Anne Nakamoto

PhD Candidate
Department of Biomolecular Engineering and Bioinformatics | Genomics Institute
University of California, Santa Cruz

aanakamo@ucsc.edu | annenakamoto.github.io | ORCID:0000-0002-6753-7238 | @annenakamoto

About Me

I am an evolutionary genomicist and bioinformatician whose research uses landscape-scale comparative genomics to inform biodiversity conservation. My work spans diverse taxa, including fish, mammals, birds, plants, herps, and invertebrates in California, as well as fungal pathogens affecting a native tree in Hawai‘i.

Education

2023- PhD Biomolecular Engineering & Bioinformatics, University of California, Santa Cruz, USA

2018-22 BA Molecular & Cell Biology, University of California, Berkeley, USA

Emphasis in Genetics, Genomics, and Development
Minor in Computer Science

Research Experience

2024- Graduate Student Researcher, Dissertation research

Dr. Russ Corbett-Detig Lab, Department of Biomolecular Engineering, University of California, Santa Cruz

2023-24 Graduate Student Researcher, Research rotations

Dr. Russ Corbett-Detig Lab, Department of Biomolecular Engineering
Dr. Joanna Kelley Lab, Department of Ecology and Evolutionary Biology
Dr. Shelbi Russell Lab, Department of Biomolecular Engineering, University of California, Santa Cruz

2022-23 Staff Research Associate II, Dr. Ksenia Krasileva Lab, Department of Plant and Microbial Biology, University of California, Berkeley

2020-22 Undergraduate Researcher, Dr. Ksenia Krasileva Lab, Department of Plant and Microbial Biology, University of California, Berkeley

Fellowships

2026 Achievement Rewards for College Scientists (ARCS) Foundation Fellowship

2024 T32 Genome Sciences Training Fellowship, University of California, Santa Cruz

2023 National Science Foundation Graduate Research Fellowship (NSF-GRFP)

2021 Summer Undergraduate Research Fellowship (SURF), University of California, Berkeley

2021 Undergraduate Research Apprenticeship Program Summer Award, University of California, Berkeley (not accepted due to accepting SURF Award)

Awards & Honors

2025 Graduate Dean’s Research Travel Grant, University of California, Santa Cruz

2025 Advancement to PhD Candidacy with Honors, Department of Biomolecular Engineering & Bioinformatics, University of California, Santa Cruz. Thesis Proposal: “Conservation genomics at the landscape scale.”

Publications

(*authors contributed equally)

Peer-Reviewed Journal Articles

2026 Anne Nakamoto, Lisa Keith, Qingyi Yu, Lionel Sugiyama, Xiaohua Wu, Blaine Luiz, MaryAnn Villalun, Jodie Jacobs, Russ Corbett-Detig, Ariana Cisneros, Harrison D. Heath, Cole Shanks, Faith Okamoto, Alexis Abigail Aroma Albura, Kyle Henricson, Yi Jun Lan, Henry Moore, William Seligmann, Yulia Zybina. Genome sequence of Ceratocystis huliohia, a fungal pathogen of the native ‘ōhi‘a tree in Hawai‘i. Microbiology Resource Announcements, 0:e00236-26.

2026 Jodie Jacobs, Alexandra Lum, Elyse Mina, Camryn N. Morey, Darren D. Lee, Emry Gutierrez, Jonah Dionisio, Cade Mirchandani, Luke Sylvester, Anne Nakamoto, Hailey Loucks, Ciara Wanket, Ariana Cisneros, Alessandro Calicchio, Alexis N. Enstrom, Camille Headrick, Faith Okamoto, Harrison D. Heath, Kseniya Malukhina, Petria Russell, Sagorika Nag, Thomas Gillespie, William Sobolewski, Zia Truong, Shelbi L. Russell. Complete de novo assembly of Wolbachia endosymbiont of contemporary Drosophila simulans using long-read genome sequencing. Microbiology Resource Announcements, 0:e00992-25.

2025 Landen Gozashti, Anne Nakamoto, Shelbi Russell, Russell Corbett-Detig. Horizontal transmission of functionally diverse transposons is a major source of new introns. Proc. Natl. Acad. Sci., 122 (21) e2414761122.

2024 Lionel Sugiyama, Brian Bushe, Eva Brill, MaryAnn Villalun, Anne Nakamoto, Lisa Keith. First Report of Leaf Spot Caused by Paramyrothecium roridum on Coffea arabica in Hawai‘i, U.S.A. Plant Disease, 108 (10), 3198.

2024 Jodie Jacobs,* Anne Nakamoto,* Mira Mastoras, Hailey Loucks, Cade Mirchandani, Lily Karim, Gabriel Penunuri, Ciara Wanket, Shelbi L Russell. Complete de novo assembly of Wolbachia endosymbiont of Drosophila willistoni using long-read genome sequencing. Scientific Reports, 14 (1), 17770.

