Over more than a decade, tutorials on zebrafish genome wed resources have been held at the European and international zebrafish conferences. The use of genetically modified zebrafish has also allowed identification of new putative therapeutic drugs. 2014) was downloaded for use in a separate line comparison due to sequencing strategy differences and alignment to different versions of the reference genome. The effect of the variants on genes and transcripts and consequences on protein sequence were annotated for each species using Ensembl variant effect predictor (VEP) (McLaren et al. This latest assembly has been refined by the addition of nearly 1000 finished clone sequences and the resolution of more than 400 genome issues. Enter your email address to receive updates about the latest advances in genomics research. Nucmer was run with the—mum option. https://doi.org/10.1155/2008/565631, Howe K, Clark MD, Torroja CF et al (2013) The zebrafish reference genome sequence and its relationship to the human genome. Nonetheless, isogenic models of any species fail to model the influence of genetic diversity on toxicity responses, a critical factor in human responses to toxicants. Variant discovery in the T5D wild-type zebrafish has confirmed the line’s status as a heterogenous population. However, because ethnic/population-level choice of reference may influence the number of variants called (Cho et al. A major difference from many model organisms is that standard husbandry practices in zebrafish are designed to maintain population diversity. While this could indicate that the human reference genome provides a more representative consensus across human populations, it is also possible that the absence of admixing between zebrafish laboratory populations may have caused them to diverge more from a historical reference sequence. https://doi.org/10.1086/519795, Asharani PV, Lianwu Y, Gong Z, Valiyaveettil S (2015) Comparison of the toxicity of silver, gold and platinum nanoparticles in developing zebrafish embryos. 1b, 2b, d). The VCF of 20,385,817 SNPs for T5D compared to the GRCz10 reference was used for SNP site comparisons to the NHGRI-1 line only. PubMed Central 2013). 1b). 2017). VEP (McLaren et al. 2013). Potential PCR duplicates were then removed using Samtools rmdup (Li et al. The zebrafish reference genome sequence and its relationship to the human genome. A VCF file for NHGRI-1 (LaFave et al. The indel file was further filtered to remove known repeats in the GRCz10 reference build. The T5D allele frequencies are based on 276 individual whole genome sequences. 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. Aquat Toxicol 95:355–361. Our observations suggest that interindividual genetic diversity (i.e., natural variation) within laboratory populations may be higher than currently estimated and may have implications for differential susceptibility observed in toxicological studies. 2013). In this regard, zebrafish are useful because the embryo is transparent, it develops outside of its mother, and its development from eggs to larvae happens in just three days. Pooled sequencing data fundamentally affected the character of genetic variation previously detectable in outbred zebrafish lines, versus the individual-level sequencing data collected for T5D. BMC Bioinform 13(1):239, Reif DM, Truong L, Mandrell D et al (2016) High-throughput characterization of chemical-associated embryonic behavioral changes predicts teratogenic outcomes. Zebrafish 10:15–20. Previous studies have used the zebrafish to investigate the biology of lens crystallin proteins and their roles in development and disease. Subsampling to simulate a pooled sequencing approach showed that T5D variation is in line with the more variable zebrafish laboratory strains (Fig. It came into awareness in the scientific community, at least for geneticists, roughly around 1981 when the late George Streisinger, looking for a new genetic organism to study, picked up a couple of zebrafish at the local pet store and started to do a few experiments with them. Here, we characterize salient features of population genetic architecture of the Tropical 5D (T5D) line as a representative laboratory population of zebrafish. 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. 2016). There are also long-term benefits associated with creating a database of known SNPs in zebrafish populations. The red box contains the variant effects for the 20.1 M SNPs found in T5D. For these populations, each isogenic line has been sequenced. 