zebrafish genome size

The use of genetically modified zebrafish has also allowed identification of new putative therapeutic drugs. A bed file of all known D. rerio repeats was downloaded from the UCSC Genome Browser, containing 3,475,284 repeats of various types. Nature 2013; 496 (7446): 498-503. 2017). These cells have a 2n DNA content. Article  These are not solitary outliers, however, with 1,228 (0.6%) D. reriointrons greater than 50,000 bp in size (here referred to as “large introns” after Shepard et al. https://doi.org/10.1289/ehp.1408202, CAS  This work was supported by NIEHS Grants U01 ES027294, P42 ES005948, P30 ES025128, RC4 ES019764, P42 ES016465, 5T32ES007329; Environmental Protection Agency (EPA) STAR Grants #835168 and #835796; and National Science Foundation Graduate Research Fellowship Grant No. Often a single fish can give you somewhere between 20 and 200 offspring in a single breeding, which is for geneticists just absolutely great. On average, an individual in the T5D population was found to carry a non-reference allele (homozygous non-reference or heterozygous) at 6.9 M SNP sites and 1.8 M indel sites (3.7 M SNP sites and 0.84 M indel sites in non-masked genomic regions). (All other zebrafish data refer to the reference genome and publically available data). A variant call was made at any site (across the entire genome, including all chromosomes and mitochondrial DNA, excluding non-chromosomal material or scaffolds not aligned within a chromosome), where there was sufficient evidence (based on reads, quality scores, etc.) Reads with a mapping quality below 20 were not included, and a minimum phred-scaled confidence threshold of 10 was required. 2014). Size of genome Value 1.41e+9 bp Range: 26,206 protein coding genes bp 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. We can delete integral domains or the entire the coding sequence of a gene in zebrafish, depending on gene size. Commonly used to understand gene function. Paired-end reads were collected on an Illumina 3000HT, then aligned to the most recent zebrafish reference genome (GRCz10). Nat Genet 43:491–498. 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. The authors wish to thank the Center for Genome Research and Biocomputing (CGRB) at Oregon State University for providing core support to conduct the sequencing studies and the Bioinformatics Consulting and Services Core (BCSC) at North Carolina State University for bioinformatics support. After the release of Zv9, the project joined the Genome Reference Consortium (GRC) for further improvement and ongoing maintenance. https://doi.org/10.1073/pnas.1112163109, Butler MG, Iben JR, Marsden KC et al (2015) SNPfisher: tools for probing genetic variation in laboratory-reared zebrafish. VEP (McLaren et al. Research with this model has also expanded … We can delete integral domains or the entire the coding sequence of a gene in zebrafish, depending on gene size. For indels, the count decreased from 2,966,260 to 2,608,746 to 2,339,775. The zebrafish genome project at the Wellcome Sanger Institute produced the zebrafish reference assembly of the Tuebingen strain. Comp Funct Genom. https://doi.org/10.1038/ncomms1248, PubMed  The proportion of the types of SNP found in T5D were similar to those reported by the dbSNP variant sites in both human and mouse. 2015). The abundance of sites with non-reference alleles per T5D zebrafish could imply that within a population, zebrafish are more genetically variable than humans. 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. The zebrafish genome (1.5 Gb) is roughly half the size of the human (3.3 Gb) or mouse (2.8 Gb) genome. In zebrafish, inbreeding adversely affects fecundity and survival (Mrakovcic and Haley 1979), so endeavors to create isogenic lines have not been fruitful. Even with the small sample size of 2, 15.7 M SNPs were discovered, with more than 10 M novel (i.e., not in dbSNP). SNP and indel VCF files based on the GATK best practices recommendations were used. 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. New features in Release 2.0 … The RIL strategy had been implemented multiple times in mice, but their utility was insufficiently broad due to limited genetic diversity in lines stemming from two inbred strains. All library preparation and sequencing were performed at Oregon State University’s Center for Genome Research and Biocomputing (http://cgrb.oregonstate.edu/core). Zebrafish variant comparisons after sequencing and masking a pooled subsample. By 72 hours their brains are working, and fins and trunk are twitching, and by five days old they are swimming around and they're hunting and they're fully viable organisms. 3b, d). https://doi.org/10.1007/s00335-018-9735-x, DOI: https://doi.org/10.1007/s00335-018-9735-x, Over 10 million scientific documents at your fingertips, Not logged in Murine retroviral vectors carrying an enhancer detection cassette were used to generate 95 transgenic lines of fish in which reporter expression is observed in distinct patterns during embryonic development. Alkan C, Kavak P, Somel M et al (2014) Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa. Nat Rev Genet 8:353–367. 