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Genomic insights into the evolutionary origin of Myxozoa within Cnidaria
Open accessAbstract
The Myxozoa comprise over 2,000 species of microscopic obligate parasites that use both invertebrate and vertebrate hosts as part of their life cycle. Although the evolutionary origin of myxozoans has been elusive, a close relationship with cnidarians, a group that includes corals, sea anemones, jellyfish, and hydroids, is supported by some phylogenetic studies and the observation that the distinctive myxozoan structure, the polar capsule, is remarkably similar to the stinging structures (nematocysts) in cnidarians. To gain insight into the extreme evolutionary transition from a free-living cnidarian to a microscopic endoparasite, we analyzed genomic and transcriptomic assemblies from two distantly related myxozoan species, Kudoa iwatai and Myxobolus cerebralis, and compared these to the transcriptome and genome of the less reduced cnidarian parasite, Polypodium hydriforme. A phylogenomic analysis, using for the first time to our knowledge, a taxonomic sampling that represents the breadth of myxozoan diversity, including four newly generated myxozoan assemblies, confirms that myxozoans are cnidarians and are a sister taxon to P. hydriforme. Estimations of genome size reveal that myxozoans have one of the smallest reported animal genomes. Gene enrichment analyses show depletion of expressed genes in categories related to development, cell differentiation, and cell-cell communication. In addition, a search for candidate genes indicates that myxozoans lack key elements of signaling pathways and transcriptional factors important for multicellular development. Our results suggest that the degeneration of the myxozoan body plan from a free-living cnidarian to a microscopic parasitic cnidarian was accompanied by extreme reduction in genome size and gene content.
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In the citing paper
“Thus, while strong support for Ctenophora-sister may be obtained from phylogenomic datasets (2 -6, 46, 55), our analysis suggests these results are caused by undetected systematic bias.”
From Genomic data do not support comb jellies as the sister group to all other animals (2015) · cites this paper as [55]
Experimental — accuracy not yet measuredIn the citing paper
“The topologies from Chang and Feuda are based on the same data set which is made up of 51,940 amino acid positions from 78 taxa representing a wide range of animals and 9 non-animal outgroups.”
From Six-state amino acid recoding is not an effective strategy to offset the effects of compositional heterogeneity and saturation in phylogenetic analyses (2019) · cites this paper as Chang et al. 2015
In the citing paper
“Porifera-sister generally [6], but not invariably [12, 38], emerges when site-specific differences in amino acid composition are modeled and distant outgroups (e.g., Fungi) are not included in the analyses.”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [12]
In the citing paper
“We show that two key phylogenomic datasets that previously supported Ctenophora-sister [10, 12] display strong heterogeneity in amino acid composition across sites and taxa”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [12]
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Cnidarian toxins: omics approaches and recombinant proteins
Vega-Tamayo, J. E., Alcantar-Orozco, E. D. J., Mendoza-Ramírez, R. A., Silva-Díaz, L. G., Aguilar-Salazar, J. A., Salvador-Aguilar, D. H., & Rojas‐Molina, A. (2025) · The Journal of venomous animals and toxins including tropical diseases · doi:10.1590/1678-9199-jvatitd-2025-0019 · Cited by 3
“Lastly, Endocnidozoa is a recently identified group that includes highly simplified parasitic species (e.g., Myxozoa), which inhabit their hosts and have lost many of the typical features of cnidarians [1,2].”
Genomes: Miniaturization Taken to Extremes
Giribet, G. (2020) · Current Biology · doi:10.1016/j.cub.2020.02.044 · Cited by 3
Tournière, O., Busengdal, H., Gahan, J. M., & Rentzsch, F. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-3766-1_4 · Cited by 2
Saltational Episodes of Reticulate Evolution in the Drosophila saltans Species Group
Prediger, C., Ferreira, E. A., Zorzato, S. V., Hua‐Van, A., Klasson, L., Miller, W. J., Yassin, A., & Madi-Ravazzi, L. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae250 · Cited by 5
Epidemiology of Polypodium hydriforme in American Paddlefish
Okamura, B., Hartigan, A., Long, P. F., Ruggeri, P., Smith‐Easter, K., & Schooley, J. D. (2020) · Journal of Fish Diseases · doi:10.1111/jfd.13202 · Cited by 3
Hine, P. M., Morris, D. J., Azevedo, C., Feist, S. W., & Casal, G. (2020) · Parasitology · doi:10.1017/s0031182020001717 · Cited by 3
“…polar capsules similar to cnidarian nematocysts (Lom and de Puytorac, 1965) and now myxozoans are recognized as cnidarians (Siddall et al., 1995; Jiménez-Guri et al., 2007) that form a sister clade to the cnidarian parasite Polypodium hydriforme (Chang et al., 2015; Foox and Siddall, 2015).”
