Under submission
Yoshioka et al. The mitochondrial genome of Palythoa tuberculosa (Esper, 1805) contains a novel ORF with unknown function. (Preprint is available on bioRxiv)
Published (Peer-reviewed)
* Corresponding author; † equal contribution
First/corresponding author on 17 papers; co-author on 24 papers.
2026
41. A dataset for forty complete bacterial genome sequences in cultures of the toxic dinoflagellate Ostreopsis cf. ovata.
Yoshioka Y, Ando C, Yamashita H, Kawamitsu M, Kawachi M, Tsunematsu Y*, and Shoguchi E*.
Data in Brief (accepted) (2026)
40. Efficiency of scleractinian-specific eDNA metabarcoding using specimens from Okinawa Churaumi Aquarium, Japan.
Narisoko H, Nagata F, Hisata K, Fujie M, Yoshioka Y, Nonaka M, Satoh N, and Nishitsuji K.
Zoological Science, 43(2), (in press) (2026).
39. Mitochondrial genomic datasets for 32 coral reef decapods from the Okinawa Archipelago.
Yoshioka Y†*, Kanai M†, Nagai T†, Gishitomi S, Nagata T, and Satoh N.
Data in Brief, 64, 112409 (2026).
38. The complete mitochondrial genome of Hanabira yukibana Lau, Stokvis, Imahara & Reimer, 2019 (Cnidaria: Anthozoa: Octocorallia).
Yoshioka Y†*, Kanai M†, Koido T†, Gishitomi S, Watanabe N, Satoh N, and Nagata T.
Mitochondrial DNA Part B, 11(1), 140–144 (2026).
37. The complete mitochondrial genomes of Litophyton sp. and Stereonephthya sp., members of family Nephtheidae (Cnidaria: Anthozoa: Octocorallia).
Yoshioka Y†*, Kanai M†, Koido T†, Satoh N, and Nagata T.
Mitochondrial DNA Part B, 11(1), 95–99 (2026).
2025
36. First genome sequences of the dinoflagellate Effrenium voratum strain isolated from the coral Hydnophora exesa in temperate Japanese region.
Yoshioka Y*, Kawachi M, Kawamitsu M, Murzabaev A, Satoh N, Shinzato C, and Shoguchi E*.
BMC Genomic Data, 26, 83 (2025). [Gene models can be found in Zenodo]
35. Molecular diversity of coral microbiomes shows no relationship with latitude in the western Pacific Ocean.
Gibu K*, Kise H, Yoshioka Y, Saito N, Nakajima Y, Sakai K, Suzuki A, Yasuda N, and Iguchi A.
Marine Ecology Progress Series, 772, 137–150 (2025).
34. Time-series RNA-seq of Acropora tenuis reveals molecular waves leading to synchronous mass spawning of scleractinian corals.
Yoshioka Y, Suzuki G*, Fujikura Y, Tashiro S, Uchida T, Shoguchi E, Satoh N, and Shinzato C*.
Molecular Ecology, 34(21), e70054 (2025). ● [プレスリリース]
33. An eDNA metabarcoding system for detecting scleractinian corals to the generic level along the Japanese coast.
Hisata K†, Nagata T†, Kanai M†, Sinniger F, Nagata F†, Suwa†, Yoshioka Y†, Harii S, Nonaka M, Fukami H, Arakaki S, Fujie M, Arakaki N, Zayasu Y, Narisoko H, Noda T, Koseki A, Nishitsuji K, Inoue J, Shinzato C, and Satoh N*.
Galaxea, Journal of Coral Reef Studies, 27(1), 13–29 (2025). ● [プレスリリース]
32. Complete mitochondrial genomes of Palauastrea ramosa Yabe & Sugiyama, 1941 and Stylocoeniella guentheri (Bassett-Smith, 1890) reveal their molecular phylogenetic position.
Yoshioka Y†*, Kanai M†, Tsuhako T, Satoh N, and Nagata T.
Galaxea, Journal of Coral Reef Studies, 27(1), 7–12 (2025).
31. Extensive mitochondrial genomic analyses reveal dynamic gene order rearrangements in the class Octocorallia (Cnidaria: Anthozoa).
Yoshioka Y†*, Kanai M†, Gishitomi S, Arakaki N, Koido T, Shinzato C, Inoue J, Nagata T*, and Satoh N*.
Gene Reports, 38, 102111 (2025).
30. Using underwater mini-ROV for coral eDNA survey: a case study in Okinawan mesophotic ecosystems
Satoh N*, Sinniger F, Narisoko H, Nagahama S, Okada N, Shimizu Y, Yoshioka Y, Hisata K, and Harii S.
Coral Reefs, 44, 209–219 (2025).
2024
29. Molecular phylogenetic position of the family Fungiidae (Cnidaria: Anthozoa) based on complete mitochondrial genome sequences.
