28] Morrissey, S. J., Jerry, D. R., & Kingsford, M. J. (2022). Genetic Detection and a Method to Study the Ecology of Deadly Cubozoan Jellyfish. Diversity, 14(12), 1139. https://doi.org/10.3390/d14121139
[29] Ortman, B. D., Bucklin, A., Pagès, F., & Youngbluth, M. (2010). DNA barcoding the Medusozoa using mtCOI. Hydrobiologia, 645, 3–16. https://doi.org/10.1016/j.dsr2.2010.09.017
[30] Shao, Z., Chen, Q., Wu, S., Zhang, M., & Xu, P. (2021). Mitochondrial genome of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa): A linear DNA molecule lacking tRNA genes. Frontiers in Marine Science, 8, 640527. https://doi.org/10.3389/fmars.2021.640527
[31] Minamoto, T., Miya, M., Sado, T., Seino, S., Doi, H., Kondoh, M., ... & Takahara, T. (2017). High-throughput sequencing of environmental DNA from jellyfish. PLoS One, 12(3), e0173073. https://doi.org/10.1371/journal.pone.017307
[32] Takahashi S, Sakata MK, Minamoto T, & Masuda R. (2020) Comparing the efficiency of open and enclosed filtration systems in environmental DNA quantification for fish and jellyfish. PLoS One. 15(4), e0231718. https://doi.org/10.1371/journal.pone.0231718
[33] Ogata, M., Masuda, R., & Harino, H. (2021). Environmental DNA preserved in marine sediment for detecting jellyfish blooms after a tsunami. Scientific Reports, 11, 16830. https://doi.org/10.1038/s41598-021-94286-2

Evaluating yield of DNA extraction methods across different tissues of moon jellyfish Aurelia aurita (Linnaeus, 1758)

Year 2025, Volume: 18 Issue: 3, 291 - 300

Sümeyra Zeynep Çalıcı , Buse Bayrak , Hatice Buse Yavuz , Nida Kelel , Zeynep Aslıhan Avşaroğlu , Merve Nur Aydemir

https://doi.org/10.46309/biodicon.2025.1697734

Abstract

Purpose: This study aimed to optimize DNA extraction from the moon jellyfish Aurelia aurita, a gelatinous marine invertebrate, by comparing different methodologies and evaluating the influence of tissue type and Proteinase K treatment duration on DNA yield.
Method: A total of 48 different combinations were tested using three extraction methods (salting-out, kit-based, and Trizol-based) across four tissue types (gonads, tentacles, epidermis, and gastrodermis). Each method was applied with varying Proteinase K incubation times (0, 1, 3, and 24 hours) to assess their impact on DNA yield and integrity.
Findings: Gonadal tissues consistently provided the highest DNA concentrations, likely due to their relatively high cellular density and structural robustness. Among the methods, the salting-out protocol yielded superior results, particularly with 1–3 hours of Proteinase K incubation. In contrast, highly hydrated tissues such as epidermis and gastrodermis led to underestimated yields due to distorted wet weight measurements.
Conclusion: Tissue selection, enzymatic treatment time, and extraction methodology critically affect DNA recovery from jellyfish. The salting-out method, when applied to gonadal tissue with moderate Proteinase K incubation, is recommended for efficient and reliable DNA isolation from Aurelia aurita.

Keywords

DNA isolation , DNA extraction , Aurelia aurita , salting-out method , DNA yield

Ethical Statement

Not applicable.

