scholarly journals MoG+: a database of genomic variations across three mouse subspecies for biomedical research

2021 ◽  
Author(s):  
Toyoyuki Takada ◽  
Kentaro Fukuta ◽  
Daiki Usuda ◽  
Tatsuya Kushida ◽  
Shinji Kondo ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Laboratory Mouse ◽  
Genomic Analysis ◽  
Inbred Strains ◽  
Genetic Distances ◽  
Mouse Strains ◽  
Comparative Genomic ◽  
Genome Database ◽  
Data Resource ◽  
Genomic Variations

AbstractLaboratory mouse strains have mosaic genomes derived from at least three major subspecies that are distributed in Eurasia. Here, we describe genomic variations in ten inbred strains: Mus musculus musculus-derived BLG2/Ms, NJL/Ms, CHD/Ms, SWN/Ms, and KJR/Ms; M. m. domesticus-derived PGN2/Ms and BFM/Ms; M. m. castaneus-derived HMI/Ms; and JF1/Ms and MSM/Ms, which were derived from a hybrid between M. m. musculus and M. m. castaneus. These strains were established by Prof. Moriwaki in the 1980s and are collectively named the “Mishima Battery”. These strains show large phenotypic variations in body size and in many physiological traits. We resequenced the genomes of the Mishima Battery strains and performed a comparative genomic analysis with dbSNP data. More than 81 million nucleotide coordinates were identified as variant sites due to the large genetic distances among the mouse subspecies; 8,062,070 new SNP sites were detected in this study, and these may underlie the large phenotypic diversity observed in the Mishima Battery. The new information was collected in a reconstructed genome database, termed MoG+ that includes new application software and viewers. MoG+ intuitively visualizes nucleotide variants in genes and intergenic regions, and amino acid substitutions across the three mouse subspecies. We report statistical data from the resequencing and comparative genomic analyses and newly collected phenotype data of the Mishima Battery, and provide a brief description of the functions of MoG+, which provides a searchable and unique data resource of the numerous genomic variations across the three mouse subspecies. The data in MoG+ will be invaluable for research into phenotype-genotype links in diverse mouse strains.

scholarly journals A database for risk assessment and comparative genomic analysis of foodborne Vibrio parahaemolyticus in China

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Rui Pang ◽  
Yanping Li ◽  
Moutong Chen ◽  
Haiyan Zeng ◽  
Tao Lei ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Foodborne Pathogens ◽  
Vibrio Parahaemolyticus ◽  
Foodborne Pathogen ◽  
Genomic Analysis ◽  
Food Samples ◽  
Comparative Genomic ◽  
Genome Database ◽  
Scientific Database ◽  
Need To Evaluate

Abstract Vibrio parahaemolyticus is a major foodborne pathogen worldwide. The increasing number of cases of V. parahaemolyticus infections in China indicates an urgent need to evaluate the prevalence and genetic diversity of this pathogenic bacterium. In this paper, we introduce the Foodborne Vibrio parahaemolyticus genome database (FVPGD), the first scientific database of foodborne V. parahaemolyticus distribution and genomic data in China, based on our previous investigations of V. parahaemolyticus contamination in different kinds of food samples across China from 2011 to 2016. The dataset includes records of 2,499 food samples and 643 V. parahaemolyticus strains from supermarkets and marketplaces distributed over 39 cities in China; 268 whole-genome sequences have been deposited in this database. A spatial view on the risk situations of V. parahaemolyticus contamination in different food types is provided. Additionally, the database provides a functional interface of sequence BLAST, core genome multilocus sequence typing, and phylogenetic analysis. The database will become a powerful tool for risk assessment and outbreak investigations of foodborne pathogens in China.

scholarly journals Molecular identification and mapping of a novel stripe rust resistance gene in wheat resistance line CH5389

2018 ◽  
Vol 48 (5) ◽  
Author(s):  
Haixian Zhan ◽  
Huijuan Guo ◽  
Linyi Qiao ◽  
Liping Mao ◽  
Shuosheng Zhang
Keyword(s):  
Resistance Gene ◽  
Stripe Rust ◽  
Rust Resistance ◽  
Puccinia Striiformis ◽  
Dominant Gene ◽  
Genomic Analysis ◽  
Resistance Breeding ◽  
Genetic Distances ◽  
Stripe Rust Resistance ◽  
Comparative Genomic

ABSTRACT: Stripe rust, caused by Puccinia striiformis is one of the most destructive diseases of wheat worldwide. CH5389 is a wheat-Thinopyrum intermedium derived line conferring stripe rust resistance. Genetic analyses of seedlings of F2 populations and F2:3 families developed by crossing CH5389 and susceptible common wheat revealed that stripe rust resistance in CH5389 was controlled by a single dominant gene that was designated YrCH5389. Eight SSR and EST-PCR polymorphic markers on chromosome 3AL were identified in F2 population of CH5389/Taichung29. The YrCH5389 was flanked by EST marker BE405348 and SSR marker Xwmc388 on chromosome 3AL with genetic distances of 2.2 and 4.6 cM, respectively. Comparative genomic analysis demonstrated that the orthologous genomic region of YrCH5389 covered 990 kb in rice, 640 kb in Brachypodium, and 890 kb in sorghum. Based on the locations of the markers, the resistance gene was located to chromosome deletion bin 3AL-0.85-1.00. Because there are no officially named stripe rust resistance genes on the 3AL chromosome, the YrCH5389 should be designated as a new resistance gene. These linkage markers could be useful for marker-assisted selection in wheat resistance breeding.

