2022

Ryoma Kamikawa*, Mochizuki T, Sakamoto M, Tanizawa Y, Nakayama T, Onuma R, Cenci U, Moog D, Speak S, Sarkozi K, Toseland A, van Oosterhout C, Oyama K, Kato M, Kume K, Kayama M, Azuma T, Ishii K, Miyashita H, Henrissat B, Lombard V, Win J, Kamoun S, Kashiyama Y, Mayama S, Miyagishima S, Tanifuji G, Mock T*, Nakamura Y. Genome evolution of a non-parasitic secondary heterotroph, the diatom Nitzschia putrida. Science Advances 2022 8(17), eabi5075

Azuma T, Panek T, Tice AK, Kayama M, Kobayashi M, Miyashita H, Suzaki T, Yabuki A, Brown MW*, Ryoma Kamikawa*. An enigmatic stramenopile sheds light on early evolution in Ochrophyta plastid organellogenesis. Molecular Biology and Evolution 2022 39(4), msac065

Inoue M*, Omae K, Nakamoto I, Ryoma Kamikawa, Yoshida T, Sako Y. Biome-specific distribution of Ni-containing carbon monoxide dehydrogenases. Extremophiles 2022 26:9

神川龍馬*. 系統ゲノミクス，ミトコンドリア，色素体から見た真核生物の多様性 化学と生物 2022 60(8): 393-401

2021

Kawachi M(a), Nakayama T(a), Kayama M, Nomura M, Miyashita H, Bojo O, Rhodes L, Sym S, Pienaar RN, Probert I, Inouye I, Ryoma Kamikawa*. Rappemonads are haptophyte phytoplankton. Current Biology. 31(11), 2395-2403.e4

神川龍馬. 非光合成性藻類の葉緑体進化 No photosynthesis, no life? Plastid evolution in non-photosynthetic algae. 光合成研究. 31(1), 37-49

2020

Nakayama T, Takahashi K, Ryoma Kamikawa, Iwataki M, Inagaki Y, Tanifuji G*. Putative genome features of the relic green alga-derived nuclei in the dinoflagellates and the future perspectives as model organisms. Communicative & Integrative Biology. 13:84-88

Moog D, Nozawa A, Tozawa Y, Ryoma Kamikawa*. Substrate specificity of plastid phosphate transporters in a non-photosynthetic diatom and its implication in evolution of red alga-derived complex plastids. Scientific Reports. 10:1167

Sarai C(a), Tanifuji G(a)*, Nakayama T(a), Ryoma Kamikawa(a), Takahashi K, Yazaki E, Matsuo E, Miyashita H, Ishida K, Iwataki M(b), Inagaki Y*. Dinoflagellates with relic endosymbiont nuclei as novel models for elucidating organellogenesis Proceeding of the National Academy of Sciences of the United States of America. 117(10):5364-5375

Tanifuji G*, Ryoma Kamikawa, Moore CE, Mills T, Onodera NT, Kashiyama Y, Archibald JM, Inagaki Y, Hashimoto H. Comparative plastid genomics of Cryptomonas species reveals fine-scale genomic responses to loss of photosynthesis. Genome Biology and Evolution. 12(2):3926-3937

Nomura M*, Ryoma Kamikawa, Ishida K. Fine structure observation of feeding behavior, Nephroselmis spp.-derived chloroplast enlargement, and mitotic processes in the katablepharid Hatena arenicola. Protist. 171(2):125714

Kayama M, Maciszewski K, Yabuki A, Miyashita H, Karnkowska A*, Ryoma Kamikawa*. Highly reduced plastid genomes of the non-photosynthetic dictyochophyceans Pteridomonas spp. (Ochrophyta, SAR) are retained for tRNA-Glu-based organellar heme biosynthesis. Frontiers in Plant Science 11:602455

Kayama M, Chen JF, Nakada T, Nishimura Y, Shikanai T, Azuma T, Miyashita H, Takaichi S, Kashiyama Y, Ryoma Kamikawa*. A non-photosynthetic green alga illuminates the reductive evolution of plastid electron transport systems. BMC Biology 18:126

