Isogenic laboratory mouse strains enhance reproducibility because individual animals are genetically identical. In this study, we report on the complete genome of faecalibaculum rodentium alo17, a bacterium that was isolated from the faeces of a 9. We and our collaborators have used shortread sequencing to identify snps, indels, and structural variations relative to the c57bl 6j mouse reference genome. C57bl 6 c57bl 6j c57blksj c57brcdj c57lj c58j casteij cbaj cej chdms czechiieij dba1j. On june 22, 2000, ucsc and the other members of the international human genome project consortium completed the first working draft of the human genome assembly, forever ensuring free public access to the genome and the information it contains. Reads were aligned to the published c57bl6 genome december 2011 release of the mouse reference genome mm10 from ucsc. In practice, genome sequences that are nearly complete are also called whole. Sensitive to teratogenic effects of acetazolamide 26 green et al.
Nlrp12 nodlike receptor pyrin domain containing 12 is a component of the innate immune system that regulates immune cell trafficking and cytokine production. These approaches provide an opportunity to modify the genomes of inbred mice, and allow the removal of strainspecific mutations that confound phenotypic assessment. Whole genome sequencing is ostensibly the process of determining the complete dna sequence of an organisms genome at a single time. It seems the default sequence on general database is from c57bl 6j. This event marked the start of a new era in mouse genetic research. Genetic polymorphisms among c57bl6 mouse inbred strains. Now 20 years after the first release of the mouse reference genome, c57bl 6j mice are at least 26 inbreeding. To characterize these loci at basepair resolution and to identify additional genomic variants contributing to mm pathogenesis, we performed whole genome sequencing wgs and whole exome sequencing wes. We sequenced the complete genome of the widely used c57lj mouse inbred strain. However, there are several c57bl6 substrains that are. Mouse haplotype table mhc class i mhc class ii mhc class ib mouse strains mhc haplotype h2k h2d h2l ia ie qa2 qa1 cd45 ly5 thy1 cd90 nk1.
Wholegenome sequence of the c57lj mouse inbred strain. Genomic structure and genetic drift in c57bl6 congenic. Table 2 presents the h2 gene numbering system for c57bl6 mice haplotype b that we have used in this paper. Generation of genome integrationfree induced pluripotent. Efficient analysis of mouse genome sequences reveal many. I found that data as well but my question is, does that data include all the reported snps for casteij with respect to the latest assembly of c57bl6. The nucleotide sequences were determined for the fulllength cdnas expressed by the genes h2t23, t22, t15, t5 and m5 and.
For many strains, we have carried out highdensity snp genotyping to precisely map the congenic interval and to identify any contaminating regions. Here, we report the construction and initial characterization of a genomewide panel of congenic strains derived from the donor strain dba2j on the background strain c57bl6j. Mgi derived this sequence for the c57bl6j strain version of gene. Here, we report the characterization of mutamouses whole genome sequence and its genetic variants. Here you could sequence your mouse and compare it to the reference sequence. Modification of igonad suitable for production of genome. For the most widely used isogenic strain, c57bl 6, there exists a wealth of genetic, phenotypic, and genomic data, including a highquality reference genome grcm38. However, the list of differentiating variants snps, small indels, and svs between the two genomes was newly created using novel inbuilt procedures in.
Improved genome editing via oviductal nucleic acid delivery igonad is a novel method for producing genomeedited mice in the absence of ex vivo handling of zygotes. Search for mouse snps represented in dbsnp by gene or genome region. Help pages, faqs, uniprotkb manual, documents, news archive and biocuration projects. The efficient ipsc generation we obtained by 3f introduction of c57bl6 mice using a retrovirusmediated gene transduction system prompted us to examine whether ipscs could be induced from c57bl6 mefs using a genome integrationfree vector with 3f, i. The c57bl6j mutation g to a at position 3,222,537, chr. Deep whole genome sequencing of founder mice revealed very little divergence from c57bl6nj and c57bl6n taconic. Two c57bl6specific peptides are coded for by the defcr20 and 21 genes evident in the nih c57bl6 genome but absent from the celera mixedstrain assembly, which excludes c57bl6 data and differs from the nih build with respect to the organization of the. To achieve crisprcas9mediated knockin into rosa26, we selected sgrna target sequences spanning the xbai site within the first intron, adapted to the homology regions of gene targeting vectors used for es cells that cover sequences up and downstream of this site. We used a genomewide single nucleotide polymorphism snp approach to characterize the genomic structures of four representative c57bl6 b6 congenic mutant mouse lines to include the a longchain acylcoa dehydrogenase acadl, b melanocortin 3 receptor mc3r, c endothelial nitric oxide synthase nos3, and d a replacement of mouse apolipoprotein e. This entails sequencing all of an organisms chromosomal dna as well as dna contained in the mitochondria and, for plants, in the chloroplast. Whole genome sequencing of faecalibaculum rodentium. The reference proteome of mus musculus is derived from the genome sequence of strain c57bl6j that was published in 2009. Deep genome sequencing and variation analysis of inbred.