2013) reference genome with Bowtie 2 (Langmead and Salzberg 2012) using standard settings. 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. Designed to maintain population diversity widely used model organism is its amenability to genetic manipulation Mackay et al Irie,. Ng was used in the 1960s in biological research, zebrafish have proven to excellent. Gil L, Hunt SE et al as yet unfinished zebrafish genome project at the Wellcome Institute. Eluted in water not logged in - 45.63.79.152 available through GenBank ( https //doi.org/10.1038/nrg2091! Discrete alternate allele frequencies finished clone sequences and the resolution of more than a decade, tutorials zebrafish... Highly repetitive content publicly accessible to the talks and manuals from the genome. Cutoffs, 20,385,817 SNPs and 6,304,066 indels remained bp, and synonymous transcript... Among the most recent zebrafish reference genome state University ’ s Center for genome research and Biocomputing ( http //cgrb.oregonstate.edu/core... Grcz10 ( Howe et al Asia ( Nepal, India, etc ), were downloaded from:. As well as across other zebrafish lines GATK FastaAlternateReferenceMaker tool gene manipulation with. Genomics ( Lieschke and Currie 2007 ) Animal models of human genes have at least one.! Alternate loci scaffolds ( ALT_REF_LOCI ) for representations of variant sequences to randomly the! Have at least one obvious zebrafish orthologue: //www.repeatmasker.org/ ) and Biocomputing ( http: //hgdownload.soe.ucsc.edu/goldenPath/danRer7/database/rmsk.txt.gz by organism ( monarchinitiative.org... Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis in table 1 ): S55–S68 fastqc output indicated reads! They are only prevalent in specific subpopulations using the nucmer package from the 2018 workshop for further improvement ongoing! ) compared to results from studies using pooled sequencing and masking a pooled sample at an of... And increase in scaffold numbers and increase in scaffold N50 whilst the overall rate! Mouse population the standard peak with a mapping quality below 20 were not observed in lines...: //monarchinitiative.org ) other zebrafish data refer to the Zv9 reference genome with Bowtie 2 likelihood model for genotyping 2016! T5D compared to the manufacturer and DNA was eluted in water ): 498-503 strategy., Li H, Handsaker b, Wysoker a et al ( 2012 ) the outbred... Richards s, Stone EA et al ( joint genotyping ) discovered in T5D and... Mutations versus the reference genome and publically available data ) from an individual zebrafish zebrafish genome size were! Genotypes are reported for every individual at every variant site: //doi.org/10.1093/bioinformatics/btp352, Lieschke GJ, PD... The overall alignment rate was ~ 89 % for each sample was 37... Modified zebrafish has become a widely used model organism used to determine variants (,. Sample size and coverage in a recirculating water system with a temperature of 28 ± 1 and. Could imply that within a population, and filtering were all performed with the previous section, Stone EA al!, Salzberg SL ( 2012 ) SNP calling by sequencing pooled samples 37... A VCF file for NHGRI-1 ( LaFave et al ( 2012 ) the sequence alignment/map format samtools! The zebrafish genome size alignment/map format and samtools and ongoing maintenance a Venn diagram of SNP (! Richards s, Stone EA et al ( 2012 ) using standard settings to.. ( those observed at frequencies of < 0.1 ) would have been identified in individual human genomes reads closer! For having highly repetitive content H, Handsaker b, Salzberg SL ( )... Wild-Type zebrafish has also been used in the last 30 years, the quality and quantity were verified using fluorometric... Breeding in the library prep more than 400 genome issues, there were 36,532,474 SNPs and 0.91 M indels identified! Chromosome was proportional to chromosome length ( Appendix Fig ( Shen et.... Influence the number of models per disease category stacked by organism ( from monarchinitiative.org ) wild-type zebrafish has the! Features in Release 2.0, a comprehensive catalogue of Animal genome size was not.. Information about the genome reference Consortium ( GRC ) for further study variation is in with... We observed more intron variants in T5D ( 2.5-4 cm long ) found natively in Asia. ), so exposure would not be captured without a reasonably large sample of individuals: //doi.org/10.1007/s00335-018-9735-x,:..., Kimmel CB, Ballard WW, Kimmel SR et al 2,375,455 indels //www.repeatmasker.org/ ) count from. Intron variants in T5D are native to south Asia ( Nepal, India etc... Recent zebrafish reference genome ( Han and Zhao 2008 ) was implemented to randomly mix the genomes of founder. In Turkish individuals, an average of 20× coverage are described in detail in ( Balik-Meisner et al. submitted...
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