LABORATORY OF BIORESOURCES

Specially Appointed Professor

NARUSE, Kiyoshi

Research Staff:

KANEKO, Hiroyo
HARA, Ikuyo
YANOGAWA, Azusa
Visiting Scientist:
SATO, Tadashi
NITTA, Masato
Visiting Graduate Student: IMAEDA YASSUMOTO,Tamiris
Technical Assistant:
AJIOKA, Rie
KOIKE, Chieko
KOIKE, Yukari
TESHIMA, Yuuko
TORII, Naoko
YAMAZAKI, Toko
Admin Support Staff:
SUZUKI, Tokiko

The medaka is a small egg-laying fresh water fish found inbrooks and rice paddies in Eastern Asia. This species has along history as an experimental animal, especially in Japan.
Our laboratory has conducted studies on the dynamics oftranscriptional and chromatin accsssibility landscape during
medaka development, the understanding of pigment celldifferentiation using body color mutants, genome sequenceof the Javanese medaka, Oryzias javanicus and the molecular genetic basis of diversified sexually dimorphic traits inOryzias species, In addition to these activities, our laboratory
was charged with the responsibility of leading the National
BioResource Project Medaka (NBRP Medaka) from 2007.

I. D aynamic transcriptional and chromatin
accesibikity landscape during medaka
development.

A high-quality genome sequence and a variety of genetic
tools are available for medaka. However, existing genome
annotation is still rudimentary, as it was mainly based oncomputational prediction and short-read RNA-seq data. To
overcome this situations, we conducted long-read RNA-seq,
short-read RNA-seq, and ATAC-seq coraboration with Dr.
Tu at the Institute of Genetics and Developmental Biology,
Chinese Academy of Sciences. This work constructed amuch-improved gene model set including about 17,000 novel
isoforms and identified 1600 transcription factors, 1100 longnon-coding RNAs, and 150,000 potential cis-regulatory
elements as well. The work provides the first comprehensive
omics datasets of medaka embryogenesis. The data portal(http://tulab.genetics.ac.cn/medaka_omics) will serve as adaily reference tool for the entire medaka community.

Figure 1. Overview of medaka multi-omics anslysis during development

II. T he Medaka Inbred Kiyosu-Karlsruhe(MIKK) panel and their genomic variationand epigenomic landscape

The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel is thefirst near-isogenic panel of 80 inbred lines derived from awild founder population collected from Kiyosu, Toyohashi.
Inbred lines provide fixed genomes that make it possible torepeat studies, to vary both genetic information and environmental conditions in controlled studies, as well as to conduct
functional studies. MIKK will thus make it possible to investigate phenotype-to-genotype association studies of complex
genetic traits while carefully controlling interacting factors.
Its applications are numerous, and include genetic research,human health, drug development, and fundamental biology.
Using short reads from Illumina, we further characterise eachof the 80 MIKK lines according to their genetic composition,using the Southern Japanese medaka inbred strain HdrR asa reference genome. We used Oxford Nanopore long readsequencing technology to analyze 12 representative lines
from MIKK to analyze the larger and more complex structural variations. We also investigate line-specific CpG methylation and performed differential DNA methylation analysis
across these 12 lines.

III. Genome sequence of the Javanese medaka,
Oryzias javanicus, as a model for studying
seawater adaptation

Medaka fish in the genus Oryzias are an emerging model
system for studying the molecular basis of vertebrate evolution. This genus contains approximately 35 species andexhibits great morphological, ecological and physiological differences among it’s species. Among these species,
the Java medaka, Oryzias javanicus, is the species thathas most typically adapted to seawater. We sequenced
and assembled the whole genome of O. javanicus, as amodel fish species for studying molecular mechanisms ofseawater adaptation. In teleost fish, the major osmoregulatory organs are the gills, intestine and kidney, and these playdifferent roles to maintain body fluid homeostasis. Manygenes encoding hormones, receptors, osmolytes, transporters, channels and cellular junction proteins are potentiallyinvolved in this osmotic regulation. In addition to the osmoregulation, hatching enzyme activity dramatically changes indifferent salt conditions. At the hatching stage, fish embryos
secrete a specific cocktail of enzymes in order to dissolve theenvelope. In the medaka O. latipes, digestion of the envelope