BackgroundChong, R. S.-M. (2022) · Elsevier eBooks · doi:10.1016/b978-0-12-812211-2.00044-5 · Cited by 2
Kaneko, T., Tanaka, S., Sugiyama, M., Kaise, S., Inui, H., & Ushida, K. (2024) · Glycobiology · doi:10.1093/glycob/cwae090 · Cited by 2
The Notch pathway in Metazoa: a comparative analysis across cnidarians and beyond
Lövy, A., Kyslík, J., Picard‐Sánchez, A., Holzer, A. S., Krejčí, A., & Fiala, I. (2025) · EvoDevo · doi:10.1186/s13227-025-00246-6 · Cited by 2
“This reduction extends to their genome, with sizes ranging from 22,5 to 206 Mb and a limited gene repertoire [21, 22].”
Couso-Pérez, S., Rangel, L. F., Santos, M. J., Ares-Mazás, E., & Goméz-Couso, H. (2021) · Parasitology Research · doi:10.1007/s00436-021-07201-z · Cited by 2
Checklists of Protozoans and Myxozoans of Freshwater and Marine Fishes of Basrah Province, Iraq
Mhaisen, F. T., Ali, A. H., & Khamees, N. R. (2022) · Mesopotamian Journal of Marine Sciences · doi:10.58629/mjms.v31i1.108 · Cited by 2
“A recent phylogenomic analysis demonstrated by Chang et al. (2015) confirmed that myxozoans are cnidarians.”
BackgroundThe compact genome of the sponge Oopsacas minuta (Hexactinellida) is lacking key metazoan core genesPreprint
Santini, S., Schenkelaars, Q., Jourda, C., Duschene, M., Belahbib, H., Rocher, C., Selva, M., Riesgo, A., Vervoort, M., Leys, S. P., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.26.501511 · Cited by 2
Morphological data, phylogenomics and recalcitrant nodes
DeSalle, R., & Tessler, M. (2025) · Cladistics · doi:10.1111/cla.12615 · Cited by 2
“For molecules, we used 12 phylogenomic datasets (ch1, ch2, ch3, ch4, wh1, wh2, wh3, wh4, si1, si2, si3, rye, ryg; see Ryan et al., 2013; Chang et al., 2015; Whelan et al., 2015; Simion et al., 2017; Neumann et al., 2021).”
Fleming, J. F., & Struck, T. H. (2026) · Systematic Biology · doi:10.1093/sysbio/syag009 · Cited by 1
“These data sets, originally based on the Chang et al. (2015) tree, were generated by applying a scaling factor to all branches of the original tree, from 1 to 20.”
Law, S. T. S., Li, Y., Li, C., Nong, W., Chan, K. K. L., Or, C. K. M., Qiu, J., & Hui, J. H. L. (2026) · BMC Biology · doi:10.1186/s12915-026-02579-7 · Cited by 1
“…in sequencing technologies, a wealth of genomic resources has been amassed over the last decade for different cnidarian taxa, including the corals [1–3], sea anemones [4–7], hydroids [8, 9], myxozoans [10, 11], true jellyfishes/scyphozoans[12], and stalked jellyfishes/ staurozoans [13].”
