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Cited by 2Coral and Marine Ecosystems StudiesProtist diversity and phylogenyMarine Invertebrate Physiology and Ecology

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Positive Selection of a Starch Synthesis Gene and Phenotypic Differentiation of Starch Accumulation in Symbiotic and Free-Living Coral Symbiont Dinoflagellate Species

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Ishii, Yuu, Kanamori, Shunsuke, Deguchi, Ryusaku, Kawata, Masakado, Maruyama, Shinichiro, Yoshida, Takashi, Kamikawa, Ryoma·2025·Genome Biology and Evolution
DOI 10.1093/gbe/evaf133PMC PMC12284398

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Abstract

Symbiosis is a basis for species diversification through interactions between organisms. In tropical and subtropical oceans, dinoflagellate symbionts belonging to the family Symbiodiniaceae, including the genus Symbiodinium, support the flourishment of cnidarian hosts, including corals, and thereby the ecology of oligotrophic oceans through their photosynthate carbon transfers. Although the genus Symbiodinium includes both free-living and symbiotic species, the detailed genetic background of their lifestyle differences remains unclear. In this study, we identified candidate genes involved in the evolutionary acquisition or maintenance of symbiosis in Symbiodinium spp. by detecting genes that have undergone positive selection during symbiotic and free-living lifestyle diversification. Using multiple Symbiodinium genomes to detect positive selection, 35 genes were identified, including a gene encoding soluble starch synthase SSY1 and genes related to metabolite secretion, which may be preferred for symbiotic lifestyles. In particular, our in silico analyses revealed that the SSY1 gene family has undergone extensive gene duplications in an ancestral dinoflagellate, and that the mutations detected as positive selection have occurred in the intrinsically disordered region of one of the homologs. Consistent with molecular evolution, the phenotypes of intracellular starch synthesis/accumulation were distinct between the symbiotic and free-living species of Symbiodinium when cultured under different pH and nitrogen conditions. These results provide molecular and phenotypic insights into symbiotic Symbiodinium-coral relationships.

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Metadata

Authors
Ishii, Y., Kanamori, S., Deguchi, R., Kawata, M., Maruyama, S., Yoshida, T., & Kamikawa, R.
Affiliations
  • Kyoto University (JP)
  • Tohoku University (JP)
  • Miyagi University of Education (JP)
  • The University of Tokyo (JP)
Corresponding author
  • Ishii, Yuu
  • Maruyama, Shinichiro
  • Kamikawa, Ryoma
ORCID
Venue
Genome Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2025-07
Volume
17
Issue
7
ISSN
1759-6653 (ISSN-L)
DOI
10.1093/gbe/evaf133
PMC
PMC12284398
OpenAlex
W4411965598
Cited by
2
References
3
Citations by year
2026: 1 · 2025: 1
FWCI
1.06
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome Biology and Evolution (publishedVersion, cc-by-nc)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • Institutional Repositories DataBase (IRDB) (submittedVersion)
  • Kyoto University Research Information Repository (Kyoto University) (submittedVersion, cc-by-nc)
Funders
  • JSPS KAKENHI (20K15871, 23KJ2228, 24K18190, 23K23960, 23H04962, 24H01462, 24K21929, 25K02334, 21H05057)
  • Starch Technologies Co., Ltd
Topics
  • Physical Sciences › Environmental Science › Ecology › Coral and Marine Ecosystems Studies
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Protist diversity and phylogeny
  • Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Marine Invertebrate Physiology and Ecology
Keywords
Symbiodinium, zooxanthellae, coral symbiosis, positive selection, starch accumulation, gene duplication, intrinsically disordered regions, metabolite secretion, coral-algal symbiosis
MeSH terms
Animals, Dinoflagellida, Phenotype, Phylogeny, Selection, Genetic, Starch, Starch Synthase, Symbiosis, Evolution, Molecular, Anthozoa

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