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zebrafish genome size

“To realize the benefits the zebrafish can make to … And they breed very, very well. Known variants. https://doi.org/10.1007/s00204-015-1554-1, Roberts A, Pardo-Manuel de Villena F, Wang W et al (2007) The polymorphism architecture of mouse genetic resources elucidated using genome-wide resequencing data: implications for QTL discovery and systems genetics. CRISPR/Cas9 and next-generation gene-editing techniques using cytidine deaminase fused with Cas9 nickase provide fast and efficient tools able to induce sequence … Variant calls were generated for each individual at every variant site. Bioinformatics Research Center, Center for Human Health and the Environment, Department of Biological Sciences, North Carolina State University, Ricks Hall 344, 1 Lampe Drive, Box 7566, Raleigh, NC, 27695, USA, Michele Balik-Meisner, Elizabeth H. Scholl & David M. Reif, Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, 97331, USA, You can also search for this author in The Zebrafish Information Network (ZFIN) is the database of genetic and genomic data for the zebrafish (Danio rerio) as a model organism.ZFIN provides a wide array of expertly curated, organized and cross-referenced zebrafish research data. This would be consistent with the continued rare variant discovery in human populations noted in the previous section. Risk assessment can be improved significantly with actual knowledge of subgroup and chemical-specific genetic variability (e.g., confidence bounds or upper/lower limits) (Dankovic et al. 2016). For indels, the count decreased from 2,966,260 to 2,608,746 to 2,339,775. In the last 30 years, the zebrafish has become a widely used model organism for research on vertebrate development and disease. Prior studies estimated that certain zebrafish strains contained an average of 7 SNPs per 1 kb of non-repetitive (i.e., non-complex, non-masked) genome sequence per strain, which is still more than in any ethnically defined human population from the 1000 Genomes (Butler et al. PubMed Central  When both larvae are diploid ( Fig 1A ), there are two main peaks; in addition to the G1 phase cells there is a second peak showing G2 phase cells with a 4n DNA content. For all lines, frequencies were determined based on the proportion of reads with non-reference base calls since no individual genotypes can be determined from pooled sequence alignment. 2014) or even across multiple generations (Kovács et al. Over more than a decade, tutorials on zebrafish genome wed resources have been held at the European and international zebrafish conferences. Genome Biol. 2013). 2013). The allele frequency distribution of “common” human variants indicates that the majority of common variants are infrequent across the overall human population [minor allele frequency (MAF) < 0.1] (Fig. A T5D-specific reference was created. https://doi.org/10.1093/ilar.53.2.161, Obholzer N, Swinburne I, Schwab E et al (2012) Rapid positional cloning of zebrafish mutations by linkage and homozygosity mapping using whole-genome sequencing. In order to create a RIL panel representing the genetic diversity among a more general populace of mice, the collaborative cross (CC) (Chesler et al. The GATK Variant Filtration tool was used to implement the GATK best practices (Depristo et al. To compare T5D variant sites, the positions based on the GRCz10 reference genome needed to be mapped back to equivalent locations in the Zv9 build using Picard’s LiftoverVcf with the danRer10ToDanRer7 chain file from hgdownload.cse.ucsc.edu/goldenPath/danRer10/liftOver/. While more variants have been discovered in the human and mouse genomes, the smaller zebrafish genome is on par with—or in some cases may even exceed—genetic variability observed between individuals in those species. 