Mating experiences with the same partner enhanced mating activities of naive male medaka fish

Mating experience shapes male mating behavior across species, from insects, fish, and birds, to rodents. Here, we investigated the effect of multiple mating experiences on male mating behavior in "naive" (defined as sexually inexperienced) male medaka fish. The latency to mate with the same female partner significantly decreased after the second encounter, whereas when the partner was changed, the latency to mate was not decreased. These findings suggest that mating experiences enhanced the mating activity of naive males for the familiar female, but not for an unfamiliar female. In contrast, the mating experiences of "experienced" (defined as those having mated > 7 times) males with the same partner did not influence their latency to mate. Furthermore, we identified 10 highly and differentially expressed genes in the brains of the naive males after the mating experience and revealed 3 genes that are required for a functional cascade of the thyroid hormone system. Together, these findings suggest that the mating experience of naive male medaka fish influences their mating behaviors, with neural changes triggered by thyroid hormone activation in the brain

Mate-guarding behavior enhances male reproductive success via familiarization with mating partners in medaka fish

Background: Male-male competition and female mating preference are major mechanisms of sexual selection, which influences individual fitness. How male-male competition affects female preference, however, remains poorly understood. Under laboratory conditions, medaka (Oryzias latipes) males compete to position themselves between a rival male and the female (mate-guarding) in triadic relationships (male, male, and female). In addition, females prefer to mate with visually familiar males. In the present study, to examine whether mate-guarding affects female preference via visual familiarization, we established a novel behavioral test to simultaneously quantify visual familiarization of focal males with females and mate-guarding against rival males. In addition, we investigated the effect of familiarization on male reproductive success in triadic relationships. Results: Three fish (female, male, male) were placed separately in a transparent three-chamber tank, which allowed the male in the center (near male) to maintain closer proximity to the female than the other male (far male). Placement of the wild-type male in the center blocked visual familiarization of the far male by the female via mate-guarding. In contrast, placement of an arginine-vasotocin receptor mutant male, which exhibits mate-guarding deficits, in the center, allowing for maintaining close proximity to the female, did not block familiarization of the far male by the female. We also demonstrated that the reproductive success of males was significantly decreased by depriving females visual familiarization with the males. Conclusions: Our findings indicated that, at least in triadic relationships, dominance in mate-guarding, not simply close proximity, allows males to gain familiarity with the female over their rivals, which may enhance female preference for the dominant male. These findings focusing on the triadic relationships of medaka may contribute to our understanding of the adaptive significance of persistent mate-guarding, as well as female preference for familiar mates

Mate-guarding behavior enhances male reproductive success via familiarization with mating partners in medaka fish

[Background] Male-male competition and female mating preference are major mechanisms of sexual selection, which influences individual fitness. How male-male competition affects female preference, however, remains poorly understood. Under laboratory conditions, medaka (Oryzias latipes) males compete to position themselves between a rival male and the female (mate-guarding) in triadic relationships (male, male, and female). In addition, females prefer to mate with visually familiar males. In the present study, to examine whether mate-guarding affects female preference via visual familiarization, we established a novel behavioral test to simultaneously quantify visual familiarization of focal males with females and mate-guarding against rival males. In addition, we investigated the effect of familiarization on male reproductive success in triadic relationships. [Results] Three fish (female, male, male) were placed separately in a transparent three-chamber tank, which allowed the male in the center (near male) to maintain closer proximity to the female than the other male (far male). Placement of the wild-type male in the center blocked visual familiarization of the far male by the female via mate-guarding. In contrast, placement of an arginine-vasotocin receptor mutant male, which exhibits mate-guarding deficits, in the center, allowing for maintaining close proximity to the female, did not block familiarization of the far male by the female. We also demonstrated that the reproductive success of males was significantly decreased by depriving females visual familiarization with the males. [Conclusions] Our findings indicated that, at least in triadic relationships, dominance in mate-guarding, not simply close proximity, allows males to gain familiarity with the female over their rivals, which may enhance female preference for the dominant male. These findings focusing on the triadic relationships of medaka may contribute to our understanding of the adaptive significance of persistent mate-guarding, as well as female preference for familiar mates