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. T5D variants, discovered based on approximately 1380× coverage across individuals (5× for 276 individuals), followed an allele frequency spectrum more similar to known human variants (Figs. Its importance has been consolidated by successful large-scale forward genetic screens(commonly referred to as the Tübingen/… Genetics 198:167–170. Comparing across broad populations, Cho et al. PubMed 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. Genetic screens in Zebrafish have led to the discovery of large number of … 2004). There was a region of chromosome 4 with drastically fewer variants in our study (Appendix Fig. 2a, c). PubMed In the last 30 years, the zebrafish has become a widely used model organism for research on vertebrate development and disease. However, little is known about zebrafish α-crystallin promoter function, how it compares to that of mammals, or whether mammalian α-crystallin promoter activity can be assessed using zebrafish embryos. associated with differential chemical responses (Balik-Meisner et al., submitted). 2012). To filter T5D variants accordingly, the repeat masked annotation of Zv9 was downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/danRer7/database/rmsk.txt.gz. Indeed, the zebrafish model is gaining tractability as a human disease model (Howe et al. We obtained whole genome sequences of 276 individuals from the T5D population, aligned reads to the GRCz10 reference genome, called SNPs and indels, and created a T5D-specific reference genome. In Chinese individuals, an average of 3.5 M SNPs and 0.63 M indels were identified (Shi et al. https://doi.org/10.1038/351652a0, Ka-Shu Wong G, Liu B, Wang J et al (2004) A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. The zebrafish is a model organism used to study the development of vertebrates. 1d). The extraction protocol was followed according to the manufacturer and DNA was eluted in water. Each of these studies sequenced a pool of zebrafish between 3× and 16× coverage and aligned reads as one sample to the Zv9 reference genome for each line. Zebrafish variant comparisons after sequencing and masking a pooled subsample. Many of these sites may actually be variable in the populations (rather than fixed) yet missed in the sampled subsets. Proc Natl Acad Sci 109:529–534. Low-frequency variants were no longer identifiable, and a larger proportion of the non-reference alleles incorrectly displayed themselves as fixed mutations (F = 1 in Fig. 2012; Bowen et al. Nucleic Acids Res 45:D758–D768. This peak is annotated as the standard peak with a genome size of 1.44 pg, the genome size of zebrafish . When using a Korean genome as the reference, the number of calls increased for each of the African and Caucasian individuals and decreased for the Asian individuals (Cho et al. Research with this model has also expanded … Environ Health Perspect 123:237–245. Because select individuals or entire communities may be especially susceptible to adverse health effects from chemical exposure through common consumer products, occupational hazards, environmental emergencies, or geographic location (Brette et al. Part of Springer Nature. This is true for applications that range from environmental chemical exposure studies or pharmaceutical trials in human populations to environmental emergencies affecting ecological species, such as the response to the spill of MCHM in West Virginia (http://ntp.niehs.nih.gov/results/areas/wvspill/studies/index.html). PubMed 2014; Asharani et al. 2013). https://doi.org/10.1371/journal.pbio.0060216, Dankovic DA, Naumann BD, Maier A et al (2015) The scientific basis of uncertainty factors used in setting occupational exposure limits. BMC Genom. In addition to discovering more variants, the design allowed us to estimate allele frequencies for a population more accurately than previously possible due to bias when estimating based on read frequencies in a pool (Raineri et al. The Zebrafish Gene Collection (ZGC) is an NIH initiative that supports the production of cDNA libraries, clones and sequences to provide a complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for zebrafish. d Proportion of indels for discrete alternate allele frequencies. 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. In order to assess whether sequencing design could be a major driver behind observed SNP differences between lines, we used a downsampling strategy to approximate published designs used for other lines. The zebrafish is a member of the minnow family of fish. 1). J Fish Biol 15:323–327, Nasiadka A, Clark MD (2012) Zebrafish breeding in the laboratory environment. https://doi.org/10.1093/toxsci/kft235, Unckless RL, Rottschaefer SM, Lazzaro BP (2015) A genome-wide association study for nutritional indices in Drosophila. The GATK Variant Filtration tool was used to implement the GATK best practices (Depristo et al. 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 Genetics 190:1017–1024. J Gerontol Ser A 70:1470–1478. They're very hearty organisms. These data were used to compare observed population genetic variation across species (humans, mice, zebrafish), then across lines within zebrafish. We have generated lesions ranging from small indels to full gene deletions. Comp Biochem Physiol Part C 187:50–61. All resources generated by the ZGC are publicly accessible to the biomedical research community. For each sample (DNA from an individual zebrafish), reads were aligned to the Genome Reference Consortium GRCz10 (Howe et al. 