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opencc-zeroNov 2023View details →

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

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 Oryzias latipes species group has larger numbers of chromosome arms than the other groups, with most chromosomes being metacentric. The O. javanicus species group has similar numbers of chromosomes to the O. latipes species group, but smaller arm numbers, with most chromosomes being acrocentric. The O. celebensis 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 O. latipes, O. javanicus, and O. celebensis, 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.

opencc-zeroMar 2022View details →

Morphological measurements Oryzias eversi, Oryzias nigrimas and hybrids

The evolution of complex phenotypes like reproductive strategies is challenging to understand as they often depend on multiple adaptations, which only jointly result in a specific functionality. Sulawesi ricefishes (Adrianichthyidae) evolved a reproductive strategy termed pelvic brooding. In contrast to the more common transfer brooding, female pelvic brooders carry an egg-bundle connected to their body for weeks until the fry hatches. To examine the genetic architecture of pelvic brooding, we crossed the pelvic brooding Oryzias eversi and the transfer brooding O. nigrimas (species divergence time: ~ 3.6 my). We hypothesize, that a low number of loci and modularity have facilitated the rapid evolution of pelvic brooding. Traits associated to pelvic brooding, like rib length, pelvic fin length and morphology of the genital papilla were correlated in the parental species but correlations were reduced or lost in their F1 and F2 hybrids. Using the Castle-Wright estimator, we found that generally few loci underlie the studied traits. Further, both parental species showed modularity in their body plans. In conclusion, morphological traits related to pelvic brooding were based on a few loci and the mid-body region likely could evolve independently from the remaining body parts. Both factors presumably facilitated the rapid evolution of pelvic brooding.

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Figure 39 in A phylogenetic analysis and taxonomic revision of ricefishes, Oryzias and relatives (Beloniformes, Adrianichthyidae)

Figure 39. Oryzias carnaticus (Jerdon, 1849), Trincomalee, Sri Lanka, AMNH 20650, male, 26.5 mm SL.

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Figure 22 in A phylogenetic analysis and taxonomic revision of ricefishes, Oryzias and relatives (Beloniformes, Adrianichthyidae)

Figure 22. Adrianichthys roseni, holotype, MZB 6732, adult female, 90 mm SL. Radiograph.

opencc-zeroMay 2023View details →

Data from: Rearing in strontium-enriched water induces vaterite otoliths in the Japanese rice fish, Oryzias latipes

Sagittal otoliths, typically composed of aragonite, are frequently laid down rather as vaterite during growth in hatchery-reared fish populations. Sagittal vateritisation is believed to impair individual hearing/balancing abilities, but the causal mechanism remains unclear. Here we experimentally demonstrated that rearing in Sr-rich water induces sagittal vateritisation in the HdrR-II1 inbred strain of the Japanese rice fish, Oryzias latipes. Both sagittae were partly vateritised in 70% of individuals subjected to the Sr2+ treatment (n = 10), whereas fish reared in normal tap water showed no sagittal vateritisation (n = 8). Our result is consistent with the theoretical prediction that vaterite becomes thermodynamically more stable than aragonite as the Sr2+ concentration in solution increases. A vateritic layer develops surrounding the original aragonitic sagitta in vateritised otoliths, some of which take on a comma-like shape. Electron probe microanalysis demonstrates that the vateritised phase is characterised by lower Sr2+ and higher Mg2+ concentrations than the aragonitic phase. It is unlikely that increased environmental Sr2+ is responsible for the sagittal vateritisation in farmed fish. However, our findings likely help to establish an in vivo assay using O. latipes to understand the physiological process underlying the sagittal vateritisation in farmed fish.

publicNov 2023View details →

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

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publicMar 2022View details →

Morphological measurements Oryzias eversi, Oryzias nigrimas and hybrids

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publicJul 2025View details →

The transgenerational physiological and molecular data of Oryzias melastigma under seawater acidification stress

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publicMay 2023View details →

Data from: Rearing in strontium-enriched water induces vaterite otoliths in the Japanese rice fish, Oryzias latipes

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publicJun 2025View details →

Inter-population variation in fin sexual dimorphism in medaka (Oryzias latipes)

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FIGURE 4 in Genetic diversity of the regionally endangered Chinese ricefish (Oryzias sinensis) in Taiwan, with comments on its conservation status

FIGURE 4. Molecular phylogenetic tree of Chinese ricefish in Taiwan based on combined COI and D-loop sequences constructed with the maximum likelihood method. Bootstrap values less than 50 are not shown.

FIGURE 2 in Genetic diversity of the regionally endangered Chinese ricefish (Oryzias sinensis) in Taiwan, with comments on its conservation status

FIGURE 2. Molecular phylogenetic tree of Chinese ricefish in Taiwan based on the D-loop sequence constructed with the maximum likelihood method (bootstrap values less than 50 not shown). The sample size of each haplotype is given in parentheses after the OTU. Haplotypes from Tzeng et al. (2006) are shown with GenBank accession numbers.