2019

Dorrell RG*, Azuma T, Nomura M, Audren de Kerdrel G, Paoli L, Yang S, Bowler C, Ishii K, Miyashita H, Gile GH, Ryoma Kamikawa*. 2019. Principles of plastid reductive evolution illuminated by non-photosynthetic chrysophytes. Proceeding of the National Academy of Sciences of the United States of America 116(14):6914-6923

2018

Brown MW, Heis AA, Ryoma Kamikawa, Inagaki Y, Yabuki A, Tice AK, Shiratori T, Ishida K, Hashimoto T, Simpson AGB, Roger AJ*. 2018. Phylogenomics places orphan protistan lineages in a novel eukaryotic super-group. Genome Biology and Evolution 10(2):427-433

Tanifuji G, Takabayashi S, Kume K, Takagi M, Nakayama T, Ryoma Kamikawa, Inagaki Y, Hashimoto T*. 2018. The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites. PLoS One 13(3):e0194487

 Cenci U, Sibbald SJ, Curtis BA, Ryoma Kamikawa, Eme L, Moog D, Henrissat B, Marechal E, Chabi M, Djemiel C, Roger AJ, Kim E, Archibald JM*. 2018. Nuclear genome sequence of the plastid- lacking cryptomonad Goniomonas avonlea: phylogenomic and metabolic insights into the evolution of secondary plastids. BMC Biology 16: 140

 Ryoma Kamikawa*, Azuma T, Ishii K, Matsuno Y, Miyashita H. 2018. Diversity of organellar genomes in non-photosynthetic diatoms. Protist 169(3):351-361

Ryoma Kamikawa*, Yazaki E, Tahara M, Sakura S, Eriko Matsuo, Nagamune K, Hashimoto T, Inagaki Y*. Fates of evolutionarily distinct, plastid-type glyceraldehyde 3-phosphate dehydrogenase genes in kareniacean dinoflagellates. Journal of Eukaryotic Microbiology 65: 669-678.

神川龍馬. ミトコンドリアの起源・進化 In: アメーバのはなし ―原生生物・人・感染症―（永宗・島野・矢吹 編）. 

2017

Leger MMa, Kolisko Ma, Ryoma Kamikawaa, Stairs CW, Kume K, Čepicka I, Silberman JD, Andersson JO, Xu F, Yabuki A, Eme L, Zhang Q, Takishita K, Inagaki Y, Simpson AGB, Hashimoto T*, Roger AJ*. 2017. Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes. Nature Ecology and Evolution 1:0092

Roger AJ*, Muñoz-Gómez SA, Ryoma Kamikawa. 2017. The origin and diversification of mitochondria. Current Biology 27(21):R1177-R1192.

Muto T, Nishikawa T, Ryoma Kamikawa, Miyashita H*. 2017. The symbiotic green alga in eggs of the endemic amphibian of Japan, Hynobius nigrescens. Phycological Research 65(2):171-174

Yang J, Harding T, Ryoma Kamikawa, Simpson AGB, Roger AJ*. 2017. Mitochondrial genome evolution and a novel RNA editing system in deep-branching heteroloboseids. Genome Biology and Evolution 9(5):1161-1174.

Ryoma Kamikawa*, Moog D, Zauner S, Tanifuji G, Mayama S, Ishida K, Miyashita H, Hashimoto T, Archibald JM, Inagaki Y. 2017. A non-photosynthetic diatom reveals early steps of reductive evolution in plastids. Molecular Biology and Evolution 34(9):2355-2366

Ishii K, Ryoma Kamikawa*. 2017. Growth characterization of non-photosynthetic diatoms, Nitzschia spp., inhabiting estuarine mangrove forests of Ishigaki Island, Japan. Plankton and Benthos Research 12(3):164-170.

2016

Ryoma Kamikawa*, Shiratori T, Ishida K, Miyashita H, Roger AJ. 2016. Group II intron-mediated trans-splicing in the gene-rich mitochondrial genome of an enigmatic eukaryote Diphylleia rotans. Genome Biology and Evolution 8(2):458-466.

Nishimura Y, Tanifuji G, Ryoma Kamikawa, Yabuki A, Hashimoto T, Inagaki Y. 2016. Mitochondrial genome of Palpitomonas bilix: Derived genome structure and ancestral system for cytochrome c maturation. Genome Biology and Evolution 8(10):3090-3098.