We here describe a userfriendly bioinformatics tool for revealing the sequence variations in proteincoding genes in one or more inbred strains and predicting which proteins are significantly different compared with those of the reference genome of c57bl6j inbred mice. Mouse genome sequences have been generated of tens of inbred strains. By creating a c57bl6 congenic strain carrying a 129derived chromosome 1 segment, we found that this 129 interval was sufficient to mediate the loss of tolerance to nuclear. The reference proteome of mus musculus is derived from the genome sequence of strain c57bl 6j that was published in 2009. For the most widely used isogenic strain, c57bl6, there exists a wealth of genetic, phenotypic, and genomic data, including a highquality reference genome grcm38. In this study, we sequenced the genome of the c57bl6jchr1 km b6chr1 km strain, the chromosome 1 chr 1 of which was derived from one km mouse. We carry out deep sequencing of additional inbred strains bubbnj, c57bl10j. Unirule expertly curated rules saas system generated rules.
Systems used to automatically annotate proteins with high accuracy. Within a species, the vast majority of nucleotides are identical between individuals, but sequencing multiple individuals is necessary to understand the genetic diversity. Sensitive to teratogenic effects of acetazolamide 2 6 green et al. The chinese kunming km mouse is a widely used outbred mouse stock in china. Now 20 years after the first release of the mouse reference genome, c57bl6j. We carry out deep sequencing of additional inbred strains bubbnj, c57bl 10j, c57brcdj, c58j, dba1j, ilnj, kkhij. Library and sequencing statistics for each sample are available in table s3 of additional file 1. We and our collaborators have used shortread sequencing to identify snps, indels, and structural variations relative to the c57bl6j mouse reference genome. As consequence, an intronic sequence alternative e1 in nzo is spliced to exon 2 of ifi202b in the. The national human genome research institute nhgri and the wellcome trust currently support a mouse genome sequencing project that aims to produce a robust physical map, and a high quality, finished genomic sequence of the c57bl6j strain of mus musculus this project is led by the mouse genome sequencing consortium mgsc, a collaboration consisting of four.
The presence of numerous mmtv sag isoforms might represent a heterogeneous mixture related but. Sequencing reads from each lane were aligned to the c57bl 6 j grcm38 mm10 mouse reference genome using bwamem v0. Given the difficulty in controlling for human studies of the gut microbiome, mouse models provide an alternative avenue to study such relationships. Nucleasebased technologies have been developed that enable targeting of specific dna sequences directly in the zygote. However, there was a twofold lower level of dna synthesis in c57bl 6 mice relative to c3h mice after partial hepatactomy, though partial hepatectomy is a tumour promoter in c57bl 6 but not in c3h mice bennett et al, 1995. Efficient dsbs induction at the rosa26 intronic xbai site in c57bl6 zygotes. The mutamouse transgenic rodent model is widely used for assessing in vivo mutagenicity.
Search for snps by genome region from dbsnp build 142. The popular and wellknown inbred strain c57bl6j was selected to deliver the sequence of this reference genome. A genome sequence is the complete list of the nucleotides a, c, g, and t for dna genomes that make up all the chromosomes of an individual or a species. Chromosome 1 sequence analysis of c57bl6jchr1km mouse. A comparative phenotypic and genomic analysis of c57bl6j. Two wellcharacterized strains of pvm, strain 15 and strain j3666, are commonly.
Intestinal microorganisms affect host physiology, including ageing. Genomic copy number and expression variation within the. Whole genome sequence of multiple myelomaprone c57bl. Genome sequence comparisons of c57bl6n and c57bl6j mice for snps and small indels. A genomewide set of congenic mouse strains derived from. Anyone knows how to find the genome sequence information for balbc mouse.
However, there was a twofold lower level of dna synthesis in c57bl6 mice relative to c3h mice after partial hepatactomy, though partial hepatectomy is a tumour promoter in c57bl6 but not in c3h mice bennett et al, 1995. The genome of c57bl6j eve, the mother of the laboratory. One such mutation is the cdh23 ahl allele, present in. Efficient generation of rosa26 knockin mice using crispr.
We utilized pairedend alignment of c57bl6n to the reference genome c57bl6j from the 17 mouse genomes project. A vast genomic deletion in the c56bl6 genome affects. The strains that have been sequenced and are in our variation catalog are. The set of 123 snps outside the siae locus that differed between n10siae and c57bl6j also comprised 97% of the snp alleles n 128 from a pool of 538,667 snps analyzed in the wholegenome arrays that differ between c57bl6j and c57bl6n sublines but are identical to the consensus 129 alleles. We designated each h2 gene with reference to the genomic locations and designations used by others 23, 24, 26.
The inbred mouse strain c57bl6 has been the preferred choice for the generation and analysis of transgenic and knockout mice. In 2011, the initial analysis of sequence variation across 17 strains found 56. Whole genome sequencing of the mutamouse model reveals. The sequence of the mouse genome is a key informational tool for understanding. The availability of a reference genome for the mouse model organism allowed for the identification of genetic polymorphisms between different strains and enabled. A direct comparison of the genomic nzo sequence with the b6 reference genome revealed a 261,797 bp deletion including copies of the ifi200family members, ifi203, ifi205, the first exon and the 5.
The mouse genomes project is an ongoing collaborative effort to sequence the genomes of the common laboratory mouse strains. Epitope mapping and kinetics of cd4 t cell immunity to. Clinical features of disease manifestation and t cell dynamics in response to pvm j3666 infection in c57bl6 mice. The results presented in figure 1 demonstrate that there are a high number of mmtv sag isoforms in the genome of c57bl6j mice, which had been previously reported to harbor only three endogenous mmtv loci mtv8, mtv9, and mtv17 2, 4. Jci insight overview of inactivating mutations in the.
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