Single-cell analyses of tissue regeneration in two true jellyfish
Li, Y. X., Law, S. T. S., Nong, W., So, W. L., Xie, Y., Leung, T. C. N., Li, T. H., Tse, J. K. Y., Yip, H. Y., Jin, O., et al. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag128 · Cited by 1
Kudoa ogawai (Myxosporea: Kudoidae) Infection in Cultured Olive Flounder Paralichthys olivaceus
Shin, S. P., Jin, C. N., Sohn, H. C., & Lee, J. (2019) · Korean Journal of Parasitology · doi:10.3347/kjp.2019.57.4.439 · Cited by 1
“439 Myxozoans are parasites that complete a life cycle through vertebrate (mainly fish) and invertebrate (mainly annelid) hosts [1].”
BackgroundLigrone, R. (2019) · Springer eBooks · doi:10.1007/978-3-030-16057-9_8 · Cited by 1
Parasitología comparada. Modelos parasitarios
Radman, N. E., Gamboa, M. I., & Mastrantonio, F. (2023) · doi:10.35537/10915/148720 · Cited by 1
Computational genomics for understanding of DNA-DNA and protein-protein similarity
Sarin, H. (2023) · Elsevier eBooks · doi:10.1016/b978-0-323-90995-2.00004-7 · Cited by 1
Spore-forming parasites infecting muscles of freshwater fishes : ecology and epidemiology
Ahonen, H. (2017) · Jyväskylä University Digital Archive (University of Jyväskylä) · Cited by 1
Shostak, S. (2021) · Wiley eBooks · doi:10.1002/9780470015902.a0029250 · Cited by 1
Guruacharya, A. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.03.11.532225 · Cited by 1
“However, myxozoans have been reported to have undergone an extreme reduction in genome size and gene content (44), thus many neurotoxin and ion channel genes may have been lost since their divergence from free living ancestors.”
BackgroundThe highly repetitive genome of Myxobolus sp., a myxozoan parasite of fathead minnowsPreprint
Muthye, V., Leon‐Coria, A., Liu, H., Finney, C. A. M., Goater, C. P., & Wasmuth, J. D. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.09.579586 · Cited by 1
Light-induced oocyte maturation in the hydrozoan clytia hemisphaerica
Quiroga-Artigas, G. (2017) · theses.fr (ABES) · doi:10.70675/df70f614z7812z4366z9e5bz28f0d76ac26b · Cited by 1
Ahonen, H. S., Koskinen, H., Valtonen, E. T., & Taskinen, J. (2016) · Aquaculture · doi:10.1016/j.aquaculture.2016.12.018
Phylogeny: Eukaryotes to Chordates
Berman, J. J. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-817126-4.00005-9
Metadata
- Authors
- Chang, E. S., Neuhof, M., Rubinstein, N. D., Diamant, A., Philippe, H., Huchon, D., & Cartwright, P.
- Affiliations
- University of Kansas (US)
- Tel Aviv University (IL)
- Harvard University (US)
- Israel Oceanographic and Limnological Research (IL)
- Centre National de la Recherche Scientifique (FR)
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2015-11-16
- Volume
- 112
- Issue
- 48
- Pages
- 14912-14917
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC4672818
- OpenAlex
- W2176109601
- Cited by
- 262
- References
- 67
- Citations by year
- 2026: 9 · 2025: 10 · 2024: 18 · 2023: 19 · 2022: 26 · 2021: 47 · 2020: 28 · 2019: 24 · 2018: 29 · 2017: 26 · 2016: 25 · 2015: 1
- FWCI
- 8.92
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- KU ScholarWorks (University of Kansas) (submittedVersion, other-oa)
- Funders
- NSF | BIO | Division of Environmental Biology (0953571)
- NSF | BIO | Division of Integrative Organismal Systems (1321759)
- Israel Science Foundation (663/10)
- United States-Israel Binational Science Foundation (2012768)
- Topics
- Life Sciences › Immunology and Microbiology › Parasitology › Myxozoan Parasites in Aquatic Species
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Marine Invertebrate Physiology and Ecology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Myxozoa, Cnidaria, evolutionary origin, phylogenomics, Myxobolus cerebralis, polar capsules, nematocysts, genome size reduction, gene enrichment analysis, genome assembly
- MeSH terms
- Animals, Phylogeny, Genome, Evolution, Molecular, Genomics, Polypodium, Myxobolus
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