Publications in 2020-2024

†, corresponding author(s); *, equally contributed authors

• Bamba K, Harada R, Inagaki Y†. 2024 AUTOEB: A software for systematically evaluating bipartitions in a phylogenetic tree employing an approximately unbiased test. IPSJ Transactions on Bioinformatics 17:72-82. (doi: 10.2197/ipsjtio.17.72)

• 稲垣祐司†，原田亮．2024 オルガネラ局在DNAポリメラーゼの多様性と進化：現状とこれからの課題／The diversity and evolution of DNA polymerases localized in organelles: What we know and what we are uncertain about.　月刊『アグリバイオ』8(12):43-47.

• Yazaki E†, Uehara T, Sakamoto H, Inagaki Y. 2024 Dinotoms possess two evolutionary distinct autophagy-related ubiquitin-like conjugation systems.  Protist 175(6):126067. pubmed. (doi: https://doi.org/10.1016/j.protis.2024.126067)

• 原田亮†，稲垣祐司．新奇DNAポリメラーゼrdxPolAは、古のミトコンドリアDNA維持装置の遺産か？／Is rdxPolA a piece of the ancient system for DNA maintenance in mitochondria? 2024 藻類 The Japanese Journal of Phycology (Sôrui) 72(2):107-114. PDF

• Nakayama T†, Yabuki A, Nomura M, Shiba K, Inaba K, Inagaki Y.  2024 Convergent reductive evolution of cyanobacteria in symbiosis with Dinophysiales dinoflagellates. Scientific Reports 14(1):12774. pubmed  (doi: 10.1038/s41598-024-63502-0)

• Harada R, Hirakawa Y, Yabuki A, Kim E, Yazaki E, Kamikawa R, Nakano K, Eliáš M†, Inagaki Y†. 2024 Encyclopaedia of DNA polymerases localized in organelles: Evolutionary contribution of bacteria including the proto-mitochodrion.  Molecular Biology and Evolution 41(2):msae014. pubmed.  (doi: 10.1093/molbev/msae014)　プレスリリース

• Nakayama T†, Yabuki A, Nomura M, Shiba K, Inaba K, Inagaki Y.  2024 Convergent reductive evolution of cyanobacteria in symbiosis with Dinophysiales dinoflagellates. bioRχiv  (doi: 10.1101/2024.01.11.574452) The version after peer-review was published in Sci Rep in 2024. See https://doi.org/10.1038/s41598-024-63502-0

• Harada R, Inagaki Y†. 2023 Gleaning Euglenozoa-specific DNA polymerases in public single-cell transcriptome data.  Protist  174(6):125997. pubmed. (doi; 10.1016/j.protis.2023.125997)

• Kume K†, Gen T, Abe K, Komatsuzaki H, Yazaki Y, Tanifuji G, Kamikawa R, Inagaki Y, Hashimoto T. 2023 Transcriptome data sets of free-living diplomonads, Treponema sp. and Hexamita sp.  Microbiology Resource Announcements 12(11):e0050623.  pubmed. (doi: https://doi.org/10.1128/MRA.00506-23)

• Harada R, Hirakawa Y, Yabuki A, Kim E, Yazaki E, Kamikawa R, Nakano K, Eliáš M†, Inagaki Y†. 2023 Encyclopaedia of DNA polymerases localized in organelles: Evolutionary contribution of diverse bacteria including the proto-mitochodrion.  bioRχiv  https://doi.org/10.1101/2023.08.28.554543 The version after peer-review was published in Mol Biol Evol in 2024. See https://doi.org/10.1093/molbev/msae014

• Harada R, Kume K, Horie K, Nakayama T, Inagaki Y, Amagasa T†. 2023 AtLASS: A scheme for end-to-end prediction of splice sites using attention-based bi-LSTM. IPSJ Transactions on Bioinformatics 16:20-27. (doi: https://doi.org/10.2197/ipsjtbio.16.20)

• 原田亮，稲垣祐司†．2023 　遺伝子水平伝播が支配するオルガネラ局在ファミリーA型DNAポリメラーゼの進化／Evolution of organelle-localized family A DNA polymerases mediated by lateral gene transfer．月刊『細胞』 55(6):33-36

• Ishitani Y†, Caterina C, Ujiie Y, Tame A, Tiboni M, Tanifuji G, Inagaki Y, Frontalini F. 2023 Fascinating strategies of marine benthic organisms to cope with emerging pollutant: Titanium dioxide nanoparticles. Environmental Pollution 330:121538. pubmed. (doi: https://doi.org/10.1016/j.envpol.2023.121538)

• Yuyama I*, Kume K*†, Tamura T, Inagaki Y, Hashimoto T. 2023 Draft genome sequence of Aduncisulcus paluster, a free-living microaerophilic eukaryote belonging to Fornicata. Microbiology Resource Announcements 12(2):e0053922. pubmed. (doi: https://doi.org/10.1128/mra.00539-22)

• Yazaki E*†, Yabuki A*†, Nishimura Y, Shiratori T, Hashimoto T, Inagaki Y. 2022 Microheliella maris possesses the most gene-rich mitochondrial genome in Diaphoretickes.  Frontiers in Ecology and Evolution 10:1030570. (doi: 10.3389/fevo.2022.1030570) 

• 矢﨑裕規* †, 矢吹彬憲*†, 稲垣祐司. Microheliella marisが繋ぐクリプチスタと一次植物の絆．2022 藻類 The Japanese Journal of Phycology (Sôrui) 70:199-204. PDF

