Kiyoshi Kikuchi

• The University of Tokyo

Selective breeding is a powerful tool for improving aquaculture production. A well-managed breeding program is essential, as populations can otherwise lose genetic diversity, leading to reduced selection response and inbreeding excesses. In such cases, genetic diversity in broodstock must be restored by introducing individuals from external populat...

In the marine realm, unidirectional ocean currents often lead to high migration rates of marine organisms and, therefore, inhibit the formation of their latitudinal genetic structure. In contrast, cryptic latitudinal structures associated with local adaptation may frequently exist in widespread species generally exposed to a strong environmental he...

Two large abalone species prevalent in the Japanese archipelago, Haliotis discus discus and H. madaka , are considered to have different morphological characteristics, and previous population genomics analyses have suggested that they have distinct genomic features. However, integrated analyses comparing the genetic and morphological data from thes...

Selective breeding is a powerful tool for improving aquaculture production. A well-managed breeding program is essential, as populations can otherwise lose genetic diversity, leading to reduced selection response and inbreeding excesses. In such cases, genetic diversity in broodstock must be restored by introducing individuals from external populat...

Fish farming relies on fishmeal (FM) as a primary protein source in aquafeeds. Particularly, tiger pufferfish (Takifugu rubripes) diets containing 70–80% FM. However, the rising cost of FM and the depletion of fish stocks necessitate sustainable alternatives. Our study assessed the feasibility of incorporating low-fishmeal (LFM) diets into tiger pu...

Sex identification markers are of considerable value to aquaculture and fisheries as they enable pre-maturity prediction of the genotypic sex of individuals as well as of the sex ratio in offspring. For these reasons, extensive investigations of the mechanisms of sex determination have been conducted in commercially important finfish species, resul...

Cartilaginous fishes are divided into holocephalans and elasmobranchs, and comparative studies involving them are expected to elucidate how variable phenotypes and distinctive genomic properties were established in those ancient vertebrate lineages. To date, molecular-level studies on holocephalans have concentrated on the family Callorhinchidae, w...

Extinct lineages can leave legacies in the genomes of extant lineages through ancient introgressive hybridization. The patterns of genomic survival of these extinct lineages provide insight into the role of extinct lineages in current biodiversity. However, our understanding on the genomic landscape of introgression from extinct lineages remains li...

The genetic basis of speciation in free‐spawning marine invertebrates is poorly understood. Although gene copy number variations (GCNVs) and nucleotide variations possibly trigger the speciation of these organisms, empirical evidence for such a hypothesis is limited. In this study, we searched for genomic signatures of GCNVs that may contribute to...

Significance Although turnover of sex chromosomes is very common in many vertebrate lineages, the transition process is still elusive. We studied the sex-determining region (SDR) of 12 congeneric fish species of Takifugu fish that compose an important model for the study of genomics and sex determination. We found that while nine species retained t...

The rising price of fishmeal and the need for sustainable use of fishery resources have encouraged efforts by the aquaculture industry to identify alternative protein sources including plants and single cell organisms. This is particularly the case for the tiger pufferfish, Takifugu rubripes, which is fed a high level of fishmeal as the protein sou...

Selection acting across environmental gradients, such as latitudes, can cause spatial structuring of genomic variants even within panmictic populations. In this study, we focused on the within‐generation latitudinal selection between northernmost and southernmost individuals of the North Pacific population of a tropical eel Anguilla marmorata, whic...

We focus on the ichthyofauna on continental shelves and slopes of the Enshu-nada Sea—an area of the northwest Pacific Ocean off the coast of Southern Japan as one of the essential trawl fishery grounds in Japan. We conducted market samplings of the trawl catches from the Enshu-nada Sea, and trawl surveys of bycatch species by commercial trawlers. A...

Hybridization induced by human activities, such as crossbreeding between invasive and native species, can adversely affect the natural biodiversity of an ecosystem. In Japan, the endemic turtle species Mauremys japonica is known to hybridize with the alien species Mauremys reevesii, and putative hybrids have been encountered in the wild. If M. japo...

Recent studies have revealed a surprising diversity of sex chromosomes in vertebrates. However, the detailed mechanism of their turnover is still elusive. To understand this process, it is necessary to compare closely related species in terms of sex-determining genes and the chromosomes harboring them. Here, we explored the genus Takifugu , in whic...