FIGURE 1 in Genetic diversity of the regionally endangered Chinese ricefish (Oryzias sinensis) in Taiwan, with comments on its conservation status

FIGURE 1. Sampling sites in northern Taiwan. Detailed localities and rivers are shown in the upper right image.

FIGRUE 3 in Genetic diversity of the regionally endangered Chinese ricefish (Oryzias sinensis) in Taiwan, with comments on its conservation status

FIGRUE 3. Molecular phylogenetic tree of Chinese ricefish in Taiwan based on COI sequences constructed with the maximum likelihood method. Bootstrap values less than 50 are not shown. Two haplotypes of Chinese ricefish from South Korea from Kim et al. (unpublished data, 2016) are shown with GenBank accession numbers.

opencc-by-4.0Jul 2023View details →

Assembly data files Oryzias dopingdopingensis

Identification and masking of repetitive elements in the genome sequence of O. dopingdopingensis was performed with the following bioinformatic tool case. Nucleotides were masked using the DUST algorithm with dustmasker (version 1.0.0, part of blast+ 2.9.0 (Altschul et al., 1990; Camacho et al., 2009) (Kuzio et al., unpublished but described in (Morgulis et al., 2006). Tandem Repeats were identified with Tandem Repeat Finder (trf version 4.09) (Benson, 1999). A species-specific de novo repeat library was built with RepeatModeler v1.0.11 (<a href="http://www.repeatmasker.org/RepeatModeler/">http://www.repeatmasker.org/RepeatModeler/</a>). Repeat Elements were located in the genome sequence using RepeatMasker (version 4.1.0) (<a href="http://www.repeatmasker.org/">http://www.repeatmasker.org</a>) with the de novo and Danio rerio libraries. The information from all four repeat analyses was merged and the genome was softmasked with bedtools (2.29.2) (Quinlan & Hall, 2010) PMID: 20110278; PMCID: PMC2832824.]. All steps of masking repetitive regions were performed with scripts provided by the sigenae platform, following the workflow from (Feron et al., 2020). For the identification of genes the masked genome was annotated with funannotate (Palmer & Stajich, 2019). The sequences were sorted by length with the ‘funannotate sort’ function, followed by a gene prediction with ‘funannotate predict’. No training based on RNA-Seq data was performed since it was not available for this species. Additional external evidence from transcripts and proteins was added. As transcript evidence, gene predictions from Oryzias latipes (NCBI Bioproject:PRJNA183868; Assembly: GCF_002234675.1) (Kasahara et al., 2007) and Oryzias melastigma (NCBI Bioproject: PRJNA401159 ; Assembly: ASM292280v2) (Kim et al., 2018) were used. As protein evidence, a protein set from Oryzias javanicus (NCBI Bioprject : PRJNA505405 ; Assembly: GCA_003999625.1) (Lee et al., 2020), manually annotated reference sequences from UniProt Knowledgebase (UniProtKB) (Release 2020_02 (22-Apr-2020) UniProtKB/Swiss-Prot with 562,253 entries ) (Apweiler et al., 2004) and a set of orthologous sequences generated in this study. Furthermore, the de novo gene predictors were trained with the Busco dataset of actinopterygii_odb10. Gene prediction resulted in a total of 56658 genes.

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Data from: Starvation causes female to male sex reversal through lipid metabolism in the teleost fish, medaka (Oryzias latipes)

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publicMar 2020View details →

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Data from: Natural allelic variations of xenobiotic metabolizing enzymes affect sexual dimorphism in Oryzias latipes

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publicOct 2014View details →

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Figure 54 in A phylogenetic analysis and taxonomic revision of ricefishes, Oryzias and relatives (Beloniformes, Adrianichthyidae)

Figure 54. Oryzias sarasinorum (Popta, 1905), Lake Lindu, Sulawesi Tengah, Indonesia, female, CMK 6557, 53.4 mm SL, carrying a cluster of embryos between pelvic fins and body.

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Figure 42. Oryzias hubbsi Roberts, 1998 in A phylogenetic analysis and taxonomic revision of ricefishes, Oryzias and relatives (Beloniformes, Adrianichthyidae)

Figure 42. Oryzias hubbsi Roberts, 1998, laboratory stock of fish collected in Jakarta, Java, Indonesia, CAS 92322, paratype, male, 14.5 mm SL.

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Figure 30 in A phylogenetic analysis and taxonomic revision of ricefishes, Oryzias and relatives (Beloniformes, Adrianichthyidae)

Figure 30. Cladogram of relationships among ricefish species, classified herein in two monophyletic genera, Adrianichthys and Oryzias. Character states at each lettered node are described and discussed in the text. Nodes marked by solid circles are supported by at least one synapomorphy; those marked by an open circle are supported only by homoplasies under a fast character state optimization. Character support at each node is discussed in the Phylogenetic analysis.