Gawlyruck R, Ryoma Kamikawa, Stairs CW, Silberman JD, Brown MW, Roger AJ. 2016. The earliest stages of mitochondrial adaptation to low oxygen revealed in a novel rhizarian. Current Biology 26(20): 2729–2738

神川龍馬*. 光合成能力を失った種と葉緑体の進化・多様性 ～環境と栄養性の進化関係の解明へ向けて～. 生物の科学 遺伝 70(2), 115-120

2015

神川龍馬. Nitzschia、光合成やめるってよ. 藻類63(3): 196-200.

石井 健一郎*, 神川 龍馬, 澤山 茂樹, 宮下 英明, 石川 輝, 今井 一郎. 珪藻類の休眠期細胞を利用した応用科学. 生物の科学 遺伝 69(5): 421-429.

Ryoma Kamikawa*, Tanifuji G, Kawachi M, Miyashita H, Hashimoto T, Inagaki Y. Plastid genome-based phylogeny pinpointed the origin of the green-colored plastid in the dinoflagellate Lepidodinium chlorophorum. Genome Biology and Evolution 7(4):1133–1140.

Ryoma Kamikawa*, Yubuki N, Yoshida M, Taira M, Nakamura N, Ishida K, Leander BS, Miyashita H, Hashimoto T, Mayama S, Inagaki Y. Multiple losses of photosynthesis in Nitzschia (Bacillariophyceae). Phycological Research 63(1): 19–28.

[One of the top ten accessed articles from the Phycological Research in 2015 (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1440-1835/homepage/MostAccessed.html)]

Ryoma Kamikawa*, Tanifuji G, Ishikawa SA, Ishii K, Matsuno Y, Onodera NT, Ishida K, Hashimoto T, Miyashita H, Mayama S, Inagaki Y. Proposal of a twin arginine translocator system-mediated constraint against Loss of ATP synthase genes from

nonphotosynthetic plastid genomes. Molecular Biology and Evolution 32(10):2598–2604.

Takeuchi F*, Sekizuka T, Ogasawara Y, Yokoyama H, Ryoma Kamikawa, Inagaki Y, Nozaki T, Sugita-Konishi Y, Ohnishi T, Kuroda M. The mitochondrial genomes of a myxozoan genus Kudoa are extremely divergent in Metazoa. PLoS ONE 10(7): e0132030

Ishikawa SA, Ryoma Kamikawa, Inagaki Y*. Multiple conversion between the genes encoding bacterial class-I release factors. Scientific Reports 5:12406

Chiba Y*, Ryoma Kamikawa, Nakada-Tsukui K, Saito-Nakano Y, Nozaki T. Discovery of PPi-type phosphoenolpyruvate carboxykinase genes in eukaryotes and bacteria. Journal of Biological Chemistry 290(39):23960-23970.

2014

Ryoma Kamikawa*, Kolisko M, Nishimura Y, Brown MW, Yabuki A, Ishikawa AS, Ishida K, Roger AJ, Hashimoto T, Inagaki Y. 2014. Gene-content evolution in discobid mitochondria deduced from the phylogenetic position and complete mitochondrial genome of Tsukubamonas globosa. Genome Biology and Evolution 6:306-315.

Yabuki Aa*, Ryoma Kamikawaa, Ishikawa SA, Kolisko M, Kume K, Kim E, Tanabe AS, Ishida K, Inagaki Y. 2014. Palpitomonas bilix represents a basal cryptist lineage: insight into the character evolution in Cryptista. Scientific Reports 4:4614.

Nishimura Y, Ryoma Kamikawa, Hashimoto T, Inagaki Y*. 2014. An intronic open reading frame was released from one of group II introns in the mitochondrial genome of a haptophyte Chrysochromulina sp. NIES-1333. Mobile Genetic Elements 4:e29384. 

Ryoma Kamikawa*, Inagaki Y, Hashimoto T. Secondary loss of a cis-spliced intron during the divergence of Giardia intestinalis assemblages. BMC Research Notes 7:413. 

Nakayama T*, Ryoma Kamikawa, Tanifuji G, Kashiyama Y, Okohchi N, Archibald JM, Inagaki Y. 2014. Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle. Proceedings of the National Academy of Sciences of the United States of America. 111(31): 11407-11412.