Yoshioka Y*, Nagata F, Nonaka M, and Satoh N.
Galaxea, Journal of Coral Reef Studies, 26(1), 43–47 (2024).
28. Deciphering mechanisms of UV filter (benzophenone-3)- and high temperature-induced adverse effects in the coral Acropora tenuis, using ecotoxicogenomics.
Nishioka S, Miyata K, Inoue Y, Aoyama K, Yoshioka Y, Miura N, Yamane M, Honda H*, and Takagi T*.
Science of The Total Environment, 954, 176018 (2024). ● [プレスリリース]
27. Azooxanthellate Palythoa (Cnidaria: Anthozoa) genomes reveal toxin-related gene clusters and loss of neuronal genes in hexacorals.
Yoshioka Y, Yamashita H, Uchida T, Shinzato C, Kawamitsu M, Fourreau CJL, Castelló GM, Fiedler BK, van den Eeckhout TM, Borghi S, Reimer JD*, and Shoguchi E*.
Genome Biology and Evolution, 16(9), evae197 (2024). [Gene models can be found on Dryad]
26. Genome and tissue-specific transcriptomes of the large-polyp coral, Fimbriaphyllia (Euphyllia) ancora: a recipe for a coral polyp.
Shikina S*, Yoshioka Y, Chiu YL, Uchida T, Chen E, Cheng YC, Lin TC, Chu YL, Kanda M, Kawamitsu M, Fujie M, Takeuchi T, Zayasu Y, Satoh N, and Shinzato C*.
Communications Biology, 7, 899 (2024). ● [研究紹介] [Genome browser]
25. Asymmetric genetic population structures at the range edges of a mangrove whelk.
Hamamoto K, Iguchi A*, Gibu K, Ozawa H, Kojima M, Arakaki S, Yoshioka Y, Saito N, and Fujita Y*.
Science of The Total Environment, 934, 173248 (2024).
24. Genomic data reveal diverse biological characteristics of scleractinian corals and promote effective coral reef conservation.
Shinzato C* and Yoshioka Y.
Genome Biology and Evolution, 16(2), evae014 (2024).
23. Ontogenetic shifts in Symbiodiniaceae assemblages within cultured Acropora humilis across hatchery rearing and post-transplantation phases.
Jandang S*, Viyakarn V, Yoshioka Y, Shinzato C, and Chavanich S*.
Frontiers in Marine Science, 11, 1138021 (2024).
2023
22. Genes possibly related to symbiosis in early life stages of Acropora tenuis inoculated with Symbiodinium microadriaticum.
Yoshioka Y*, Chiu YL, Uchida T, Yamashita H, Suzuki G, and Shinzato C*.
Communications Biology, 6, 1027 (2023). ● [プレスリリース]
21. Genomic and transcriptomic analyses illuminate the molecular basis of the unique lifestyle of a tubeworm, Lamellibrachia satsuma.
Uchida T, Yoshioka Y, Yoshida Y, Fujie M, Yamaki A, Sasaki A, Inoue K, and Shinzato C*.
DNA Research, 30(4), dsad014 (2023). ● [プレスリリース]
20. Genetic population structure of the precious coral Corallium japonicum in the Northwest Pacific.
Kise H, Iguchi A*, Saito N, Yoshioka Y, Uda K, Suzuki T, Nagano AJ, Suzuki A, and Iwasaki N.
Frontiers in Marine Science, 10, 1052033 (2023). ● [プレスリリース]
19. Microbial mat compositions and localization patterns explain the virulence of black band disease in corals.
Wada N, Iguchi A, Urabe Y, Yoshioka Y, Abe N, Takase K, Hayashi S, Kawanabe S, Sato Y, Tang SL*, and Mano N*.
npj Biofilms and Microbiomes, 9, 15 (2023).
2022
18. Calcification rates of a massive and a branching coral species were unrelated to diversity of endosymbiotic dinoflagellates.
Gibu K, Ikeuchi E, Bell T, Nakamura T, Yoshioka Y, Suzuki A, and Iguchi A*.
Molecular Biology Reports, 49, 9101–9106 (2022).
17. The seasonal investigation of Symbiodiniaceae in broadcast spawning, Acropora humilis and brooding, Pocillopora cf. damicornis corals.
Jandang S, Viyakarn V, Yoshioka Y, Shinzato C, and Chavanich S*.
PeerJ, 10, e13114 (2022).
16. Comparative genomics highlight the importance of lineage-specific gene families in evolutionary divergence of the coral genus, Montipora.
Yoshioka Y, Suzuki G, Zayasu Y, Yamashita H, and Shinzato C*.
BMC Ecology and Evolution, 22, 71 (2022). [Genome browser for M. cactus] [Genome browser for M. efflorescens]
15. Larval transcriptomic responses of a stony coral, Acropora tenuis, during initial contact with the native symbiont, Symbiodinium microadriaticum.