CRISPR-Cas9システムを用いた味覚受容体発現調節物質のスクリーニング系の開発

Taste recognition mediated by taste receptors is critical for the survival of animals in nature and is an important determinant of nutritional status and quality of life in humans. However, many factors including aging, diabetes, zinc deficiency, infection with influenza or cold viruses, and chemotherapy can trigger dysgeusia, for which a standard treatment has not been established. We here established an engineered strain of medaka (Oryzias latipes) that expresses green fluorescent protein (GFP) from the endogenous taste 1 receptor 3 (T1R3) gene locus with the use of the CRISPR-Cas9 system. This T1R3-GFP knock-in (KI) strain allows direct visualization of expression from this locus by monitoring of GFP fluorescence. The pattern of GFP expression in the T1R3-GFP KI fish thus mimicked that of endogenous T1R3 gene expression. Furthermore, exposure of T1R3-GFP KI medaka to water containing monosodium glutamate or the anticancer agent 5-fluorouracil resulted in an increase or decrease, respectively, in GFP fluorescence intensity, effects that also recapitulated those on T1R3 mRNA abundance. Finally, screening for agents that affect GFP fluorescence intensity in T1R3-GFP KI medaka identified tryptophan as an amino acid that increases T1R3 gene expression. The establishment of this screening system for taste receptor expression in medaka provides a new tool for the development of potential therapeutic agents for dysgeusia

Development of ethnographic digital collections

Περιέχει το πλήρες κείμενοΟι λαογραφικές συλλογές αποτελούν πολύτιμη πηγή μελέτης, εξερεύνησης και αξιολόγησης των εθνικών στερεοτύπων των διαφόρων διαμερισμάτων μιας χώρας, δεδομένου ότι στις συλλογές είναι καταχωρημένα ανόθευτα και πηγαία τα εγχώρια εθνοχαρακτηριστικά τους. Κατά κύριο λόγο η λαογραφία αναφέρεται στους μύθους, τα τραγούδια, τη μουσική, τα έθιμα, τη χειροτεχνία, την ενδυμασία, την αρχιτεκτονική και την προφορική παράδοση μιας κοινότητας. Η ιδιαιτερότητα και η ποικιλία ενός τομέα όπως της λαογραφίας δικαιολογεί απόλυτα την ύπαρξη συλλογών και υπο-συλλογών σύνθετης δομής και σημασιολογίας, όπως αυτές που αναφέρουμε παραπάνω. Επομένως η ανάπτυξη ψηφιακών συλλογών απαιτεί τη διατήρηση των στοιχείων που χρειάζονται για: (α) την περιγραφή του περιεχομένου της κάθε συλλογής χωριστά και (β) τη σωστή απεικόνιση της δομής των αντικειμένων στο εσωτερικό αυτής. Στόχος της εργασίας αυτής είναι η παρουσίαση μιας μεθοδολογίας για την ανάπτυξη ενός περιγραφικού μοντέλου μεταδεδομένων για λαογραφικές συλλογές. Το μοντέλο θα αποτελέσει βασικό εργαλείο για την περιγραφή του ψηφιοποιημένου λαογραφικού υλικού, την πρόσβαση σε αυτό από κατανεμημένους χρήστες και φυσικά την επικοινωνία του με άλλα συστήματα. Επιπλέον θα συμβάλλει στη διασύνδεση σύνθετων συλλογών και των αντικειμένων που περιλαμβάνουν είτε σημασιολογικά, είτε χρονικά, είτε θεματικά είτε με οποιονδήποτε άλλο τρόπο απαιτεί η φύση των συλλογών και οι ανάγκες των χρηστών

Mesozoic origin and ‘out-of-India’ radiation of ricefishes (Adrianichthyidae)