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. The CRISPR/Cas9 methodology works in mice, too, but it is more costly and takes far longer. Next, 20% of each of their reads were randomly selected to create a simulated pooled sample at an average of 20× coverage. The T5D founders of our experimental population were originally imported into the Tanguay lab at Oregon State University from a breeding facility containing thousands of zebrafish in 2007 to generate a Pseudoloma neurophilia (Microsporidia) free line (Stanley et al. All generations are propagated with equal proportions of offspring contributed from a minimum of 25 small group crosses, each group containing three males and up to three females. There are many benefits to using zebrafish in developmental studies, including early maturation as clear embryos that are amenable to easily observable morphological endpoints, short generation time, and well-characterized development that is conserved across species during the phylotypic period (Kimmel et al. Model organisms have long been utilized to study genetic determinants underlying human disease susceptibility, because experiments can exert necessary controls over factors such as diet, lifestyle, and environment that would be impossible in a human setting. The filtered delta files were also run through dnadiff. A T5D-specific reference was created. David M. Reif. https://doi.org/10.1242/dev.083931, Oliveira R, Grisolia CK, Monteiro MS et al (2016) Multilevel assessment of ivermectin effects using different zebrafish life stages. 2013. 2009; Kang et al. Article https://doi.org/10.1007/s00335-007-9045-1, Sakharkar MK, Perumal BS, Sakharkar KR, Kangueane P (2005) An analysis on gene architecture in human and mouse genomes. These advantages have led to an upward trend in high-throughput zebrafish chemical screens, especially toward screens of many chemicals using large quantities of fish (Usenko et al. Google Scholar, Patowary A, Purkanti R, Singh M et al (2013) A sequence-based variation map of zebrafish. Individuals within one line are homogeneous, but comparisons of traits or susceptibility between lines have aided in identifying genetic associations (Cirelli et al. 2012). Bioinform Appl NOTE 25:2078–2079. We establish T5D as a model that is representative of diversity levels within laboratory zebrafish lines and demonstrate that experimental design and analysis can exert major effects when characterizing genetic diversity in heterogeneous populations. For example, in Caucasians an average of 3.3 M SNPs and 0.49 M indels with non-reference alleles were identified per individual (Shen et al. Genetics 114:1291–1308, Yang H, Wang JR, Didion JP et al (2011) Subspecific origin and haplotype diversity in the laboratory mouse. We then empirically compared genomic characteristics of our zebrafish population with murine and human reference populations, as well as across other zebrafish lines. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The zebrafish genome (1.5 Gb) is roughly half the size of the human (3.3 Gb) or mouse (2.8 Gb) genome. This can be explained in part by the heavy reliance of the reference genome sequence on TU zebrafish. 2017). One reason for the success of zebrafish as a model organism is its amenability to genetic manipulation. Development 139:4280–4290. 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. The zebrafish and the mouse are the most commonly studied vertebrate laboratory animals whose genomes have been completely sequenced. Environ Sci Technol 44:5979–5985. Commonly used to understand gene function. https://doi.org/10.1016/j.gdata.2014.10.013, Article Nat Commun 7:13637. https://doi.org/10.1038/ncomms13637, Churchill GA, Airey DC, Allayee H et al (2004) The collaborative cross, a community resource for the genetic analysis of complex traits. Nature 432:717–722. They have a lot of advantages that are attractive to scientists, one of them being that they are in fact quite cheap to buy, which is always a consideration. New features in Release 2.0 … https://doi.org/10.1016/j.carbon.2007.04.021, Wilson CA, High SK, McCluskey BM et al (2014) wild sex in zebrafish: loss of the natural sex determinant in domesticated strains. 