Aquaculture production is expected to increase with the help of genomic selection (GS). The possibility of performing GS using only a small number of SNPs has been examined in order to reduce genotyping costs; however, the practicality of this approach is still unclear. Here, we tested whether the effects of reducing the number of SNPs impaired the...

How early stages of speciation in free-spawning marine invertebrates proceeds is poorly understood. The Western Pacific abalones, Hatiois discus, H. madaka, and H. gigantea occur in sympatry with shared breeding season and are capable of producing viable F1 hybrids in spite of being ecologically differentiated. Population genomic analyses revealed...

Crustacean aquaculture is expected to be a major source of fishery commodities in the near future. Hemocytes are key players of the immune system in shrimps; however, their classification, maturation, and differentiation are still under debate. To date, only discrete and inconsistent information on the classification of shrimp hemocytes has been re...

The novel non-targeted PCR-based genotyping system, namely Genotyping by Random Amplicon Sequencing, Direct (GRAS-Di), is characterized by the simplicity in library construction and robustness against DNA degradation and is expected to facilitate advancements in genetics, in both basic and applied sciences. In this study, we tested the utility of G...

A correction to this paper has been published: https://doi.org/10.1007/s12562-021-01505-w

COI-based DNA barcoding could be an efficient tool for species identification of deep-sea fishes and could lead to the discovery of cryptic species diversity. However, the availability of reference sequences of deep-sea fishes for DNA barcoding is limited, especially for fishes in the northwestern Pacific Ocean. In this study, we performed DNA barc...

Crustacean aquaculture is expected to be a major source of fishery commodities in the near future. Hemocytes are key players of the immune system in shrimps; however, their classification, maturation, and differentiation are still under debate. To date, only discrete and inconsistent information on the classification of shrimp hemocytes has been re...

Hybridization between divergent lineages generates new allelic combinations. One mechanism that can hinder the formation of hybrid populations is mitonuclear incompatibility, that is, dysfunctional interactions between proteins encoded in the nuclear and mitochondrial genomes (mitogenomes) of diverged lineages. Theoretically, selective pressure due...

Parasite resistance traits in aquaculture species often have moderate heritability, indicating the potential for genetic improvements by selective breeding. However, parasite resistance is often synonymous with an undesirable negative correlation with body size. In this study, we first tested the feasibility of genomic selection (GS) on resistance...

The genus Takifugu is a group of approximately 20 species of puffer fishes living in a wide range of salinity environments around East Asian countries. This group presents a broad spectrum of evolutionary stages adapted to anadromy as a result of speciation that occurred a short time (2–5 million years) ago on an evolutionary timescale. This group...

Paleoenvironmental changes in marginal seas on the coast of the northwestern Pacific during the Quaternary have caused genetic differentiation and subsequent secondary contacts between populations of coastal organisms in this region. However, little is known about how geographical isolation and the subsequent connection events associated with these...

Testes of the tiger pufferfish Takifugu rubripes are a delicacy in Japan, and selective breeding for a male precocious phenotype, i.e., with early initiation of testes development, is desirable. However, it is unknown if precocious gonad development in this species is under genetic control. Here, we investigated genetic involvement in precociousnes...

Rapid radiation associated with phenotypic divergence and convergence provides an opportunity to study the genetic mechanisms of evolution. Here we investigate the genus Takifugu that has undergone explosive radiation relatively recently and contains a subset of closely-related species with a scale-loss phenotype. By using observations during devel...

Population genetic studies of marine species sometimes find no clear patterns of genetic differentiation, but signals of geographic gene flow typified by isolation by distance (IBD) due to high dispersal ability. A previous study of mitochondrial DNA of the yellowfin goby Acanthogobius flavimanus indicated that this species also does not have clear...

Cell surface display is a useful platform to examine the interactions between two proteins of interest, such as immune receptors and ligands. This technique is also useful for studies on the immune receptors of lower vertebrates and invertebrates. However, in many cases, the commonly used cell culture temperature is relatively high for proteins fro...

The tiger pufferfish Takifugu rubripes is one of the most valuable aquaculture species in Japan. In this study, we investigated the genetic variation in resistance to heterobothriosis caused by a host-specific monogenean parasite, Heterobothrium okamotoi, in the tiger pufferfish, and examined the possibility of selective breeding for enhancing resi...

Genetic and phenotypic analyses of independent secondary contact zones between certain pairs of divergent populations offer powerful opportunities to assess whether the consequences vary with different environmental backgrounds. Populations of the ice goby Leucopsarion petersii are distributed throughout the Japanese archipelago and comprise geneti...