2013

Kawaichi S, Itoh N, Ryoma Kamikawa, Sugawara T, Yoshida T, Sako Y*. Ardenticatena maritima gen. nov., sp. nov., a ferric iron- and nitrate-reducing bacterium of the phylum Chloroflexi isolated from an iron-rich coastal hydrothermal field, and description of Ardenticatenia classis nov. International Journal of Systematic and Evolutionary Microbiology 63(8):2992-3002

Ryoma Kamikawa*, Brown MW, Nishimura Y, Sako Y, Heiss AA, Yubuki N, Gawryluk R, Simpson AGB, Roger AJ, Hashimoto T, Inagaki Y. Parallel re-modeling of EF-1α function: Divergent EF-1α genes co-occur with EFL genes in diverse distantly related eukaryotes. BMC Evolutionary Biology 13:131

2012

Shiraishi T, Ryoma Kamikawa*, Sako Y, Imai I. Monitoring harmful microalgae by using a molecular biological techneque. Food Quality, Chapter 2, 15-28. 

Nishimura Ya, Ryoma Kamikawaa, Hashimoto T, Inagaki Y*. Separate origins of group I introns in two mitochondrial genes of the katablepharid Leucocryptos marina. PLoS One 7(5): e37307.

Ishitani Y*, Ryoma Kamikawa, Yabuki A, Inagaki Y, Takishita K. Evolution of elongation factor-like (EFL) protein in Rhizaria is revised by radiolarian EFL gene sequences. Journal of Eukaryotic Microbiology 59(4): 367-373.

2011

Ryoma Kamikawa*, Inagaki Y, Hashimoto T. A novel spliceosome-mediated trans-splicing can change our view on the genome complexity of the divergent eukaryote Giardia intestinalis. Biophysical Reviews 3(4):193-197.

Ryoma Kamikawa*, Inagaki Y, Roger AJ, Hashimoto T. Splintrons in Giardia intestinalis: Spliceosomal introns in a split form. Communicative and Integrative Biology 4(4):454-456.

Ryoma Kamikawa*, Inagaki Y, Tokoro M, Roger AJ*, Hashimoto T. Split introns in the genome of a divergent eukaryote Giardia intestinalis are excised by spliceosome-mediated trans-splicing. Current Biology 21(4): 311-315.

Ryoma Kamikawa*, Yabuki A, Nakayama T, Ishida K, Hashimoto T, Inagaki Y. Cercozoa comprises both EF-1α-containing and EFL-containing members. European Journal of Protistology 47(1): 24-28.

Masuda Ia, Ryoma Kamikawa*a, Ueda M, Oyama K, Yoshimatsu S, Inagaki Y, Sako Y. Mitochondrial genomes from two red tide forming raphidophycean algae Heterosigma akashiwo and Chattonella marina var. marina. Harmful Algae10(2):130-137.

2010

Kuno S, Ryoma Kamikawa*, Yoshimatsu S, Sagara T, Nishio S, Sako Y. Genetic diversity of Gambierdiscus spp. (Gonyaulacales, Dinophyceae) in Japanese coastal areas. Phycological Research 58(1): 44-52.

Ryoma Kamikawa*, Sakaguchi M, Matsumoto T, Hashimoto T, Inagaki Y. Rooting for the root of elongation factor-like protein phylogeny. Molecular Phylogenetics and Evolution 56(4): 1082-1088.

Kuno S, Yoshida T*, Ryoma Kamikawa, Hosoda N, Sako Y. Distributions of IS607-type insertion sequence in the toxic cyanobacterium Microcystis aeruginosa and its phage. Microbes & Environments 25(4): 295-301.

2009

Ryoma Kamikawa*, Nishimura H, Sako Y. Analysis of the mitochondrial genome, transcripts, and electron transport activity of the dinoflagellate Alexandrium catenella (Gonyaulacales, Dinophyceae). Phycological Research 57(1): 1-11.

Ryoma Kamikawa*, Masuda I, Demura M, Oyama K, Yoshimatsu S, Kawachi M, Sako Y. Mitochondrial group II introns in raphidophycean flagellates Chattonella spp. suggest a diatom-to-Chattonella lateral group II intron transfer. Protist 160(3): 364-375.