The Indian subcontinent has an origin geologically different from Eurasia, but many terrestrial animal and plant species on it have congeneric or sister species in other parts of Asia, especially in the Southeast. This faunal and floral similarity between India and Southeast Asia is explained by either of the two biogeographic scenarios, ‘into-India’ or ‘out-of-India’. Phylogenies based on complete mitochondrial genomes and five nuclear genes were undertaken for ricefishes (Adrianichthyidae) to examine which of these two biogeographic scenarios fits better. We found that Oryzias setnai, the only adrianichthyid distributed in and endemic to the Western Ghats, a mountain range running parallel to the western coast of the Indian subcontinent, is sister to all other adrianichthyids from eastern India and Southeast–East Asia. Divergence time estimates and ancestral area reconstructions reveal that this western Indian species diverged in the late Mesozoic during the northward drift of the Indian subcontinent. These findings indicate that adrianichthyids dispersed eastward ‘out-of-India’ after the collision of the Indian subcontinent with Eurasia, and subsequently diversified in Southeast–East Asia. A review of geographic distributions of ‘out-of-India’ taxa reveals that they may have largely fuelled or modified the biodiversity of Eurasia.journal articl

ゲノム編集ツールを用いたメダカにおける標的遺伝子破壊

京都大学0048新制・課程博士博士(農学)甲第19765号農博第2161号新制||農||1039(附属図書館)学位論文||H28||N4981(農学部図書室)32801京都大学大学院農学研究科応用生物科学専攻(主査)教授 佐藤 健司, 教授 澤山 茂樹, 准教授 田川 正朋学位規則第4条第1項該当Doctor of Agricultural ScienceKyoto UniversityDFA

Targeted mutagenesis using CRISPR/Cas system in medaka

Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system-based RNA-guided endonuclease (RGEN) has recently emerged as a simple and efficient tool for targeted genome editing. In this study, we showed successful targeted mutagenesis using RGENs in medaka, Oryzias latipes. Somatic and heritable mutations were induced with high efficiency at the targeted genomic sequence on the DJ-1 gene in embryos that had been injected with the single guide RNA (sgRNA) transcribed by a T7 promoter and capped RNA encoding a Cas9 nuclease. The sgRNAs that were designed for the target genomic sequences without the 5′ end of GG required by the T7 promoter induced the targeted mutations. This suggests that the RGEN can target any sequence adjacent to an NGG protospacer adjacent motif (PAM) sequence, which occurs once every 8 bp. The off-target alterations at 2 genomic loci harboring double mismatches in the 18-bp targeting sequences were induced in the RGEN-injected embryos. However, we also found that the off-target effects could be reduced by lower dosages of sgRNA. Taken together, our results suggest that CRISPR/Cas-mediated RGENs may be an efficient and flexible tool for genome editing in medaka

Data from: Repositioning of centromere-associated repeats during karyotype evolution in Oryzias fishes