Supporting Institution

Scientific Research Projects Coordination Unit (BAP) of Istanbul University

Project Number

FLO-2024-40848

Thanks

Dr. Habeş Bilal AYDEMİR and Dr. Esra SU

References

[1] Putnam, N., Srivastava, M., Hellsten, U., Dirks, B., Chapman, J., … & Salamov, A. (2007). Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science, 317. https://doi.org/10.1126/science.1139158
[2] Park, E., Hwang, D.S., Lee, J.-S., Song, J.-I., Seo, T.-K., & Won, Y.-J. (2012). Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record. Molecular Phylogenetics and Evolution, 62(1), 329–345. https://doi.org/10.1016/j.ympev.2011.10.008
[3] Purcell, J. E., Uye, S., & Lo, W. (2007). Anthropogenic causes of jellyfish blooms and their direct consequences for humans: A review. Marine Ecology Progress Series, 350, 153–174. https://doi.org/10.3354/meps07093
[4] Condon, R. H., Steinberg, D. K., del Giorgio, P. A., Bouvier, T. C., Bronk, D. A., … & Graham, W. M. (2011). Jellyfish blooms result in a major microbial respiratory sink of carbon in marine systems. Proceedings of the National Academy of Sciences, 108(25), 10225–10230. https://doi.org/10.1073/pnas.1015782108
[5] Brekhman, V., Malik, A., Haas, B., (2015). Transcriptome profiling of the dynamic life cycle of the scyphozoan jellyfish Aurelia aurita. BMC Genomics, 16(74). https://doi.org/10.1186/s12864-015-1320-z
[6] Purcell, J. E. (2007). Environmental effects on asexual reproduction rates of the scyphozoan Aurelia labiata. Marine Ecology Progress Series, 348, 183–196. https://doi.org/10.3354/meps07056
[7] Miller, M.-E. C., & Graham, W. M. (2012). Environmental evidence that seasonal hypoxia enhances survival and success of jellyfish polyps in the northern Gulf of Mexico. Journal of Experimental Marine Biology and Ecology, 432–433, 113–120. https://doi.org/10.1016/j.jembe.2012.07.015
[8] Fuchs, B., Wang, W., Graspeuntner, S., Li, Y., Insua, S., Herbst, E., ... & Khalturin, K. (2014). Regulation of polyp-to-jellyfish transition in Aurelia aurita. Current Biology, 24(3), 263–268. https://doi.org/10.1016/j.cub.2013.12.003
[9] Lucas, C. H., & Dawson, M. N. (2014). What are jellyfishes and thaliaceans and why do they bloom? In Jellyfish Blooms (pp. 9–44). Springer. https://doi.org/10.1007/978-94-007-7015-7_2
[10] Brotz, L., Cheung, W. W. L., Kleisner, K., Pakhomov, E., … & Pauly, D. (2012). Increasing jellyfish populations: Trends in large marine ecosystems. Hydrobiologia, 690(1), 3–20. https://doi.org/10.1007/s10750-012-1039-7
[11] Goldstein, J., & Steiner, U. K. (2019). Ecological drivers of jellyfish blooms: The complex life history of a ‘well‐known’ medusa (Aurelia aurita). Journal of Animal Ecology, 89(3), 697–707. https://doi.org/10.1111/1365-2656.13147
[12] Purcell, J. E. (2011). Jellyfish and ctenophore blooms coincide with human proliferations and environmental perturbations. Annual Review of Marine Science, 4(1), 209–235. https://doi.org/10.1146/annurev-marine-120709-142751
[13] Richardson, A. J., Bakun, A., Hays, G. C., & Gibbons, M. J. (2009). The jellyfish joyride: Causes, consequences and management responses to a more gelatinous future. Trends in Ecology & Evolution, 24(6), 312–322. https://doi.org/10.1016/j.tree.2009.01.010
[14] Brown, D. D., & Cai, L. (2007). Amphibian metamorphosis. Developmental Biology, 306(1), 20–33. https://doi.org/10.1016/j.ydbio.2007.03.021
[15] McBrayer, Z., Ono, H., Shimell, M., Parvy, J., Beckstead, R. B., Warren, J. T., ... & O’Connor, M. B. (2007). Prothoracicotropic hormone regulates developmental timing and body size in Drosophila. Developmental Cell, 13(6), 857–871. https://doi.org/10.1016/j.devcel.2007.11.003
[16] Laudet, V. (2011). The origins and evolution of vertebrate metamorphosis. Current Biology, 21(18), R726–R737. https://doi.org/10.1016/j.cub.2011.07.030
[17] Miglioli, A., Canesi, L., Gomes, I. D. L., Schubert, M., & Dumollard, R. (2021). Nuclear receptors and development of marine invertebrates. Genes, 12(1), 52. https://doi.org/10.3390/genes12010083
[18] Fujita, S., Kuranaga, & E., Nakajima, Y. (2021). Regeneration potential of jellyfish: Cellular mechanisms and molecular insights. Genes, 12(5), 758. https://doi.org/10.3390/genes12050758