59

National Institute for Basic Biology

Evolutionary Biology and Biodiversity

occurs after the cooperative action of two kinds of hatching
enzymes: (i) the high choriolytic enzyme (HCE) and (ii) thelow choriolytic enzyme (LCE) (Yasumasu et al., 2010).The
HCE shows higher activity in freshwater than in brackish
water (Kawaguchi et al., 2013). Thus, availability of thehigh-quality reference genome in O. javanicus would facilitate further research for investigating the molecular basis ofphysiological differences including the osmotic regulationand the hatching enzyme activity among Oryzias species.

IV. National BioResource Project Medaka

Our laboratory has been acting as main facility of theMedaka BioResource Project (NBRP Medaka) in the fourthphase of NBRP, which started in 2017. We are providing
wild strains, and related species, genomic resources (approximately 400,000 cDNA clones from 30 different cDNA libraries (containing approximately 23,000 different sequences) and BAC/Fosmid clones covering the entire medakagenome), and hatchery enzymes essential for embryo manipulation and live imaging. These bioresources are available
on our website (Figure 3. https://shigen.nig.ac.jp/medaka/).
These bioresources can be searched by various methods suchas keywords, sequence homology, and expression profiles
using the database on the website. In addition, genome
browsers for the three inbred strains, phylogenetic relationships between wild strains of medaka and related species,and experiment manuals are also available. With the approvalof the second supplementary budget for FY2020, we wereable to install a cabinet-type fish tank washing machine.
This has freed up our technical support staff from the need
to wash the tanks by hand, and has allowed us to focus moreon breeding and management, which requires more humanwork. In addition, a system to remotely monitor the temperature, humidity, and illumination in the medaka breedingrooms and the water temperature in the breeding tanks wasinstalled. The air conditioner in the breeding room was alsoupgraded. We have continuously monitored the medaka
breeding conditions using these systems.
Figure 2. NBRP Medaka website

Publication List:〔Original papers〕

T., Brettell, I., Leger, A., Wolf, N., Kusminski, N.,• Fitzgerald,Monahan, J., Barton, C., Herder, C., Aadepu, N., Gierten, J., Becker, C.,••60

Hammouda, O.T., Hasel, E., Lischik, C., Lust, K., Sokolova, N., Suzuki,R., Tsingos, E., Tavhelidse, T., Thumberger, T., Watson, P., Welz, B.,Khouja, N., Naruse, K., Birney, E., Wittbrodt, J., and Loosli, F. (2022).
The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. Genome Biol.
23, 59. DOI: 10.1186/s13059-022-02623-z
Leger, A., Brettell, I., Monahan, J., Barton, C., Wolf, N., Kusminski,N., Herder, C., Aadepu, N., Becker, C., Gierten, J., Hammouda, O.T.,
Hasel, E., Lischik, C., Lust, K., Sokolova, N., Suzuki, R., Tavhelidse, T.,
Thumberger, T., Tsingos, E., Watson, P., Welz, B., Naruse, K., Loosli, F.,
Wittbrodt, J., Birney, E., and Fitzgerald, T. (2022). Genomic variations
and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe(MIKK) panel. Genome Biol. 23, 58. DOI: 10.1186/s13059-022-02602-4
Seleit, A., Ansai, S., Yamahira, K., Masengi, K. W., Naruse, K., &Centanin, L. (2021). Diversity of lateral line patterns and neuromastnumbers in the genus Oryzias. Journal of Experimental Biology, 224,jeb242490. DOI: 10.1242/jeb.242490