Studies using genome-wide single nucleotide polymorphisms (SNPs) have become commonplace in genetics and genomics, due to advances in high-throughput sequencing technologies. Since the numbers of required SNPs and samples vary depending on each research goal, genotyping technologies with high flexibility in the number of SNPs/samples and high repea...

Vertebrate sex development consists largely of two processes: “sex determination,” the initial bifurcation of sexual identity, and “sex differentiation,” which subsequently facilitates maleness or femaleness according to the sex determination signal. Steroid hormones promote multiple types of sexual dimorphism in eutherian mammals and avians [ 1 ,...

While various technologies for high‐throughput genotyping have been developed for ecological studies, simple methods tolerant to low quality DNA samples are still limited. In this study, we tested the availability of a random PCR‐based genotyping‐by‐sequencing technology GRAS‐Di (Genotyping by Random Amplicon Sequencing, Direct). We focused on popu...

Genomic Prediction for Heterobothriosis Resistance in the Tiger Pufferfish.

Objective: Selective breeding for desirable traits is becoming popular in aquaculture. In Miyagi prefecture, Japan, a selectively bred population of Coho salmon (Oncorhynchus kisutch) has been established with the original, randomly breeding population maintained separately. Since they have been bred without family records, the genetic diversity w...

There is increasing evidence for frequent turnover in sex chromosomes in vertebrates. Yet experimental systems suitable for tracing the detailed process of turnover are rare. In theory, homologous turnover is possible if the new sex-determining locus is established on the existing sex-chromosome. However, there is no empirical evidence for such an...

Number of fish with recombination between f383 and f714 in families 4–7. (XLSX)

Association test for phenotypic sex and marker genotypes, and quantitative trait loci (QTL) analysis in T. niphobles Family 2. (A) Plot of–log10 (P value) versus chromosome position for association test of T. niphobles. The chromosomal position of the markers was first inferred from the draft genome sequence of fugu, and later confirmed partially b...

The search for individuals with recombination near the sex-determining locus. “X” and “Y” indicate female-associated and male-associated alleles, respectively, inherited from the father. Empty blocks indicate non-informative markers. The first row contains marker names. There were six individuals with recombination between the markers f383 and f200...

Primer sequences for DNA sequencing. (XLSX)

Female and male meiotic map of LG (linkage group) 19 in T. niphobles Family 2. Allelic bridges are indicated by a line connecting the female (left) and male (right) linkage maps. Genetic distances in centimorgans between adjacent markers are shown. Genetic markers are ordered and placed based on both the linkage analysis of T. niphobles (in the gra...

Female and male meiotic maps of LG (linkage group) 19 in T. niphobles Family 3. Allelic bridges are indicated by a line connecting the female (left) and male (right) linkage maps. Genetic distances in centimorgans between adjacent markers are shown. (TIF)

A comparison of the Amhr2 gene between T. niphobles and fugu. Coding regions (red letters) were deduced from a comparison between the fugu Amhr2 gene sequence (fugu_Amhr2) in the fugu Chr19 (FUGU5/fr3, [36]) and its full-length cDNA sequence deposited in DDBJ (accession number AB618627). A comparison of the gene sequence between fugu and T. niphobl...

Primer sequences for microsatellite markers and their genomic position. (XLSX)

The tiger puffer Takifugu rubripes is one of the most popular aquacultural fish; however, there are two major obstacles to selective breeding. First, they have a long generation time of 2 or 3 years until maturation. Second, the parental tiger puffer has a body size (2–5 kg) much larger than average market size (0.6–1.0 kg). The grass puffer Takifu...

How parasites recognize their definitive hosts is a mystery; however, parasitism is reportedly initiated by recognition of certain molecules on host surfaces. Fish ectoparasites make initial contact with their hosts at body surfaces, such as skin and gills, which are covered with mucosa that are similar to those of mammalian guts. Fish are among th...

This study investigated the expression of aquaporin 2 (AQP2) and its newly found alternatively spliced isoform (alternative AQP2) and the functions of these AQP2 isoforms in the cellular hyperosmotic tolerance in the bottlenose dolphin Tursiops truncatus. mRNA sequencing revealed that alternative AQP2 lacks the fourth exon and instead has a longer...