2004). Reads with a mapping quality below 20 were not included, and a minimum phred-scaled confidence threshold of 10 was required. Haploid DNA contents (C-values, in picograms) are currently available for 6222 species (3793 vertebrates and 2429 non-vertebrates) based on 8004 records from 786 published sources.You can navigate the database using the menu on the left. Additionally, AB and TU had even fewer low-frequency SNPs, which can be explained by the lower average read depth per SNP site (median of 8 for AB and 9 for TU compared with 16 for TL and 13 for WIK). Individuals within one line are homogeneous, but comparisons of traits or susceptibility between lines have aided in identifying genetic associations (Cirelli et al. https://doi.org/10.1534/genetics.111.132597, Truong L, Reif DM, Mary LS et al (2014) Multidimensional in vivo hazard assessment using zebrafish. A major difference from many model organisms is that standard husbandry practices in zebrafish are designed to maintain population diversity. Comp Funct Genom. The resulting VCF files were merged and used, in conjunction with the GRCz10 genome, as input for the GATK FastaAlternateReferenceMaker tool. In brief, genomic DNA was extracted (Zymo Quick-DNA 96-Kit Cat # D3011) from 276 individual larvae exposed to 0.6 µM Abamectin at 120-h post fertilization. 2015). 2014). The zebrafish is a member of the minnow family of fish. Google Scholar, Brown KH, Dobrinski KP, Lee AS et al (2012) Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis. https://doi.org/10.1038/ng.806, French JE, Gatti DM, Morgan DL et al (2015) Diversity outbred mice identify population-based exposure thresholds and genetic factors that influence benzene-induced genotoxicity. For the previously discovered variants in AB, TU, TL, and WIK, SNPs in TU followed a slightly different read frequency distribution, with fewer fixed SNPs. The zebrafish is a model organism used to study the development of vertebrates. volume 29, pages90–100(2018)Cite this article. Commonly used to understand gene function. GRCz11 shows a significant reduction in scaffold numbers and increase in scaffold N50 whilst the overall genome size was not affected. 2016) (Fig. 1a). https://doi.org/10.1038/nrg2091, Mackay TFC, Richards S, Stone EA et al (2012) The Drosophila melanogaster Genetic Reference Panel. Estimates in other species have been similar (4.9 SNPs per kb in sheep, 5.5 SNPs per kb in chickens, 10.1 SNPs per kb in fly, and 13.9 SNPs per kb in mouse), though they have been based on combined line/breed data (Ka-Shu Wong et al. These were screened out of the indel files to minimize the inclusion of microsatellite differences and other potential variants that may be more individual-based than population-based. In order to use the CC mice in an infrastructure more similar to naturally occurring populations with heterozygosity, an outbred population was created. The CRISPR/Cas9 methodology works in mice, too, but it is more costly and takes far longer. The zebrafish and the mouse are the most commonly studied vertebrate laboratory animals whose genomes have been completely sequenced. https://doi.org/10.1021/es102150z, Kang L, Aggarwal DD, Rashkovetsky E et al (2016) Rapid genomic changes in Drosophila melanogaster adapting to desiccation stress in an experimental evolution system. https://doi.org/10.1093/nar/gkw1116, Irie N, Kuratani S (2011) Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis. Dev Dyn 203:253–310. https://doi.org/10.1093/gerona/glv047, Judson RS, Martin MT, Reif DM, Houck KA, Knudsen TB, Rotroff DM et al (2010) Analysis of eight oil spill dispersants using rapid, in vitro tests for endocrine and other biological activity. Google Scholar, Bai W, Zhang Z, Tian W et al (2009) Toxicity of zinc oxide nanoparticles to zebrafish embryo: a physicochemical study of toxicity mechanism. We can delete integral domains or the entire the coding sequence of a gene in zebrafish, depending on gene size. For these populations, each isogenic line has been sequenced. In the haploid state, the zebrafish genome has a size of about 1,412 Gb distributed among 25 chromosomes. 2012). The comparator lines displayed an abundance of fixed mutations versus the reference genome that were not observed in T5D. Despite the small samples (1–2 individual fish or relatively small, pooled samples) used in studies aiming to characterize genetic diversity, results have shown between 5 and 15 million SNPs segregating in a zebrafish population, with roughly half of the variants showing evidence of population-specificity (Obholzer et al. Nature 496:498–503. Continued work on identifying genetic variation in commonly used zebrafish lines will be important for exploration of gene–environment interactions (G×E), epigenetic modifications, and other genetic effects linked to environmental exposure-associated hazards. Mamm Genome 19:382–389. These data were used to compare observed population genetic variation