Genomic and Phenotypic Characterization of a Wild Medaka Population : Towards the Establishment of an Isogenic Population Genetic Resource in Fish

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

A genome database for a Japanese population of the larvacean Oikopleura dioica

The larvacean Oikopleura dioica is a planktonic chordate, and is tunicate that belongs to the closest relatives to vertebrates. Its simple and transparent body, invariant embryonic cell lineages, and short life cycle of five days make it a promising model organism for developmental biology research. The genome browser OikoBase was established in 2013 using Norwegian O. dioica. However, genome information for other populations is not available, even though many researchers have studied local populations. In the present study, we sequenced using Illumina and PacBio RSII technologies the genome of O. dioica from a southwestern Japanese population that was cultured in our laboratory for three years. The genome of Japanese O. dioica was assembled into 576 scaffold sequences with a total length and N50 length of 56.6 Mb and 1.5 Mb, respectively. A total of 18,743 gene models (transcript models) were predicted in the genome assembly, named as OSKA2016. In addition, 19,277 non-redundant transcripts were assembled using RNA-seq data. The OSKA2016 has global sequence similarity of only 86.5% when compared with the OikoBase, highlighting the sequence difference between the two far distant O. dioica populations on the globe. The genome assembly, transcript assembly, and transcript models were incorporated into ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and blast searches. Moreover, screening of the male-specific scaffolds revealed that over 2.6 Mb of sequence were included in the male-specific Yregion. The genome and transcriptome resources from two distinct populations will be useful datasets for developmental biology, evolutionary biology, and molecular ecology using this model organism

Genome Features of “Dark-Fly”, a Drosophila Line Reared Long-Term in a Dark Environment

Organisms are remarkably adapted to diverse environments by specialized metabolisms, morphology, or behaviors. To address the molecular mechanisms underlying environmental adaptation, we have utilized a Drosophila melanogaster line, termed “Dark-fly”, which has been maintained in constant dark conditions for 57 years (1400 generations). We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness. Using next-generation sequencing technology, we determined the whole genome sequence of Dark-fly and identified approximately 220,000 single nucleotide polymorphisms (SNPs) and 4,700 insertions or deletions (InDels) in the Dark-fly genome compared to the genome of the Oregon-R-S strain, a control strain. 1.8% of SNPs were classified as non-synonymous SNPs (nsSNPs: i.e., they alter the amino acid sequence of gene products). Among them, we detected 28 nonsense mutations (i.e., they produce a stop codon in the protein sequence) in the Dark-fly genome. These included genes encoding an olfactory receptor and a light receptor. We also searched runs of homozygosity (ROH) regions as putative regions selected during the population history, and found 21 ROH regions in the Dark-fly genome. We identified 241 genes carrying nsSNPs or InDels in the ROH regions. These include a cluster of alpha-esterase genes that are involved in detoxification processes. Furthermore, analysis of structural variants in the Dark-fly genome showed the deletion of a gene related to fatty acid metabolism. Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Summary of genome sequencing.

<p>The results of genome sequencing using an Illumina Genome Analyzer II are summarized. Flybase Dmel 5.22 genome (168,736,537 bases) was used as a reference genome.</p

Genes carrying nsSNPs and cInDels in the Dark-fly ROH regions.

<p>The chromosomal position and length of the Dark-fly ROH regions showing significantly high homozygosity are listed. Genes carrying nsSNPs and InDels in each ROH region are shown. Details regarding nsSNPs and cInDels are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033288#pone.0033288.s004" target="_blank">File S1</a>.</p

History of Dark-fly.

<p>In 1954, a fly population derived from one pair of Oregon-R-S flies was divided into 6 populations. Three of them (aL, bL and cL populations) were reared in normal light-dark cycling conditions and the remaining three populations (dD, eD, and fD populations) were reared in constant dark conditions. Unfortunately, all of the L lines were lost by 2002. The dD and eD lines were lost in 1965 and 1967, and only the fD line has been maintained until now. In 2008, we started to rear the fD line and designated it “Dark-fly”. We have maintained Dark-fly in a minimum medium as done before (black lines), and in a standard cornmeal medium (white lines) in parallel. The population size of Dark-fly has not been controlled but has usually been about 100 flies each in several culture vials.</p

Survival curves of Dark-fly and Oregon-R-S.

<p>The viability of male flies (A) and female flies (B) reared together is plotted versus time (days). Dark-fly (red lines) and Oregon-R-S (blue lines) were reared under LD (dotted lines) and DD (solid lines) conditions. The viability of virgin females (C) was also measured in a similar manner. n = 92–100 flies. Oregon-R-S virgin females showed longer longevity than the mated ones, whereas Dark-fly virgin females showed shorter longevity than the mated ones.</p

Alignment of read sequences around CG4594 gene.

<p>A view of Integrated Genomics Viewer around the CG4594 gene. The numerous small gray bars represent reads of genome sequencing. A region of about 500 bases in the CG4594 gene (red thick bar) was not covered by any read sequences of the Dark-fly genome (upper), but was fully covered by the sequences of the Oregon-R-S genome (lower). Numbers on a horizontal line indicate nucleotide position on chromosome 2L. Numbers on vertical alignment indicate read depth.</p