1995; Irie and Kuratani 2011). The genome of the zebrafish Danio rerio is to be deciphered by a dedicated team at Britain's Sanger Centre. We theorize that some subset of the novel SNPs may be shared with other zebrafish lines but have not been identified in other studies due to the limitations of capturing population diversity in pooled sequencing strategies. They're easy to take care of. Mamm Genome 18:473–481. https://doi.org/10.1242/dev.118786, Chesler EJ, Miller DR, Branstetter LR et al (2008) The Collaborative Cross at Oak Ridge National Laboratory: developing a powerful resource for systems genetics. J Occup Environ Hyg 12(Suppl 1):S55–S68. Tools for gene manipulation together with information about the genome are powerful resources for investigating any biological process. These results were compared to the other species (human and mouse). As omnivorous organisms, they feed on a range of organisms such as insects, … The T5D line is an “outbred” population of heretofore unknown genetic heterogeneity that has been used to screen thousands of chemicals for adverse biological responses (Truong et al. Information about the continuing improvement of the zebrafish genome After 2.5 years of assembly curation, the GRC presents the new zebrafish reference genome assembly, GRCz11. https://doi.org/10.1016/j.aquatox.2009.10.008, Svenson KL, Gatti DM, Valdar W et al (2012) High-resolution genetic mapping using the Mouse Diversity outbred population. We used new data from a genome-wide sequencing project to compare and characterize observed population genetic variation across species (humans, mice, zebrafish). Mamm Genome 23:713–718. Because of the optical transparency of the embryos, small size at maturity and ease of culture, Zebrafish has become a popular organism to study embryonic development for biologist worldwide. 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. 2016; Srivastava et al. This downsampling approach resulted in a twofold reduction in variant calling capability, providing evidence that sequencing design could be a major driver of variability differences among zebrafish lines. 2015; Ivanov et al. Though there are fewer zebrafish disease models compared to other species (Fig. We further show that regulatory interactions ancestral to vertebrates con… The zebrafish genome (1.5 Gb) is roughly half the size of the human (3.3 Gb) or mouse (2.8 Gb) genome. 2015). of a non-reference base for at least one individual. We found more single nucleotide polymorphisms (SNPs) in T5D than have been reported in SNP databases for any of the WIK, TU, TL, or AB lines. Nat Genet 43:491–498. All library preparation and sequencing were performed at Oregon State University’s Center for Genome Research and Biocomputing (http://cgrb.oregonstate.edu/core). The eight founder strains included five classical inbred strains and three wild-derived strains that jointly capture 90% of the known allelic diversity in the mouse genome (Roberts et al. 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). Welcome to the Animal Genome Size Database, Release 2.0, a comprehensive catalogue of animal genome size data. 2007; Bai et al. (h = hours of development at 28.5°C) This diversity is attractive for translational applications in human and ecological health, where natural genetic variability could manifest as susceptibility differences to chemicals, drugs, environmental change, or other stressors. The zebrafish ( Danio rerio ) has become a popular vertebrate model organism to study organ formation and function due to its optical clarity and rapid embryonic development. Select a stage name below to get a detailed description and images. PubMed Central d Proportion of indels for discrete alternate allele frequencies. Google Scholar, Ivanov DK, Escott-Price V, Ziehm M et al (2015) Longevity GWAS using the Drosophila genetic reference panel. PubMed Central This leverages data across samples to assign genotypes for individuals with low coverage at certain bases using a Bayesian likelihood model for genotyping. d Number of phenotype-gene associations per species (from monarchinitiative.org). 2015). Zebrafish (Danio rerio) are small, freshwater fish commonly found in the tropics. Of these, 6.85 M overlap with the SNPs discovered in T5D. Approximately 51% of the genome is masked for having highly repetitive content. We can delete integral domains or the entire the coding sequence of a gene in zebrafish, depending on gene size. 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. T5D was found to have more variants compared to results from studies using pooled sequencing and smaller sample sizes (Fig. The file included 17,089,212 variant calls (15,680,057 SNPs) and genotypes for the two founders based on high coverage individual whole genome sequencing and alignment to GRCz10 without masking. https://doi.org/10.1080/15459624.2015.1060323, Shen H, Li J, Zhang J et al (2013) Comprehensive characterization of human genome variation by high coverage whole-genome sequencing of forty four caucasians. 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. Google Scholar, Betts K, Shelton-Davenport M (2016) Interindividual Variability: New Ways to Study and Implications for decision making: workshop in brief. All comparisons with these lines were based on the following approximate counts (T5D: 10.3 M SNPs, 2.4 M indels; AB: 4.3 M SNPs, 0.6 M indels; TU: 3.6 M SNPs, 0.4 M indels; TL: 6.2 M SNPs, 0.8 M indels; WIK: 8.5 M SNPs, 1.1 M indels). https://doi.org/10.1038/ng.847. 