Divergent evolution of the myosin heavy chain gene family in fish and tetrapods: evidence from comparative genomic analysis

2007 ◽  
Vol 32 (1) ◽  
pp. 1-15 ◽  
Author(s):  
Daisuke Ikeda ◽  
Yosuke Ono ◽  
Phil Snell ◽  
Yvonne J. K. Edwards ◽  
Greg Elgar ◽  
...  
Keyword(s):  
Myosin Heavy Chain ◽  
Heavy Chain ◽  
Genomic Analysis ◽  
Divergent Evolution ◽  
Comparative Genomic ◽  
Chain Gene ◽  
Takifugu Rubripes ◽  
Genome Database ◽  
Genomic Regions ◽  
Syntenic Analysis

Myosin heavy chain genes ( MYHs) are the most important functional domains of myosins, which are highly conserved throughout evolution. The human genome contains 15 MYHs, whereas the corresponding number in teleost appears to be much higher. Although teleosts comprise more than one-half of all vertebrate species, our knowledge of MYHs in teleosts is rather limited. A comprehensive analysis of the torafugu ( Takifugu rubripes) genome database enabled us to detect at least 28 MYHs, almost twice as many as in humans. RT-PCR revealed that at least 16 torafugu MYH representatives (5 fast skeletal, 3 cardiac, 2 slow skeletal, 1 superfast, 2 smooth, and 3 nonmuscle types) are actually transcribed. Among these, MYH M743-2 and MYH M5 of fast and slow skeletal types, respectively, are expressed during development of torafugu embryos. Syntenic analysis reveals that torafugu fast skeletal MYHs are distributed across five genomic regions, three of which form clusters. Interestingly, while human fast skeletal MYHs form one cluster, its syntenic region in torafugu is duplicated, although each locus contains just a single MYH in torafugu. The results of the syntenic analysis were further confirmed by corresponding analysis of MYHs based on databases from Tetraodon, zebrafish, and medaka genomes. Phylogenetic analysis suggests that fast skeletal MYHs evolved independently in teleosts and tetrapods after fast skeletal MYHs had diverged from four ancestral MYHs.

scholarly journals Multiple trait measurements in 43 inbred mouse strains capture the phenotypic diversity characteristic of human populations

2007 ◽  
Vol 102 (6) ◽  
pp. 2369-2378 ◽  
Author(s):  
Karen L. Svenson ◽  
Randy Von Smith ◽  
Phyllis A. Magnani ◽  
Heather R. Suetin ◽  
Beverly Paigen ◽  
...  
Keyword(s):  
High Fat Diet ◽  
Phenotypic Diversity ◽  
Inbred Mouse ◽  
Inbred Strains ◽  
Mouse Strains ◽  
Human Populations ◽  
Large Set ◽  
Inbred Mouse Strains ◽  
High Fat ◽  
Mineral Density

The breadth of genetic and phenotypic variation among inbred strains is often underappreciated because assessments include only a limited number of strains. Evaluation of a larger collection of inbred strains provides not only a greater understanding of this variation but collectively mimics much of the variation observed in human populations. We used a high-throughput phenotyping protocol to measure females and males of 43 inbred strains for body composition (weight, fat, lean tissue mass, and bone mineral density), plasma triglycerides, high-density lipoprotein and total cholesterol, glucose, insulin, and leptin levels while mice consumed a high-fat, high-cholesterol diet. Mice were fed a chow diet until they were 6–8 wk old and then fed the high-fat diet for an additional 18 wk. As expected, broad phenotypic diversity was observed among these strains. Significant variation between the sexes was also observed for most traits measured. Additionally, the response to the high-fat diet differed considerably among many strains. By the testing of such a large set of inbred strains for many traits, multiple phenotypes can be considered simultaneously and thereby aid in the selection of certain inbred strains as models for complex human diseases. These data are publicly available in the web-accessible Mouse Phenome Database ( http://www.jax.org/phenome ), an effort established to promote systematic characterization of biochemical and behavioral phenotypes of commonly used and genetically diverse inbred mouse strains. Data generated by this effort builds on the value of inbred mouse strains as a powerful tool for biomedical research.

