start-ver=1.4
cd-journal=joma
no-vol=10
cd-vols=
no-issue=11
article-no=
start-page=3883
end-page=3895
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=202011
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=A Reference Genome from the Symbiotic Hydrozoan, Hydra viridissima
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Various Hydra species have been employed as model organisms since the 18(th) century. Introduction of transgenic and knock-down technologies made them ideal experimental systems for studying cellular and molecular mechanisms involved in regeneration, body-axis formation, senescence, symbiosis, and holobiosis. In order to provide an important reference for genetic studies, the Hydra magnipapillata genome (species name has been changed to H. vulgaris) was sequenced a decade ago (Chapman et al., 2010) and the updated genome assembly, Hydra 2.0, was made available by the National Human Genome Research Institute in 2017. While H. vulgaris belongs to the non-symbiotic brown hydra lineage, the green hydra, Hydra viridissima, harbors algal symbionts and belongs to an early diverging clade that separated from the common ancestor of brown and green hydra lineages at least 100 million years ago (Schwentner and Bosch 2015; Khalturin et al., 2019). While interspecific interactions between H. viridissima and endosymbiotic unicellular green algae of the genus Chlorella have been a subject of interest for decades, genomic information about green hydras was nonexistent. Here we report a draft 280-Mbp genome assembly for Hydra viridissima strain A99, with a scaffold N50 of 1.1 Mbp. The H. viridissima genome contains an estimated 21,476 protein-coding genes. Comparative analysis of Pfam domains and orthologous proteins highlights characteristic features of H. viridissima, such as diversification of innate immunity genes that are important for host-symbiont interactions. Thus, the H. viridissima assembly provides an important hydrozoan genome reference that will facilitate symbiosis research and better comparisons of metazoan genome architectures.
en-copyright=
kn-copyright=

en-aut-name=HamadaMayuko
en-aut-sei=Hamada
en-aut-mei=Mayuko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=SatohNoriyuki
en-aut-sei=Satoh
en-aut-mei=Noriyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=KhalturinKonstantin
en-aut-sei=Khalturin
en-aut-mei=Konstantin
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

affil-num=1
en-affil=Ushimado Marine Institute, Okayama University
kn-affil=

affil-num=2
en-affil=Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University
kn-affil=

affil-num=3
en-affil=Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University
kn-affil=
en-keyword=green hydra
kn-keyword=green hydra
en-keyword=Hydra viridissima A99
kn-keyword=Hydra viridissima A99
en-keyword=whole genome sequencing
kn-keyword=whole genome sequencing
en-keyword=de novo assembly
kn-keyword=de novo assembly
en-keyword=symbiosis
kn-keyword=symbiosis
END

start-ver=1.4
cd-journal=joma
no-vol=G3: Genes Genomes Genetics
cd-vols=
no-issue=1
article-no=
start-page=217
end-page=228
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2019
dt-pub=201901
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Medaka Population Genome Structure and Demographic History Described via Genotyping-by-Sequencing
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Medaka is a model organism in medicine, genetics, developmental biology and population genetics. Lab stocks composed of more than 100 local wild populations are available for research in these fields. Thus, medaka represents a potentially excellent bioresource for screening disease-risk- and adaptation-related genes in genome-wide association studies. Although the genetic population structure should be known before performing such an analysis, a comprehensive study on the genome-wide diversity of wild medaka populations has not been performed. Here, we performed genotyping-by-sequencing (GBS) for 81 and 12 medakas captured from a bioresource and the wild, respectively. Based on the GBS data, we evaluated the genetic population structure and estimated the demographic parameters using an approximate Bayesian computation (ABC) framework. The genome-wide data confirmed that there were substantial differences between local populations and supported our previously proposed hypothesis on medaka dispersal based on mitochondrial genome (mtDNA) data. A new finding was that a local group that was thought to be a hybrid between the northern and the southern Japanese groups was actually an origin of the northern Japanese group. Thus, this paper presents the first population-genomic study of medaka and reveals its population structure and history based on chromosomal genetic diversity.
en-copyright=
kn-copyright=

en-aut-name=KatsumuraTakafumi
en-aut-sei=Katsumura
en-aut-mei=Takafumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=OdaShoji
en-aut-sei=Oda
en-aut-mei=Shoji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=MitaniHiroshi
en-aut-sei=Mitani
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=OotaHiroki
en-aut-sei=Oota
en-aut-mei=Hiroki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

affil-num=1
en-affil=Graduate School of Natural Science and Technology, Okayama University
kn-affil=

affil-num=2
en-affil=Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo
kn-affil=

affil-num=3
en-affil=Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo
kn-affil=

affil-num=4
en-affil=Department of Anatomy, Kitasato University School of Medicine
kn-affil=
en-keyword=local population
kn-keyword=local population
en-keyword=freshwater fish
kn-keyword=freshwater fish
en-keyword=demography
kn-keyword=demography
en-keyword=RAD-seq
kn-keyword=RAD-seq
en-keyword=bioresource
kn-keyword=bioresource
END