Yoshioka Y, Yamashita H, Suzuki G, and Shinzato C*.
Scientific Reports, 12, 2854 (2022).
2021
14. Whole-genome sequencing highlights conservative genomic strategies of a stress-tolerant, long-lived scleractinian coral, Porites australiensis Vaughan, 1918.
Shinzato C*, Takeuchi T, Yoshioka Y, Tada I, Kanda M, Broussard C, Iguchi A, Kusakabe M, Marin F, Satoh N, and Inoue M.
Genome Biology and Evolution, 13(12), evab270 (2021). [Genome browser]
13. Divalent metal transporter-related protein restricts animals to marine habitats.
Sassa M, Takagi T, Kinjo A, Yoshioka Y, Zayasu Y, Shinzato C, Kanda S, Murakami-Sugihara N, Shirai K, and Inoue K*.
Communications Biology, 4, 463 (2021). ● [プレスリリース]
12. Genomics and transcriptomics of the green mussel explain the durability of its byssus.
Inoue K*, Yoshioka Y, Tanaka H, Kinjo A, Sassa M, Ueda I, Shinzato C, Toyoda A, and Itoh T.
Scientific Reports, 11, 5992 (2021). ● [プレスリリース]
11. Whole-genome transcriptome analyses of native symbionts reveal host coral genomic novelties for establishing coral-algae symbioses.
Yoshioka Y, Yamashita H*, Suzuki G, Zayasu Y, Tada I, Kanda M, Satoh N, Shoguchi E, and Shinzato C*.
Genome Biology and Evolution, 13(1), evaa240 (2021).
10. Eighteen coral genomes reveal the evolutionary origin of Acropora strategies to accommodate environmental changes.
Shinzato C*, Khalturin K, Inoue J, Zayasu Y, Kanda M, Kawamitsu M, Yoshioka Y, Yamashita H, Suzuki G, and Satoh N.
Molecular Biology and Evolution, 38(1), 16–30 (2021). ● [プレスリリース]
2020
9. De novo transcriptome assembly from the gonads of a scleractinian coral, Euphyllia ancora: molecular mechanisms underlying scleractinian gametogenesis.
Chiu YL, Shikina S*, Yoshioka Y, Shinzato C*, and Chang CF*.
BMC Genomics, 21, 732 (2020).
8. Extensive gene flow among populations of the cavernicolous shrimp at the northernmost distribution margin in the Ryukyu Islands, Japan.
Yorisue T*, Iguchi A, Yasuda N, Mizuyama M, Yoshioka Y, Miyagi A, and Fujita Y.
Royal Society Open Science, 7(10), 191731 (2020).
7. Transcriptome analyses of immune system behaviors in primary polyp of coral Acropora digitifera exposed to the bacterial pathogen Vibrio coralliilyticus under thermal loading.
Takagi T*, Yoshioka Y, Zayasu Y, Satoh N, and Shinzato C.
Marine Biotechnology, 22(6), 748–759 (2020).
6. Evaluating the effect of overharvesting on genetic diversity and genetic population structure of the coconut crab.
Yorisue T*, Iguchi A*, Yasuda N, Yoshioka Y, Sato T, and Fujita Y.
Scientific Reports, 10, 10026 (2020). ● [プレスリリース]
5. Correlation between organelle genetic variation and RNA editing in dinoflagellates associated with the coral Acropora digitifera.
Shoguchi E†*, Yoshioka Y†, Shinzato C, Arimoto A, Bhattacharya D, and Satoh N.
Genome Biology and Evolution, 12(3), 203–209 (2020).
4. Deep-sea amphipods around cobalt-rich ferromanganese crusts: Taxonomic diversity and selection of candidate species for connectivity analysis.
Iguchi A*, Nishijima M, Yoshioka Y, Miyagi A, Miwa R, Tanaka Y, Kato S, Matsui T, Igarashi Y, Okamoto N, and Suzuki A.
PLoS One, 15(2), e0228483 (2020).
2019
3. RADseq population genomics confirms divergence across closely related species in blue coral (Heliopora coerulea).
Iguchi A*, Yoshioka Y, Forsman HZ, Knapp ISS, Toonen RJ, Hongo Y, Nagai S, and Yasuda N*.
BMC Evolutionary Biology, 19, 187 (2019).
2018
2. Evaluating the occurrence of cryptic invasions of a rocky shore barnacle, Semibalanus cariosus, between the north-eastern Pacific and Japan.
Yorisue T*, Yoshioka Y, Sakuma K, and Iguchi A.
Biofouling, 34(2), 183–189 (2018).
2017
1. The presence of genes encoding enzymes that digest carbohydrates in coral genomes and analysis of their activities.
Yoshioka Y, Tanabe T, and Iguchi A*.
PeerJ, 5, e4087 (2017).