<p>The karyotype, which is the number and shape of chromosomes, is a fundamental characteristic of all eukaryotes. Karyotypic changes play an important role in many aspects of evolutionary processes, including speciation. In organisms with monocentric chromosomes, it was previously thought that chromosome number changes were mainly caused by centric fusions and fissions, whereas chromosome shape changes, that is changes in arm numbers, were mainly due to pericentric inversions. However, recent genomic and cytogenetic studies have revealed examples of alternative cases, such as tandem fusions and centromere repositioning, found in the karyotypic changes within and between species. Here, we employed comparative genomic approaches to investigate whether centromere repositioning occurred during karyotype evolution in medaka fishes. In the medaka family (Adrianichthyidae), the three phylogenetic groups differed substantially in their karyotypes. The <em>Oryzias latipes</em> species group has larger numbers of chromosome arms than the other groups, with most chromosomes being metacentric. The <em>O. javanicus</em> species group has similar numbers of chromosomes to the <em>O. latipes</em> species group, but smaller arm numbers, with most chromosomes being acrocentric. The <em>O. celebensis</em> species group has fewer chromosomes than the other two groups and several large metacentric chromosomes that were likely formed by chromosomal fusions. By comparing the genome assemblies of <em>O. latipes</em>, <em>O. javanicus</em>, and <em>O. celebensis</em>, we found that repositioning of centromere-associated repeats might be more common than simple pericentric inversion. Our results demonstrated that centromere repositioning may play a more important role in karyotype evolution than previously appreciated.</p><p>Funding provided by: Japan Science and Technology Agency<br>Crossref Funder Registry ID: https://ror.org/00097mb19<br>Award Number: JPMJCR20S2</p><p>Funding provided by: Ministry of Education, Culture, Sports, Science and Technology<br>Crossref Funder Registry ID: https://ror.org/048rj2z13<br>Award Number: 22H04983</p><p>Funding provided by: Ministry of Education, Culture, Sports, Science and Technology<br>Crossref Funder Registry ID: https://ror.org/048rj2z13<br>Award Number: 16H06279</p><p><strong>De novo assembly of <em>Oryzias celebensis</em> genome</strong></p> <p>For reference genome assembly of <em>O. celebensis</em> with improved continuities, PacBio continuous long reads (CLRs) (PacBio RSII with P6/C4v2 chemistry; 7.5 million reads; 88.1 Gb; ~110x coverage; PacBio, Menlo Park, CA, USA) (<a href="https://ddbj.nig.ac.jp/resource/sra-experiment/DRX230016">DRX230016</a>) acquired in our previous study (Ansai et al., 2021) were assembled using NextDeNovo 2.5.2 (Hu et al., 2023). The assembled contig sequences were then polished with the PacBio reads used for the assembly and the Illumina short reads (Illumina HiSeq 2500; 2 x 250 bp; 296 millions reads; 148Gb; ~185x coverage; San Diego, CA, USA) (<a href="https://ddbj.nig.ac.jp/resource/sra-experiment/DRX230015">DRX230015</a>) using NextPolish 1.4.1 (Hu et al., 2020).</p> <p>              To scaffold the contigs into chromosome-level assemblies, a linkage map was constructed using an F<sub>2</sub> family obtained by crossing an <em>O. celebensis</em> female with a male of a closely-related species <em>O. woworae</em> (2n = 42; (Myosho et al., 2018)) generated in a previous study (Ansai et al., 2021). Genotypes of the F<sub>2</sub> family, consisting of two grandparents and 164 F<sub>2</sub> fish, were determined using double digest restriction site-associated DNA sequencing (ddRAD-seq) (<a href="https://ddbj.nig.ac.jp/resource/sra-submission/DRA010679">DRA010679</a>). The ddRAD-seq reads were trimmed using Trim Galore 0.4.3 (<a href="https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/">https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/</a>) with cutadapt 1.12 (Martin, 2011) and mapped to the assembled contigs using BWA-backtrack 0.7.17 (Li & Durbin, 2009). The polymorphisms in the RAD tags were called using Stacks Version 2.64 (Rochette et al., 2019). A linkage map was constructed using 3,757 informative markers in lep-map3 (Rastas, 2017). After calling the parental genotypes using the <em>ParentCall2</em> module, markers with high segregation distortion (dataTolerance=0.001) and an excess number of missing genotypes (>10% of individuals; missingLimit=0.1) were removed using the <em>Filtering2</em> module. The 1,756 markers were assigned to 18 linkage groups (LGs) by grouping the markers with pairwise LOD score higher than 10 (lodLimit=10) using the <em>SeparateChromosomes2</em> module, resulting in the total number of LGs equal to the haploid chromosome number of <em>O. celebensis</em> (n = 18). The order of the markers within each LG was determined by maximizing the likelihood of 50 iterations for each LG (numMergeIterations=50) using the <em>OrderMarkers2</em> module.</p> <p>              Based on the linkage map, three contigs in which four or more markers were aligned to two different linkage groups were split into two different contigs. Their breakpoints were determined based on a cross-species synteny map between <em>O. celebensis</em> and <em>O. latipes</em> by aligning the cDNA sequences of <em>O. latipes</em> (Ensembl Release 104; <a href="http://www.ensembl.org/">http://www.ensembl.org/</a>) to the reassembled contigs of <em>O. celebensis</em> using minimap2-2.24 (r1122) (Li, 2018). Finally, chromosomal sequences were reconstructed using the positional information of 1,755 markers of the genetic map with ALLMAPS in JCVI utility libraries v1.2.7 (Tang et al., 2015). The number of LG was determined based on the syntenic chromosomes of <em>O. latipes</em>. The names of the fused chromosomes correspond to all syntenic chromosomes (e.g., LG1_19_17 is syntenic to LG1, LG19, and LG17 of the <em>O. latipes</em> chromosomes).</p&gt