The zebrafish reference genome sequence and its relationship to the human genome
Kerstin HoweMatthew D. ClarkCarlos TorrojaJames TorranceCamille BerthelotMatthieu MuffatoJohn CollinsSean HumphrayStuart McLarenLucy MatthewsStuart McLarenIan SealyMario CáccamoCarol ChurcherCarol ScottJeffrey C. BarrettRomke KochGerd-Jörg RauchSimon WhiteWilliam ChowBritt KilianLeonor QuintaisJosé Afonso Guerra‐AssunçãoYi ZhouYong Q. GuJennifer YenJan-Hinnerk VogelT. A. EyreSeth RedmondRuby BanerjeeJianxiang ChiBeiyuan FuElizabeth LangleySean MaguireGavin K. LairdDavid LloydEmma J. KenyonSarah DonaldsonHarminder SehraJ. P. AlmeidaJane LovelandStephen J. TrevanionMatthew C. JonesMike QuailDave WilleyAdrienne HuntJohn H. BurtonSarah SimsKirsten McLayBob PlumbJoy DavisChris M. CleeKaren OliverRichard ClarkClare RiddleDavid ElliottGlen ThreadgoldGlenn HardenDarren WareSharmin BegumBeverley MortimoreGiselle KerryP. D. HeathBenjamin PhillimoreAlan TraceyN. CorbyMatthew DunnChristopher M. JohnsonJonathan WoodSusan ClarkSarah PelanGuy GriffithsMichelle SmithRebecca GlitheroPhilip HowdenNicholas BarkerChristine LloydChristopher StevensJoanna HarleyKaren HoltGeorgios PanagiotidisJ. LovellHelen BeasleyCarl HendersonDaria GordonKatherine A. AugerDeborah WrightJoanna CollinsClaire RaisenLauren DyerKenric LeungLauren RobertsonKirsty AmbridgeDaniel LeongamornlertSarah McGuireRuth GilderthorpChris GriffithsDeepa ManthravadiSarah NicholGary BarkerSiobhan WhiteheadMike KayJacqueline BrownClare MurnaneEmma GrayMatthew HumphriesNeil SycamoreDarren BarkerDavid SaundersJ. M. WallisAnne BabbageSian HammondM. Mashreghi-MohammadiLucy BarrSancha MartinPaul WrayAndrew EllingtonNicholas MatthewsMatthew EllwoodRebecca WoodmanseyGraham ClarkJames D. CooperA. TromansDarren GrafhamC. D. SkuceRichard PandianRobert AndrewsElliot HarrisonAndrew KimberleyJ. GarnettNigel FoskerR. E. HallP. GarnerDaniel KellyChristine BirdSophie PalmerInes GehringAndrea BergerChristopher M. DooleyZübeyde Ersan-ÜrünCigdem EserHorst GeigerMaria GeislerLena KarotkiA KirnJudith KonantzMartina KonantzMartina OberländerSilke Rudolph-GeigerMathias TeuckeChrista LanzGünter RaddatzKazutoyo OsoegawaBaoli ZhuAmanda RappSara WidaaCordelia LangfordFengtang YangStephan C. SchusterNigel P. CarterJennifer HarrowZemin NingJavier HerreroSteve SearleAnton J. EnrightRobert GeislerRonald H.A. PlasterkCharles LeeMonte WesterfieldPieter J. de JongLeonard I. ZonJohn H. PostlethwaitChristiane Nüsslein–VolhardTim HubbardHugues Roest CrolliusJane RogersDerek L. Stemple
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A high-quality sequence assembly of the zebrafish genome reveals the largest gene set of any vertebrate and provides information on key genomic features, and comparison to the human reference genome shows that approximately 70% of human protein-coding genes have at least one clear zebrafish orthologue. The genome of the zebrafish — a key model organism for the study of development and human disease — has now been sequenced and published as a well-annotated reference genome. Zebrafish turns out to have the largest gene set of any vertebrate so far sequenced, and few pseudogenes. Importantly for disease studies, comparison between human and zebrafish sequences reveals that 70% of human genes have at least one obvious zebrafish orthologue. A second paper reports on an ongoing effort to identify and phenotype disruptive mutations in every zebrafish protein-coding gene. Using the reference genome sequence along with high-throughput sequencing and efficient chemical mutagenesis, the project's initial results — covering 38% of all known protein-coding genes — they describe phenotypic consequences of more than 1,000 alleles. The long-term goal is the creation of a knockout allele in every protein-coding gene in the zebrafish genome. All mutant alleles and data are freely available at go.nature.com/en6mos . Zebrafish have become a popular organism for the study of vertebrate gene function1,2. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease3,4,5. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes6, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.Keywords:
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Zebrafish (danio rerio) is a small, tropical freshwater teleost fish that belongs to the Cyprinidae family and lives in natural waters and rice fields in South Asia, North India, and Pakistan. Zebrafish has become a popular vertebrate model organism for biomedical research due to its numerous advantages such as their small size, short life cycle, accessibility in large numbers and inexpensive maintenance. In addition, fertilization happens externally in zebrafish and allows zebrafish to be manipulated directly. As another important advantage, the embryos are transparent thus the stages of development can be easily identified. Zebrafish can have multiple co-orthologs for human genes. In the 1930s, the zebrafish was first used as a model for developmental and embryological studies and in 1981, was introduced as a genetic model by Streisinger by force of developed genetic techniques in zebrafish such as cloning, mutagenesis and transgenesis. In the 1990s, various genetic manipulations were introduced. These improvements have contributed to the popularity of zebrafish. After that zebrafish was used in various research areas including genetics, biomedicine, neurobiology, toxicology, pharmacology as well as in human disease models. Zebrafish is also becoming a popular model organism in dental research. It is preferred in dental material toxicity studies and in research related to the genetic and molecular factors in tooth formation and craniofacial development. This review provides information on the use of zebrafish in dental research, focusing on tooth formation and dentition (pharyngeal dentition) of zebrafish and the dental research performed using zebrafish.
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Zebrafish; an emerging model organism for studying toxicity and biocompatibility of dental materials
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