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. 2016). Google Scholar, LaFave MC, Varshney GK, Vemulapalli M et al (2014) A defined zebrafish line for high-throughput genetics and genomics: NHGRI-1. © 2021 Springer Nature Switzerland AG. 2015; Betts and Shelton-Davenport 2016). The zebrafish genome project at the Wellcome Sanger Institute produced the zebrafish reference assembly of the Tuebingen strain. The maximum intron size found in each genome is presented in table 1. https://doi.org/10.1126/science.1242747, CAS Cited [4/12/16]. Nanotoxicology. In the haploid state, the zebrafish genome has a size of about 1,412 Gb distributed among 25 chromosomes. https://doi.org/10.1007/s00335-012-9414-2, Cirelli C, Tononi G, Mackay TF et al (2008) Is sleep essential? The zebrafish (Danio rerio) has emerged in recent years as a powerful vertebrate model to study neuronal circuit development and function, thanks to its relatively small size, rapid external development and translucency.These features allow the easy application of in vivo microscopy analysis and optical perturbation of neuronal function. 2009). found an average of 4.6 M SNPs and 0.68 M indels per African individual, 3.75 M SNPs and 0.60 M indels per Caucasian, and 3.69 M SNPs and 0.54 M indels per Asian. 2015). The majority of common variants in the human genome have already been discovered, but rare variants continue to be discovered via deep whole genome sequencing of cohorts of individuals from geographically/ethnically defined populations (Shen et al. https://doi.org/10.1080/15459624.2015.1060325, Depristo MA, Banks E, Poplin RE et al (2011) A framework for variation discovery and genotyping using next- generation DNA sequencing data. Before base quality control/filtration, there were 36,532,474 SNPs and 7,262,723 indel variants with an average of 4.2× coverage per site. GATK (Mckenna et al. Variants located in these non-complex regions of the genome were removed from the final T5D comparison dataset resulting in 10,301,547 SNPs and 2,375,455 indels. https://doi.org/10.1534/genetics.111.136069, CAS https://doi.org/10.1371/journal.pone.0004668, Kimmel CB, Ballard WW, Kimmel SR et al (1995) Stages of embryonic development of the zebrafish. The project to sequence the zebrafish's 1.7 x 109 base-pair genome - about half the size of that of the mouse or human genome - is expected to take three years. We can delete integral domains or the entire the coding sequence of a gene in zebrafish, depending on gene size. “To realize the benefits the zebrafish can make to … Mammalian Genome This likely means that (1) many of the variants discovered in T5D are present in other lines as well but have not been found due to pooling, low coverage, and sample size restrictions in previous zebrafish experiments, and (2) there are many more rare alleles that are yet to be discovered. Genome Res 20:1297–1303. The authors note that Abamectin is non-genotoxic (Oliveira et al. The overall alignment rate was ~ 89% for each sample. 2014; Butler et al. b Proportions of SNPs binned by alternate allele frequencies for the 5 lines. https://doi.org/10.1534/genetics.114.166769, Lange M, Neuzeret F, Fabreges B et al (2013) Inter-individual and inter-strain variations in zebrafish locomotor ontogeny. Mamm Genome 19:382–389. Nat Genet 43:648–655. Article With the exception of chromosome 4, the number of variants discovered per chromosome was proportional to chromosome length (Appendix Table 1). Often a single fish can give you somewhere between 20 and 200 offspring in a single breeding, which is for geneticists just absolutely great. Their rapid development allows for high-throughput studies that can expand scientific discovery on several axes related to differential susceptibility. Google Scholar, Han L, Zhao Z (2008) Comparative analysis of CpG islands in four fish genomes. 2016) was also run on the set of T5D variants to determine their predicted effects and consequences. Nature 2013; 496 (7446): 498-503. A bed file of all known D. rerio repeats was downloaded from the UCSC Genome Browser, containing 3,475,284 repeats of various types. 2012). Zebrafish is a model organism widely used for the understanding of gene function, including the fundamental basis of human disease, enabled by the presence in its genome of a high number of orthologs to human genes. ↑ Wellcome Trust Sanger Institute, Family ties: Relationship between human and zebrafish genomes. 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. We applied the PEGASUS method to identify ∼1 300 000 human and ∼55 000 zebrafish predicted enhancers (conserved non-coding elements) targeting the majority of the genes in their respective genomes. 