2023 Anne Nakamoto,* Pierre Joubert,* Ksenia Krasileva. Intraspecific variation of transposable elements reveals differences in the evolutionary history of fungal phytopathogen pathotypes. Genome Biology and Evolution, 15 (12), evad206.

Preprints

Genomic Resources

2026 Genome assembly of Ceratocystis huliohia isolate C25-5, NCBI GenBank GCA_054512535.1. Long-read assembly generated using Nanopore sequencing, with gene annotations (Bioproject: PRJNA1400107)

2026 Mitochondrial genome assembly of Ceratocystis huliohia isolate C25-5, NCBI GenBank PX891014.1. Generated using long-read Nanopore sequencing, with genes annotated.

Conference Presentations

Talks

2026 Biomolecular Engineering Research Retreat, University of California, Santa Cruz. “Comparative mutation load in the California Conservation Genomics Project.”

2025 Evolution Conference, Athens, GA. “Investigating deleterious mutation burden across populations and landscapes in the California Conservation Genomics Project.”

2024 Joint Idaho and Washington Chapters of the Wildlife Society Meeting, Coeur d’Alene, Idaho. “Investigating Mammalian Hibernation Phenotypes using Comparative Transcriptomics.”

2022 Plant and Microbial Biology Department Retreat, University of California, Berkeley. Speed Talk: “Investigating the role of transposable elements in fungal plant pathogen genome evolution.”

2021 Summer Undergraduate Research Fellowship Program Conference, University of California, Berkeley. “Investigating the role of transposable elements in fungal plant pathogen genome evolution.”

Posters

2026 NHGRI Training Conference, St. Louis, MO. “From orientation to publication: training in genome sequencing and assembly for new graduate students.”

2025 Bay Area Population Genomics Conference, Stanford University, CA. “Comparative mutation load in the California Conservation Genomics Project.”

2025 The 12th Wolbachia Conference, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan. “Mining for novel bacterial symbiont genomes of invertebrate metazoan hosts through de novo assembly.”

2023 Biology of Genomes, Cold Spring Harbor Laboratory. “Investigating the role of transposable elements in fungal plant pathogen genome evolution.”

2022 Center for Computational Biology Retreat, University of California, Berkeley. “Investigating the role of transposable elements in fungal plant pathogen genome evolution.”

2022 Plant and Microbial Biology Department Retreat, University of California, Berkeley. “Investigating the role of transposable elements in fungal plant pathogen genome evolution.”

Seminars

2025 Biomolecular Engineering Seminar Series, University of California, Santa Cruz. Seminar: “Investigating deleterious mutation burden across populations and landscapes in the California Conservation Genomics Project.”

2025 Dr. Peter Sudmant Lab, University of California, Berkeley. Seminar: “Investigating deleterious mutation burden across populations and landscapes in the California Conservation Genomics Project.”

2021 Dr. Daniel Croll Lab, University of Neuchâtel. Virtual seminar: “Investigating the role of transposable elements in fungal plant pathogen genome evolution.”

Teaching & Mentorship

2026- Rebecca Abraham - undergraduate student mentee (Biomolecular Engineering, UCSC), bioinformatics techniques for transposable element analysis in the California Conservation Genomics Project

2025-26 Faith Okamoto - Science Support Network mentee, Program in Biomedical Sciences & Engineering, University of California, Santa Cruz

2024,25 Instructor for the BMEB Bootcamp, a two-week orientation for incoming PhD and Masters students led by the T32 Genome Sciences Fellows, Department of Biomolecular Engineering & Bioinformatics, University of California, Santa Cruz, USA.

Co-developed and led a training program introducing new students to genome sequencing and bioinformatic analyses
Students completed a full genome assembly workflow, gained experience with the research and publication process, contributed meaningful results, and built community through collaborative activities early in their graduate careers.

2022,23 Instructor for the Genomes and Plant Health Workshop, Summer 2022 and 2023, one session for undergraduate students and one for high school students each summer, hosted by Ksenia Krasileva Lab, Department of Plant and Microbial Biology, University of California, Berkeley.

A workshop designed to engage students from diverse backgrounds in genomics and data science
I taught a module on genomics and computational biology, and led a hands-on tutorial teaching transposable element annotation.

Professional Activities

Meetings

2025 Kelp Mapping & Genetics Workshop participant. A collaborative effort to align the Strategic Mapping of Giant Kelp and Bull Kelp Genomic Diversity project with management needs in California.

2021 5th Uppsala Transposon Symposium (virtual) attendee.

Professional Memberships

2026- Society for the Study of Evolution

2026- Genetics Society of America

2026- American Society for Microbiology

Work Experience

2019-21 Intermittent Lab Assistant at Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii, USA