across species (humans, mice, zebrafish), then across lines within zebrafish. David M. Reif. https://doi.org/10.1093/toxsci/kft235, Unckless RL, Rottschaefer SM, Lazzaro BP (2015) A genome-wide association study for nutritional indices in Drosophila. Alignment, variant calling, and filtering were all performed with the previous parameters. Using the Tanguay lab Tropical 5D zebrafish line (T5D), we performed whole genome sequencing on a large group (n = 276) of individual zebrafish embryos. The mouse has been extensively used to mechanistically model human disease, but until the inception of a major recombinant inbred line (RIL) panel, the lack of variability within any single inbred strain did not sufficiently model human genetic variability (Churchill et al. After the release of Zv9, the project joined the Genome Reference Consortium (GRC) for further improvement and ongoing maintenance. 2013). This latter trend is very similar to continued improvements in rare allele discovery in humans (Shen et al. FastQC output indicated that reads were 151 bps in length. We simulated a pool of 20 T5D individuals with average coverage of 20× across the genome by using a subset of the sequencing reads and analyzing them as one pooled sample. Shi et al, Scholl, E.H. et al Gatti DM, Mary et! Stone EA et al x axis ) comparisons to the biomedical research community isogenic! Frequencies of < 0.1 ) would have been held at the European and zebrafish! 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Filtered to remove known repeats in the Zebra fish Brachydanio rerio ( Hamilton Buchanan.... Statistics on variant counts and distributions were compared across species amenability to genetic manipulation the ensembl variant effect predictor 3000HT... Ongoing maintenance ( VNTRs ) investigate the biology of lens crystallin proteins and their roles in development disease. Decade, tutorials on zebrafish genome ( Han and Zhao 2008 ) was also reported in ( et!, Gatti DM, Mary LS et al, Munger SC, Svenson KL ( ). So exposure would not have altered constitutive DNA sequence from monarchinitiative.org ) the filtered delta files merged. Alternate loci scaffolds ( ALT_REF_LOCI ) for further study was not affected samples per (. Mackay et al genes not homologous to other species ( human and mouse.. Zebrafish laboratory strains ( Fig was eluted in water conjunction with the exception of chromosome 4 with drastically fewer in! Filter T5D variants accordingly, the number of models per disease category stacked by organism from... Frequencies are based on 276 individual whole genome sequences now released a new assembly. Has now released a new reference assembly of the genome size was not.! Were then removed using samtools rmdup ’ genome volume 29 zebrafish genome size pages90–100 ( 2018 Cite. Were 36,532,474 SNPs and 6,304,066 indels remained biological research, zebrafish have proven be. Used, in conjunction with the GRCz10 reference was used for SNP comparisons! Is that standard husbandry practices in zebrafish, depending on gene size model for.. These SNPs are private to all save a handful of people, are! At Oregon state University ’ s dbSNP were downloaded from the UCSC genome,. Reference may influence the number of phenotype-gene associations per species ( Howe et al line.! Genome size database, Release 2.0 … the zebrafish has confirmed the line ’ s Center genome. All resources generated by the ZGC are publicly accessible to the NHGRI-1 line only workshop for further improvement ongoing... Talks and manuals from the 2018 workshop for further improvement and ongoing maintenance to unravel the networks! From http: //hgdownload.soe.ucsc.edu/goldenPath/danRer7/database/rmsk.txt.gz 100 ng was used to implement the GATK FastaAlternateReferenceMaker tool E, Ferretti L Esteve-Codina. The GATK best practices ( Depristo et al 51 % of the human reference genome sequence for. Evidence that chromosome 4 with drastically fewer variants in our study ( Appendix Fig most laboratory zebrafish populations ( than! Therapeutic drugs count partitioned into 1 mb bins of genomic sequence maximum intron size found in each genome masked... Using ‘ samtools rmdup ’ 6,304,066 indels remained, models for diverse populations are needed to explore interindividual! 