Macrophage colony-stimulating factor receptor (M-CSFR), a member of the group of type III protein tyrosine kinase receptors, is expressed primarily by monocyte/macrophage lineage cells. In order to describe the distribution of macrophages at the maternal-fetal interface in Neoditrema ransonnetii, a viviparous fish species, M-CSFR cDNA was sequenced...

Correlated suits of behaviors (behavioral syndrome) are commonly observed in both inter- and intraspecific studies. In order to understand the genetic basis of such a correlation between species, we compared ten behaviors classified into five categories (acclimation, feeding, normal swimming, reaction to a novel object and activity in a novel envir...

Caligus fugu is a parasitic copepod specific to the tetraodontid genus Takifugu including the commercially important Takifugu rubripes. Despite the rapid accumulation of knowledge on other aspects of its biology, the host and settlement-site recognition mechanisms of this parasite are not yet well understood. Since the infective copepodid stage sho...

The tiger pufferfish (fugu) is one of the most important food fishes in East Asia. Since its testes are regarded as a delicacy, sex determination is economically relevant. Previous studies have identified a missense single-nucleotide polymorphism (SNP) in the Amhr2 (anti-Müllerian hormone receptor type II) gene as a strong candidate for a master se...

We investigated the influence of paternal effects on progeny survival of the fugu Takifugu rubripes when multiple families were reared in communal tanks. Four males were crossed with four females in a factorial cross to give 16 families, and the half-siblings sharing the same mother were reared together. Male parentage was determined using microsat...

In fish breeding, it is essential to discover and generate fish exhibiting an effective phenotype for the aquaculture industry, but screening for natural mutants by only depending on natural spontaneous mutations is limited. Presently, reverse genetics has become an important tool to generate mutants, which exhibit the phenotype caused by inactivat...

The genetic mechanisms underlying host specificity of parasitic infections are largely unknown. After hatching, the larvae of the monogenean parasite, Heterobothrium okamotoi, attach to the gill filaments of hosts and the post-larval worms develop there by consuming nutrients from the host. The susceptibility to H. okamotoi infection differs marked...

Although the molecular mechanisms underlying many developmental events are conserved across vertebrate taxa, the lability at the top of the sex-determining (SD) cascade has been evident from the fact that four master SD genes have been identified: mammalian Sry; chicken DMRT1; medaka Dmy; and Xenopus laevis DM-W. This diversity is thought to be ass...

Closely related species have often evolved dramatic differences in body size. Takifugu rubripes (fugu) is a large marine pufferfish whose genome has been sequenced, whereas T. niphobles is the smallest species among Takifugu. We show that, unsurprisingly, the juvenile growth rate of T. rubripes is higher than that of T. niphobles in a laboratory se...

Linkage disequilibrium of the SD region of fugu. r2 and D′ values ×100 estimated for each pairwise comparison of SNPs are shown in plots (A) and (B), respectively. Darker grey in (A) indicates higher r2 (white, r2 = 0; shades of grey, 0<r2<1; black, r2 = 1), while darker red in B indicates higher D′ (white, D′<1 and LOD<2; blue, D′ = 1 and LOD<2; p...

SNP 7271 is the sole conserved SNP perfectly correlated with phenotypic sex among Takifugu species. We screened variants in exon 9 of Amhr2 and its flanking introns from 16 individuals (8 females and 8 males) of fugu, 16 individuals (8 females and 8 males) of T. pardalis and 13 individuals (7 females and 6 males) of T. poecilonotus. We combined all...

Genetic position and direction of scaffolds in and around the SD region of fugu. (XLS)

Summary of pedigreed families and the genotype of SNP7271 in them. (XLS)

Screening for variants in the 17.5 kb SD region of fugu. We demarcated 4 genomic regions for sequencing: SD2–14K region, SD3–14k region, the 5′ region of SD3 and the 3′ region of SD3. Red and green bars indicate genomic clones of X and Y chromosomes, respectively, from XY males belonging to independent families. The derivation of clones was determi...

Screening for variants. (XLS)

Marker information for association test. (XLS)

Trans-species comparison of Amhr2. (A) Comparison of Amhr2 from fugu, human and medaka. The protein sequence of fugu Amhr2D384 was aligned with human and medaka Amhr2 by ClustalW. Arrow heads indicate intron positions in fugu Amhr2D384. The kinase domain of fugu Amhr2D384 was predicted using SMART (http://smart.embl-heidelberg.de/) and is boxed in...