Ryoma Kamikawa*, Sanchez-Perez GF, Sako Y, Roger AJ, Inagaki Y. Expanded phylogenies of canonical and non-canonical types of methionine adenosyltransferase reveal a complex history of these gene families in eukaryotes. Molecular Phylogenetics and Evolution 53(2): 565-570.

神川龍馬、左子芳彦. 有毒・有害微細藻類の分子モニタリング法の開発. 日本プランクトン学会誌 56(1): 43-46.

白石智孝・今井一郎・左子芳彦・石井健一郎・神川龍馬・山本圭吾・中嶋昌紀・長井 敏. 大阪湾における有毒渦鞭毛藻Alexandrium属シストの動態に関する研究. 瀬戸内海 58: 48-50.

2008

Ryoma Kamikawa*, Hosoi-Tanabe S, Yoshimatsu S, Oyama K, Masuda I, Sako Y. Development of a novel molecular marker on mitochondrial genomes in a toxic dinoflagellate Alexandrium spp., and its application in single cell PCR. 2008. Journal of Applied Phycology 20(2): 153-159.

Ryoma Kamikawa, Inagaki Y*, Sako Y. Direct phylogenetic evidence for lateral transfer of elongation factor-like gene. 2008. Proceedings of the National Academy of Sciences of the United States of America 105(19): 6965-6969.

Shiraishi T*, Hiroishi S, Ryoma Kamikawa, Sako Y, Taino S, Ishikawa T, Hayashi Y, Imai I. Population dynamics of the shellfish-killing dinoflagellate Heterocapsa circularisquama monitored by an indirect fluorescent antibody technique and real-time PCR assay in Uranouchi Inlet, Kochi Prefecture, Japan. Proceedings of 5th World Fisheries Congress, 6c_1006, TerraPub, Tokyo.

神川龍馬、左子芳彦. 西日本に分布するGambierdiscus属近縁種の遺伝的多様性. 日本水産学会誌 74(5): 911-912.

神川龍馬. アピコンピレクサ類のアピコプラストと渦鞭毛藻類の色素体のミッシングリング―色を纏った寄生虫の親戚―. 藻類56(2): 119-121.

神川龍馬. シアノファージの多様な感染戦略. 藻類 56(3): 209-211.

2007

Ryoma Kamikawa*, Nagai S, Hosoi-Tanabe S, Itakura S, Yamaguchi M, Uchida Y, Baba T, Sako Y. Application of real-time PCR assay for detection and quantification of Alexandrium tamarense and A. catenella cysts from marine sediments. Harmful Algae 6(2): 413-420.

Ryoma Kamikawa*a, Inagaki Ya, Sako Y. Fragmentation of mitochondrial large subunit rRNA in the dinoflagellate Alexandrium catenella and the evolution of rRNA structure in alveolate mitochondria. Protist 158(2): 239-245.

Ryoma Kamikawa*, Masuda I, Oyama K, Yoshimatsu S, Sako Y. Genetic variation in mitochondrial genes and intergenic spacer region of harmful algae Chattonella species. Fisheries Science 73(4): 871-880.

神川龍馬、左子芳彦. リアルタイム定量PCR法を用いた有害・有毒微細藻の現場モニタリング. 日本水産学会誌、73(2): 299-301.

田辺(細井)祥子、神川龍馬、左子芳彦. 貝毒原因プランクトンの分子モニタリング. In: 今井一郎、福代康夫・広石伸互 (編) 「貝毒研究の最先端―現状と展望」、水産学シリーズ 153、55-64.

神川龍馬、左子芳彦. 有害有毒微細藻ゲノム情報の応用. 海洋と生物、29(5): 418-422.

2006

Ryoma Kamikawa*, Asai J, Miyahara T, Murata T, Oyama K, Yoshimatsu Y, Yoshida T, Sako Y. Application of a real-time PCR assay to a comprehensive method for monitoring harmful algae. Microbes & Environments 21(3): 163-173.

神川龍馬、田辺（細井）祥子、左子芳彦. 有害・有毒微細藻の包括的モニタリング法の開発. Brain Techno NEWS 117号: 28-31.

2005

Ryoma Kamikawa*, Hosoi-Tanabe S., Nagai S., Itakura S., Sako Y. Development of a quantification assay for the cysts of the toxic dinoflagellate Alexandrium tamarense using real-time polymerase chain reaction assay. Fisheries Science 71(5): 987-991.