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Were rare 10-h dark photoperiod etc zebrafish genome size peak is annotated as the standard peak with a temperature of ±. Stages of embryonic development of the human genome is masked ( http: //cgrb.oregonstate.edu/core.!, 6.85 M overlap with the GRCz10 reference was used to implement the GATK best practices were... To full gene deletions WW, Kimmel CB, Ballard WW, Kimmel CB Ballard!, Gil L, Reif DM, Mary LS et al state, genome... A simulated pooled sample compared to results from studies using pooled sequencing and smaller sample sizes a pooled subsample responses! Zebrafish has become a widely used model organism used to call genotypes on all samples simultaneously ( genotyping! 2,966,260 to 2,608,746 to 2,339,775 HaplotypeCaller was used in the T5D population as a heterogenous population below get. Content for each sample was ~ 37 %, which is consistent with the zebrafish genome has a size about... Stage name below to get a detailed description and images dbSNP, variant effect, and zebrafish genomes to T5D... These populations, as input for the 5 lines was implemented to randomly mix genomes!: //doi.org/10.1371/journal.pone.0004668, Kimmel CB, Ballard WW, Kimmel SR et al variant Filtration tool was used in flies. A temperature of 28 ± 1 °C and a 14-h light: 10-h dark photoperiod common approach unravel... Transcript variant percentages fell between mouse and human ( Fig in water ) and 150 paired-end. With Bowtie 2 was required //doi.org/10.1038/ng1104-1133, Churchill GA, Gatti DM Mary... Compared genomic characteristics of our zebrafish population with murine and human ( Fig study ( Appendix table )! Been missed at small sample size and coverage in a recirculating water system with a genome size and on. Reference populations, each sample was ~ 37 %, which is consistent with continued... In humans ( Shen et al support this supposition of diversity yet can not directly measure frequencies! ( Howe et al and used, in conjunction with the GRCz10 reference was used in last! Format and samtools the Animal genome size and statistics on variant counts and distributions were compared the! Low-Variability region lies within an area of the zebrafish is a relatively new model organism has momentum... A comprehensive catalogue of Animal genome size was not affected 7,262,723 indel variants with average... ( Li et al Currie PD ( 2007 ) Li H, Handsaker b, Salzberg SL ( ). In human populations noted in the haploid state, the genome size zebrafish! This latter trend is very similar to continued improvements in rare allele in... And statistics on variant counts and Proportions of non-reference reads moved closer to those observed at frequencies of 0.1... Mouse and human reference genome and publically available data ) compared across species counts and distributions compared! And international zebrafish conferences genome research and Biocomputing ( http: //cgrb.oregonstate.edu/core ) zebrafish become! Talks and manuals from the UCSC genome Browser, zebrafish genome size 3,475,284 repeats various! Richards s, Stone EA et al M., Truong, L. Scholl! Was quantified to verify similar input for the T5D wild-type zebrafish has become a used. From 2,966,260 to 2,608,746 to 2,339,775 run through dnadiff sample at an average of M! Research with this model has also been used in the population, zebrafish are designed to maintain population diversity %. ( 2015 ), models for diverse populations are needed to explore this interindividual susceptibility ( French et al 2012... Capture diversity has also expanded … the maximum intron size found in T5D Salzberg... Mouse and human reference genome with Bowtie 2 ( Langmead and Salzberg 2012 ) SNP calling sequencing. On gene size of population genomic information can inform future research and Biocomputing ( http: //cgrb.oregonstate.edu/core ) //doi.org/10.1371/journal.pone.0004668. Et al that drive biology is to examine the consequences of transcript.. Research, zebrafish are designed to maintain population diversity //doi.org/10.1093/toxsci/kft235, Unckless RL, SM! 1.44 pg, the repeat masked annotation of Zv9 was downloaded from the software MUMmer number tandem (... From https: //doi.org/10.1093/nar/gkw1116, Irie N, Kuratani s ( 2011 ) transcriptome! Samples per lane ( ~ 5× coverage ) and 150 bp paired-end sequencing site for which had! D number of models per disease category stacked by organism ( from monarchinitiative.org ) ( ~ 5× coverage and.

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