[19] Cunningham, K., Anderson, D. J., & Weissbourd, B. (2024). Jellyfish for the study of nervous system evolution and function. Current Opinion in Neurobiology, 88, 102903. https://doi.org/10.1016/j.conb.2024.102903
[20] Kurchaba, N., Cassone, B. J., Northam, C., Ardelli, B. F., & LeMoine, C. M. R. (2020). Effects of MP polyethylene microparticles on microbiome and inflammatory response of larval zebrafish. Toxics, 8(3), 55. https://doi.org/10.3390/toxics8030055
[21] Yang, B., Liu, B., & Chen, Z. (2020). DNA Extraction with TRIzol Reagent Using a Silica Column. Analytical Sciences, 37(7), 1033–1037. https://doi.org/10.2116/analsci.20p361
[22] Sugrue, V. J., Prescott, M., Glendining, K. A., Bond, D. M., Horvath, S., Anderson, G. M., ... & Hore, T. A. (2025). The androgen clock is an epigenetic predictor of long-term male hormone exposure. Proceedings of the National Academy of Sciences, 122(3), e2420087121. https://doi.org/10.1073/pnas.2420087121
[23] Martínez, G., Shaw, E. M., Carrillo, M., & Zanuy, S. (1998). Protein Salting-Out Method Applied to Genomic DNA Isolation from Fish Whole Blood. BioTechniques, 24(2), 238–239. https://doi.org/10.2144/98242bm14
[24] Desjardins, P., & Conklin, D. (2010). NanoDrop Microvolume Quantitation of nucleic acids. Journal of Visualized Experiments, 1. https://doi.org/10.3791/2565
[25] Sthle, L., & Wold, S. (1989). Analysis of variance (ANOVA). Chemometrics and Intelligent Laboratory Systems, 6(4), 259–272. https://doi.org/10.1016/0169-7439(89)80095-4
[26] Sevindik, E., Coşkun, F., Selvi, S., & Alkaç, S. A. (2013). Comparative analysis of the genomic DNA isolation methods on some Silene L. (Caryophyllaceae). Biological Diversity and Conservation, 6(3), 67-71.
[27] Dawson, M. N., & Jacobs, D. K. (2001). Molecular evidence for cryptic species of Aurelia aurita (Cnidaria, Scyphozoa). Biological Bulletin, 200(1), 92–96. https://doi.org/10.2307/1543089
[28] Morrissey, S. J., Jerry, D. R., & Kingsford, M. J. (2022). Genetic Detection and a Method to Study the Ecology of Deadly Cubozoan Jellyfish. Diversity, 14(12), 1139. https://doi.org/10.3390/d14121139
[29] Ortman, B. D., Bucklin, A., Pagès, F., & Youngbluth, M. (2010). DNA barcoding the Medusozoa using mtCOI. Hydrobiologia, 645, 3–16. https://doi.org/10.1016/j.dsr2.2010.09.017
[30] Shao, Z., Chen, Q., Wu, S., Zhang, M., & Xu, P. (2021). Mitochondrial genome of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa): A linear DNA molecule lacking tRNA genes. Frontiers in Marine Science, 8, 640527. https://doi.org/10.3389/fmars.2021.640527
[31] Minamoto, T., Miya, M., Sado, T., Seino, S., Doi, H., Kondoh, M., ... & Takahara, T. (2017). High-throughput sequencing of environmental DNA from jellyfish. PLoS One, 12(3), e0173073. https://doi.org/10.1371/journal.pone.017307
[32] Takahashi S, Sakata MK, Minamoto T, & Masuda R. (2020) Comparing the efficiency of open and enclosed filtration systems in environmental DNA quantification for fish and jellyfish. PLoS One. 15(4), e0231718. https://doi.org/10.1371/journal.pone.0231718
[33] Ogata, M., Masuda, R., & Harino, H. (2021). Environmental DNA preserved in marine sediment for detecting jellyfish blooms after a tsunami. Scientific Reports, 11, 16830. https://doi.org/10.1038/s41598-021-94286-2

There are 33 citations in total.

Details

Primary Language	English
Subjects	Genetics (Other), Zoology (Other)
Journal Section	Research Articles
Authors	Sümeyra Zeynep Çalıcı 0009-0006-0348-1884 Buse Bayrak 0009-0000-6916-5776 Hatice Buse Yavuz 0009-0008-1919-3910 Nida Kelel 0009-0002-5540-9981 Zeynep Aslıhan Avşaroğlu 0009-0004-9084-2515 Merve Nur Aydemir 0000-0001-6328-626X
Project Number	FLO-2024-40848
Early Pub Date	September 25, 2025
Publication Date	October 4, 2025
Submission Date	May 12, 2025
Acceptance Date	August 13, 2025
Published in Issue	Year 2025 Volume: 18 Issue: 3

Cite

APA	Çalıcı, S. Z., Bayrak, B., Yavuz, H. B., … Kelel, N. (2025). Evaluating yield of DNA extraction methods across different tissues of moon jellyfish Aurelia aurita (Linnaeus, 1758). Biological Diversity and Conservation, 18(3), 291-300. https://doi.org/10.46309/biodicon.2025.1697734

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