Primer sequences. (XLS)

Heterogametic sex chromosomes have evolved independently in various lineages of vertebrates. Such sex chromosome pairs often contain nonrecombining regions, with one of the chromosomes harboring a master sex-determining (SD) gene. It is hypothesized that these sex chromosomes evolved from a pair of autosomes that diverged after acquiring the SD gen...

Artificial cultivation of the Japanese eel has not been feasible due to difficulties in seed production and larval rearing, leading to poor seed and larval survival. We have focused on the importance of the thymus and T-cell function in eel larval stages because only the thymus, of all the immune system organs, develops well in eel leptocephalus. I...

A skin mucus lectin exhibiting a homodimeric structure and an S–S bond between subunits of ∼40 kDa was purified from flathead Platycephalus indicus (Scorpaeniformes). This lectin, named FHL (FlatHead Lectin), exhibited mannose-specific activity in a Ca2+-dependent manner. Although FHL showed no homology to any previously reported lectins, it did ex...

The compact genome of fugu (Takifugu rubripes) has been used widely as a reference genome for understanding the evolution of vertebrate genomes. However, the fragmented nature of the fugu genome assembly has restricted its use for comparisons of genome architecture in vertebrates. To extend the contiguity of the assembly to the chromosomal level, w...

In mammals, professional APCs induce adaptive immunity via the activation of T cells. During this process, B7 family molecules present upon APCs are known to play crucial roles in optimal T cell stimulation. In contrast, the confirmation of APCs in a nonmammalian vertebrate has yet to be achieved. To obtain further insights into the evolutionary or...

Melatonin synthesis in the retina as well as in the pineal gland exhibits daily variations with higher levels during the dark phase of light-dark cycles. To analyze the molecular mechanism of melatonin synthesis in the retina, we have cloned, sequenced and characterized a putative cDNA for arylalkylamine N-acetyltransferase (AANAT; EC 2.3.1.87), a...

We have investigated the characteristics of CD8+ leukocytes by using an anti-CD8alpha antiserum raised in mouse by DNA-immunization. The magnetically sorted CD8alpha+ peripheral blood leukocyte (PBL) population comprised lymphocytes/thrombocytes and monocytes, whereas CD8alpha- PBLs consisted of lymphocytes/thrombocytes, monocytes, and neutrophils....

Torafugu Takifugu rubripes is an attractive vertebrate model organism for genomics by virtue of its smallest genome among vertebrates and available whole-genome database. Our group has constructed the torafugu linkage map with over 400 markers. In this study, we screened superior trait-related genes of torafugu by using the genome database and link...

The primary structures of a CXC chemokine (CXCL8) and two CXC receptors (CXCR) have been characterized in fugu, Takifugu rubripes. Unlike mammalian and avian species, CXCL8 of teleosts including fugu lacks the ELR motif that appears to be important in ligand/receptor interactions on neutrophils. Genomic organization shows that fugu CXCL8 gene consi...

We have cloned cDNAs encoding the alpha and beta chains of CD8 from the tiger pufferfish (fugu), Takifugu rubripes. The cDNA sequences encode a putative leader peptide, extracellular immunoglobulin variable region-like domain, stalk region, transmembrane region, and cytoplasmic tail. A protein tyrosine kinase p56lck binding motif was not found in t...

The skin mucus IgM is an important molecule in the mucosal immune system of teleost skin. However, the transport mechanism associated with this molecule has yet to be clarified. In this study, we isolated a gene encoding a polymeric Ig receptor (pIgR) from a species of teleost fish, Takifugu rubripes (fugu). This gene is known to be an Ig transport...

The tiger pufferfish (fugu), Takifugu rubripes, is a model fish that has had its genome entirely sequenced. By performing genomewide linkage analyses, we show that the sex of fugu is determined by a single chromosomal region on linkage group 19 in an XX-XY system.

Pufflectin-s, identified in the skin mucus of the fugu Takifugu rubripes, is a novel mannose-specific lectin with similar structure to monocotyledonous plant lectins. In the present study, mutational analysis was used to reveal the mannose-binding sites of pufflectin-s. Putative binding sites were mutated as follows: binding site 1; rPL-D32E (Asp32...

Here, we report two distinct genes in teleosts that are homologous to interleukin (IL)-15. The two genes, isolated from fugu (Takifugu rubripes), resemble to mammalian IL-15 but differ from IL-2 and IL-21 in their amino acid sequences, the possessing of an extraordinary long signal peptide and more widespread tissue localization. In addition, multi...