• Yoshinaga M, Nakayama T, Inagaki Y†. A novel structural maintenance of chromosomes (SMC)-related protein family specific to Archaea. 2022 Frontiers in Microbiology 13:913088. pubmed. (doi: 10.3389/fmicb.2022.913088) 

• Matsuo E*, Morita K*, Nakayama T*, Yazaki E, Takahashi K, Sarai C, Iwataki M†, Inagaki Y†.  Comparative plastid genomics of green-colored dinoflagellates unveils parallel genome compaction and RNA editing. 2022 Frontiers in Plant Science 13:918543. pubmed. (doi:10.3389/fpls.2022.918543) 

• Yazaki E*†, Yabuki A*†, Imaizumi A, Kume K, Hashimoto T, Inagaki Y. The closest relative of Archaeplastida is revealed by phylogenomic analyses that include Microheliella maris. 2022 Open Biology 12:210376. pubmed. (doi: 10.1098/rsob.210376)　プレスリリース

• Yoshinaga M, Inagaki Y†. Ubiquity and origins of structure maintenance of chromosomes (SMC) proteins in eukaryotes. 2021 Genome Biology and Evolution 13(12):evab256. pubmed. (doi: 10.1093/gbe/evab256) 

• Yazaki E*, Yabuki A*, Imaizumi A, Kume K, Hashimoto T, Inagaki Y. Phylogenomics invokes the clade housing Cryptista, Archaeplastida, and Microheliella maris. 2021 bioRχiv website. (doi: 10.1101/2021.08.29.458128)  The version after peer-review was published in Open Biol in 2022.

• Yoshinaga M, Inagaki Y†. Ubiquity and origins of structure maintenance of chromosomes (SMC) proteins in eukaryotes. 2021 bioRχiv website. (doi: 10.1101/2021.05.15.444277) The version after peer-review was published in Genome Biol Evol in 2021

• Yazaki E*, Miyata R*, Chikami Y, Harada R, Kawakubo T, Tanifuji G, Nakayama T, Yahata K, Hashimoto T, Inagaki Y†. Signs of the plastid: Enzymes involved in plastid-localized metabolic pathways in a eugregarine species. 2021 Parasitology International 83:102364. pubmed. (do: 10.1016/j.parint.2021.102364) プレスリリース

• Harada R, Inagaki Y†. Phage origin of mitochondrion-localized family A DNA polymerases in kinetoplastids and diplonemids. 2021 Genome Biology and Evolution 13(2):evab003. pubmed. (doi: 10.1093/gbe/evab003)

• Omori Y†, Saeki A, Wada S, Inagaki Y, Hama T. Experimental analysis of diurnal variations in humic-like fluorescent dissolved organic matter in surface seawater. 2020 Frontiers in Marine Science 7:589064. website (doi: 10.3389/fmars.2020.589064)

• Harada R, Inagaki Y†. Phage origin of mitochondrion-localized family A DNA polymerases in kinetoplastids and diplonemids. 2020 bioRχiv website. (doi: 10.1101/2020.09.26.314351) The version after peer-review was published in Genome Biol Evol in 2021

• Yazaki E†, Kume K, Shiratori T, Eglit Y, Tanifuji G, Harada R, Simpson AGB, Ishida K, Hashimoto T, Inagaki Y†. Barthelonids represent a deep-branching matamonad clade with mitochondrion-related organelles predicted to generate no ATP.  Proceedings of the Royal of Sciences B: Biological Sciences 287(1934): 20201538 pubmed. (doi: 10.1098/rspb.2020.1538 ) プレスリリース（eng. ver.）

• Nakayama T, Takahashi K, Kamikawa R, 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(1):84-88. website pubmed. (doi: 10.1080/19420889.2020.1776568)

• Nishimura Y*, Kume K*, Sonehara K, Tanifuji G, Shiratori T, Ishida K, Hashimoto T, Inagaki Y†, Ohkuma M. Mitochondrial genomes of Hemiarma marina and Leucocryptos marina revised the evolution of cytochrome c maturation in Cryptista. 2020 Frontiers in Ecology and Evolution 8:140. website (doi: 10.3389/fevo.2020.00140)

• Harada R, Hirakawa Y, Yabuki A, Kashiyama Y, Maruyama M, Onuma R, Soukal P, Miyagishima S, Hampl V, Tanifuji G, Inagaki Y†. Inventory and evolution of mitochondrion-localized family A DNA polymerases in Euglenozoa. 2020 Pathogens 9(4):257. pubmed. (doi: 10.3390/pathogens9040257)

• Sarai C*, Tanifuji G*†, Nakayama T*, Kamikawa R*, Takahashi K, Yazaki E, Matsuo E, Miyashita H, Ishida K, Iwataki M†, Inagaki Y†. Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesis. 2020 Proceedings of the National Academy of Sciences of the United States of America 117(10):5364-5375. pubmed. (doi: 10.1073/pnas.1911884117)  プレスリリース：筑波大（eng ver.），PR Times，東北大．

• Tanifuji G†, Kamikawa R, Moore CE, Mills T, Onodera NT, Kashiyama Y, Archibald JM, Inagaki Y, Hashimoto T. Comparative plastid genomics of Cryptomonas species reveals fine-scale genomic responses to loss of photosynthesis. 2020 Genome Biology and Evolution 12(2):3926-3937. pubmed. (doi: 10.1093/gbe/evaa001)