The Japanese medaka, Oryzias latipes, is a vertebrate teleost model with a long history of genetic research. A number of unique features and established resources distinguish medaka from other vertebrate model systems. A large number of laboratory strains from different locations are available. Due to a high tolerance to inbreeding, many highly inbred strains have been established, thus providing a rich resource for genetic studies. Furthermore, closely related species native to different habitats in Southeast Asia permit comparative evolutionary studies. The transparency of embryos, larvae, and juveniles allows a detailed in vivo analysis of development. New tools to study diverse aspects of medaka biology are constantly being generated. Thus, medaka has become an important vertebrate model organism to study development, behavior, and physiology. In this review, we provide a comprehensive overview of established genetic and molecular-genetic tools that render medaka fish a full-fledged vertebrate system.

https://www.genetics.org/content/genetics/199/4/905.full.pdf

The Genomic and Genetic Toolbox of the Teleost Medaka (Oryzias latipes)

Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here, we perform de novo long-read genome assembly of three inbred medaka strains that are derived from geographically isolated subpopulations and undergo speciation. Using single-molecule real-time (SMRT) sequencing, we obtain three chromosome-mapped genomes of length ~734, ~678, and ~744Mbp with a resource of twenty-two centromeric regions of length 20-345kbp. Centromeres are positionally conserved among the three strains and even between four pairs of chromosomes that were duplicated by the teleost-specific whole-genome duplication 320-350 million years ago. The centromeres do not all evolve at a similar pace; rather, centromeric monomers in non-acrocentric chromosomes evolve significantly faster than those in acrocentric chromosomes. Using methylation sensitive SMRT reads, we uncover centromeres are mostly hypermethylated but have hypomethylated sub-regions that acquire unique sequence compositions independently. These findings reveal the potential of non-acrocentric centromere evolution to contribute to speciation.

/pdf/centromere-evolution-and-cpg-methylation-during-vertebrate-25xy1l82ij.pdf

Centromere evolution and CpG methylation during vertebrate speciation

This review summarizes the achievements and novel perspectives that our fish mitochondrial genome (mitogenome) project has brought to molecular phylogenetics and evolution of fishes during the last 15 years (1999–2014). To date, we have assembled ≈1,340 whole mitogenome sequences from fishes, publishing 83 mitogenomic papers on all major fish lineages (except agnathans). Those papers have been cited 5,303 times in total as of 30 September 2014 and have been featured in many textbooks and scientific articles as well as various media. These results have not only had a significant impact on the scientific community, but also attracted considerable attention from the general public. The success of the project largely owes to our own development of a novel, PCR-based approach for sequencing whole mitogenomes (ca. 16,500 bp), which opened a new avenue toward addressing higher-level relationships of fishes based on longer DNA sequences from a number of taxa. Shortly after the development of the method, we explicitly demonstrated the phylogenetic utility of mitogenomic data and actually resolved a long-standing issue in basal teleostean relationships. On the basis of those encouraging results from the initial studies, we published a series of four mitogenomic papers in 2003, which together encompass the whole of actinopterygian diversity and provided a “big picture” phylogenetic framework for the group. Those four studies offered a useful phylogenetic basis for subsequent studies (i.e., with a different choice of outgroups and targeted taxa) and have facilitated massive sequencing efforts for a wide variety of fishes from chondrichthyians to higher teleosts living in diverse habitats from freshwaters to the deep sea. We highlight some of the 83 mitogenomic papers by subject and briefly refer to the phylogenetic and evolutionary significances of those studies. Finally, we argue that intensive taxonomic sampling from an interface between species and populations together with the massive character sampling from mitogenome sequences using next-generation sequencing (NGS) technologies would enable simultaneous attempts to delimit species boundaries and to reconstruct evolutionary relationships at much finer scale, eventually unraveling the fish part of the Tree of Life in a bottom-up manner with more accurate estimations of species diversity.

/pdf/the-mitogenomic-contributions-to-molecular-phylogenetics-and-38hbh0b9ux.pdf

The mitogenomic contributions to molecular phylogenetics and evolution of fishes: a 15-year retrospect

Oryzias latipes (medaka) has been established as a vertebrate genetic model for more than a century and recently has been rediscovered outside its native Japan. The power of new sequencing methods now makes it possible to reinvigorate medaka genetics, in particular by establishing a near-isogenic panel derived from a single wild population. Here we characterize the genomes of wild medaka catches obtained from a single Southern Japanese population in Kiyosu as a precursor for the establishment of a near-isogenic panel of wild lines. The population is free of significant detrimental population structure and has advantageous linkage disequilibrium properties suitable for the establishment of the proposed panel. Analysis of morphometric traits in five representative inbred strains suggests phenotypic mapping will be feasible in the panel. In addition, high-throughput genome sequencing of these medaka strains confirms their evolutionary relationships on lines of geographic separation and provides further evidence that there has been little significant interbreeding between the Southern and Northern medaka population since the Southern/Northern population split. The sequence data suggest that the Southern Japanese medaka existed as a larger older population that went through a relatively recent bottleneck approximately 10,000 years ago. In addition, we detect patterns of recent positive selection in the Southern population. These data indicate that the genetic structure of the Kiyosu medaka samples is suitable for the establishment of a vertebrate near-isogenic panel and therefore inbreeding of 200 lines based on this population has commenced. Progress of this project can be tracked at http://www.ebi.ac.uk/birney-srv/medaka-ref-panel.

/pdf/genomic-and-phenotypic-characterization-of-a-wild-medaka-2pxirjd2kq.pdf

Kazumi Hosoya

Papers

Oryzias sakaizumii, a new ricefish from northern Japan (Teleostei: Adrianichthyidae)