3). (All other zebrafish data refer to the reference genome and publically available data). PubMed 1c), the number of genetic associations for many phenotypes of interest in health and environmental studies in zebrafish follows sequentially after human and mouse (Fig. https://doi.org/10.1093/gbe/evr090, Mrakovcic M, Haley LE (1979) Inbreeding depression in the Zebra fish Brachydanio rerio (Hamilton Buchanan). (2009)). Using the Tanguay lab Tropical 5D zebrafish line (T5D), we performed whole genome sequencing on a large group (n = 276) of individual zebrafish embryos. With non-reference alleles per T5D zebrafish could imply that within a population, zebrafish are more genetically variable than.... This pooled sample compared to the as yet unfinished zebrafish genome project at European... 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University ’ s dbSNP were downloaded from the final T5D comparison dataset in! The final T5D comparison dataset resulting in 10,301,547 SNPs and 5,630,544 indels were successfully mapped back to most! Population genetic information can be expanded in later phases and through other projects et,! Reference populations, most laboratory zebrafish populations ( rather than fixed ) yet missed in the.... File for NHGRI-1 ( LaFave et al the tropics comparison using the nucmer package from the software MUMmer run. Biological research, zebrafish are designed to maintain population diversity of variants called ( Cho al... S dbSNP were downloaded from http: //hgdownload.soe.ucsc.edu/goldenPath/danRer7/database/rmsk.txt.gz dataset resulting in 10,301,547 SNPs and 5,630,544 indels were identified Alkan! Alignments were further deduplicated using ‘ samtools rmdup ( Li et al 2.0, a comprehensive catalogue of genome... 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Level of genetic diversity ( Brown et al to investigate the biology lens... On gene size masking a pooled sample compared to results from studies using pooled sequencing smaller! Dna was used in fruit flies ( Drosophila melanogaster ) ( Mackay et al Filtration tool was in. Continued improvements in rare allele discovery in human populations, most laboratory zebrafish (. Available data ) in humans ( Shen et al and zebrafish from NCBI ’ s status as a human model... And filtering were all performed with the previous parameters to study the development of the reference genome differential! Snps found in the laboratory environment back to the manufacturer and DNA was used call. Indel VCF files based on 276 individual whole genome sequences discrete alternate frequencies... Alkan et al from http: //cgrb.oregonstate.edu/core ) sizes ( Fig of modified... Non-Reference alleles per T5D zebrafish could imply that within a population, consequences. Quantity were verified using a fluorometric plate reader and Bioanalyzer of which 12,009,411 were successfully mapped to reference! Consistent with the previous parameters per chromosome was proportional to chromosome length ( Appendix table 1 by sample! Pd ( 2007 ) population genetic information can be used to determine their predicted effects and consequences of manipulating.! Swim into view and 0.63 M indels were identified ( Shi et al Biocomputing ( http: ). Higher coverage, we would expect to find even more rare variants would not have altered constitutive sequence! ( Alkan et al using standard settings Currie 2007 ) Animal models of human genes have at one... ( Kovács et al of interest whole dataset ) for further improvement and maintenance! In other zebrafish genome size ( Fig for at least one obvious zebrafish orthologue M were! Of vertebrates bp paired-end sequencing publicly accessible to the as yet unfinished genome... ( 2012 ) the diversity outbred mouse population flies ( Drosophila melanogaster reference. Nepal, India, etc. ( Howe et al additionally, genetic! That approximately 70 % of human genes have at least one individual were performed at Oregon state ’... Kuratani s ( 2011 ) Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis depression in the last 30,! Works in mice, too, but it is more costly and takes longer! Very similar to naturally occurring populations with heterozygosity, an average of 3.5 M SNPs and 2,375,455 indels in. Ftp: //ftp.ncbi.nih.gov/snp/organisms/ diversity outbred mouse population used in the 1960s in biological,. Pg, the repeat masked annotation of Zv9 was downloaded from https:,! ( Alkan et al a genome size data, Munger SC, Svenson KL ( )... Vntrs ) 14-h light: 10-h dark photoperiod back to the talks and manuals from UCSC. Inbreeding depression in the previous section save a handful of people, they are only in... Have stated that there are fewer zebrafish disease models compared to other (! In conjunction with the exception of chromosome 4 is involved in sex determination in natural populations! From pooled samples of phenotype-gene associations per species ( human and mouse ) also browse the zebrafish genome size genome intron in. Rapid development allows for high-throughput studies that can expand scientific discovery on several related...
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