Dataset Information

The zebrafish reference genome sequence and its relationship to the human genome.

ABSTRACT: Zebrafish have become a popular organism for the study of vertebrate gene function. 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 disease. 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 genes, 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.

SUBMITTER: Howe K

PROVIDER: S-EPMC3703927 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature

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The zebrafish reference genome sequence and its relationship to the human genome.

Howe Kerstin K Clark Matthew D MD Torroja Carlos F CF Torrance James J Berthelot Camille C Muffato Matthieu M Collins John E JE Humphray Sean S McLaren Karen K Matthews Lucy L McLaren Stuart S Sealy Ian I Caccamo Mario M Churcher Carol C Scott Carol C Barrett Jeffrey C JC Koch Romke R Rauch Gerd-Jörg GJ White Simon S Chow William W Kilian Britt B Quintais Leonor T LT Guerra-Assunção José A JA Zhou Yi Y Gu Yong Y Yen Jennifer J Vogel Jan-Hinnerk JH Eyre Tina T Redmond Seth S Banerjee Ruby R Chi Jianxiang J Fu Beiyuan B Langley Elizabeth E Maguire Sean F SF Laird Gavin K GK Lloyd David D Kenyon Emma E Donaldson Sarah S Sehra Harminder H Almeida-King Jeff J Loveland Jane J Trevanion Stephen S Jones Matt M Quail Mike M Willey Dave D Hunt Adrienne A Burton John J Sims Sarah S McLay Kirsten K Plumb Bob B Davis Joy J Clee Chris C Oliver Karen K Clark Richard R Riddle Clare C Elliot David D Threadgold Glen G Harden Glenn G Ware Darren D Begum Sharmin S Mortimore Beverley B Kerry Giselle G Heath Paul P Phillimore Benjamin B Tracey Alan A Corby Nicole N Dunn Matthew M Johnson Christopher C Wood Jonathan J Clark Susan S Pelan Sarah S Griffiths Guy G Smith Michelle M Glithero Rebecca R Howden Philip P Barker Nicholas N Lloyd Christine C Stevens Christopher C Harley Joanna J Holt Karen K Panagiotidis Georgios G Lovell Jamieson J Beasley Helen H Henderson Carl C Gordon Daria D Auger Katherine K Wright Deborah D Collins Joanna J Raisen Claire C Dyer Lauren L Leung Kenric K Robertson Lauren L Ambridge Kirsty K Leongamornlert Daniel D McGuire Sarah S Gilderthorp Ruth R Griffiths Coline C Manthravadi Deepa D Nichol Sarah S Barker Gary G Whitehead Siobhan S Kay Michael M Brown Jacqueline J Murnane Clare C Gray Emma E Humphries Matthew M Sycamore Neil N Barker Darren D Saunders David D Wallis Justene J Babbage Anne A Hammond Sian S Mashreghi-Mohammadi Maryam M Barr Lucy L Martin Sancha S Wray Paul P Ellington Andrew A Matthews Nicholas N Ellwood Matthew M Woodmansey Rebecca R Clark Graham G Cooper James D J Tromans Anthony A Grafham Darren D Skuce Carl C Pandian Richard R Andrews Robert R Harrison Elliot E Kimberley Andrew A Garnett Jane J Fosker Nigel N Hall Rebekah R Garner Patrick P Kelly Daniel D Bird Christine C Palmer Sophie S Gehring Ines I Berger Andrea A Dooley Christopher M CM Ersan-Ürün Zübeyde Z Eser Cigdem C Geiger Horst H Geisler Maria M Karotki Lena L Kirn Anette A Konantz Judith J Konantz Martina M Oberländer Martina M Rudolph-Geiger Silke S Teucke Mathias M Lanz Christa C Raddatz Günter G Osoegawa Kazutoyo K Zhu Baoli B Rapp Amanda A Widaa Sara S Langford Cordelia C Yang Fengtang F Schuster Stephan C SC Carter Nigel P NP Harrow Jennifer J Ning Zemin Z Herrero Javier J Searle Steve M J SM Enright Anton A Geisler Robert R Plasterk Ronald H A RH Lee Charles C Westerfield Monte M de Jong Pieter J PJ Zon Leonard I LI Postlethwait John H JH Nüsslein-Volhard Christiane C Hubbard Tim J P TJ Roest Crollius Hugues H Rogers Jane J Stemple Derek L DL

Nature 20130417 7446

Zebrafish have become a popular organism for the study of vertebrate gene function. 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 disease. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes an ...[more]

PMID: 23594743

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Project description:The determination of the relationship between a pair of individuals is a fundamental application of genetics. Previously, we and others have demonstrated that identity-by-descent (IBD) information generated from high-density single-nucleotide polymorphism (SNP) data can greatly improve the power and accuracy of genetic relationship detection. Whole-genome sequencing (WGS) marks the final step in increasing genetic marker density by assaying all single-nucleotide variants (SNVs), and thus has the potential to further improve relationship detection by enabling more accurate detection of IBD segments and more precise resolution of IBD segment boundaries. However, WGS introduces new complexities that must be addressed in order to achieve these improvements in relationship detection. To evaluate these complexities, we estimated genetic relationships from WGS data for 1490 known pairwise relationships among 258 individuals in 30 families along with 46 population samples as controls. We identified several genomic regions with excess pairwise IBD in both the pedigree and control datasets using three established IBD methods: GERMLINE, fastIBD, and ISCA. These spurious IBD segments produced a 10-fold increase in the rate of detected false-positive relationships among controls compared to high-density microarray datasets. To address this issue, we developed a new method to identify and mask genomic regions with excess IBD. This method, implemented in ERSA 2.0, fully resolved the inflated cryptic relationship detection rates while improving relationship estimation accuracy. ERSA 2.0 detected all 1(st) through 6(th) degree relationships, and 55% of 9(th) through 11(th) degree relationships in the 30 families. We estimate that WGS data provides a 5% to 15% increase in relationship detection power relative to high-density microarray data for distant relationships. Our results identify regions of the genome that are highly problematic for IBD mapping and introduce new software to accurately detect 1(st) through 9(th) degree relationships from whole-genome sequence data.

Dataset Information

The zebrafish reference genome sequence and its relationship to the human genome.

Publications

The zebrafish reference genome sequence and its relationship to the human genome.

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