Homology of p53 intronic sequences between four laboratory mouse strains and Japanese wild mouse (Mus musculus molossinus Mishima)

Genome ◽  
1994 ◽  
Vol 37 (6) ◽  
pp. 1022-1026 ◽  
Author(s):  
Masayuki Tokumitsu ◽  
Katsuhiro Ogawa
Keyword(s):  
Loss Of Heterozygosity ◽  
Mus Musculus ◽  
Laboratory Mouse ◽  
Wild Mouse ◽  
P53 Gene ◽  
Inbred Strains ◽  
Mouse Strains ◽  
Restriction Enzyme Digestion ◽  
Laboratory Mice ◽  
Wild Mice

Strain variation in the mouse p53 gene sequences was investigated in various regions of the gene in 14 inbred strains of laboratory mice and one Japanese wild mouse strain (Mus musculus molossinus Mishima, M. MOL-MSM). Nucleotides within p53 introns 1 and 7, found to be identical in 10 of the laboratory strains (129/J, A/J, AKR/J, BALB/cJ, C3H/HeJ, C57BL/6J, CBA/J, CE/J, NZB, and SWR/J), were substituted for other nucleotide sequences in common with M. MOL-MSM and the four other strains (DBA/1J, DBA/2J, I/LnJ, and P/J). The latter were documented to have originated from a common ancestor. These observations thus suggested the possibility that the p53 gene may have become substituted by outcrossing of this ancestral strain with Asian mice; this is presumably related to the documentation that Japanese mice brought to western countries were used as laboratory mice early in this century. To establish p53 gene heterozygosity, female C3H/HeJ and male DBA/2J mice were mated to produce F1, hybrids (C3D2F1,). Electrophoresis of PCR fragments including polymorphic regions with or without restriction enzyme digestion, allowed clear distinction of paternal and maternal p53 alleles. These markers, therefore, should be useful for studying the loss of heterozygosity of the p53 gene during the carcinogenic process.Key words: p53 gene, polymorphism, Japanese wild mice, laboratory mice, loss of heterozygosity.

Sendai virus-induced alterations in lung structure/function correlate with viral loads and reveal a wide resistance/susceptibility spectrum among mouse strains

2005 ◽  
Vol 289 (5) ◽  
pp. L777-L787 ◽  
Author(s):  
Pedro Faisca ◽  
Dao Bui Tran Anh ◽  
Daniel J.-M. Desmecht
Keyword(s):  
Structure Function ◽  
Positional Cloning ◽  
Sendai Virus ◽  
Laboratory Mouse ◽  
Inbred Strains ◽  
Biological Properties ◽  
Mouse Strains ◽  
Viral Loads ◽  
Lung Structure ◽  
Inbred Strains Of Mice

The Paramyxoviridae family includes some of the most important and ubiquitous disease-causing viruses of infants and children, most of which cause significant infections of the respiratory tract. Evidence is accumulating in humans that genetic factors are involved in the severity of clinical presentation. As a first step toward the identification of the genes involved, this study was undertaken to establish whether laboratory mouse strains differ in susceptibility to Sendai virus, the murine counterpart of human type-1 parainfluenza virus which, historically, has been used extensively in studies that have defined the basic biological properties of paramyxoviruses in general. With this purpose in mind, double-chamber plethysmography data were collected daily for 7 days after inoculation of Sendai virus in six inbred strains of mice. In parallel, histological examinations and lung viral titration were carried out from day 5 to day 7 after inoculation. Pulmonary structure/function values closely reflected the success of viral replication in the lungs and revealed a pattern of continuous variation with resistant, intermediate, and susceptible strains. The results unambiguously suggest that BALB/c (resistant) and 129Sv (susceptible) strains should be used in crossing experiments aimed at identifying the genes involved in resistance to Paramyxoviridae by the positional cloning approach.

scholarly journals Mouse Genome Database (MGD): Knowledgebase for mouse–human comparative biology

2020 ◽  
Vol 49 (D1) ◽  
pp. D981-D987 ◽  
Author(s):  
Judith A Blake ◽  
Richard Baldarelli ◽  
James A Kadin ◽  
Joel E Richardson ◽  
Cynthia L Smith ◽  
...  
Keyword(s):  
Mouse Models ◽  
Mouse Strain ◽  
Mouse Genome ◽  
Laboratory Mouse ◽  
Model Organism ◽  
Primary Source ◽  
Mouse Genome Database ◽  
Biomedical Literature ◽  
Mouse Strains ◽  
Genome Database

Abstract The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism knowledgebase for the laboratory mouse, a widely used animal model for comparative studies of the genetic and genomic basis for human health and disease. MGD is the authoritative source for biological reference data related to mouse genes, gene functions, phenotypes and mouse models of human disease. MGD is the primary source for official gene, allele, and mouse strain nomenclature based on the guidelines set by the International Committee on Standardized Nomenclature for Mice. MGD’s biocuration scientists curate information from the biomedical literature and from large and small datasets contributed directly by investigators. In this report we describe significant enhancements to the content and interfaces at MGD, including (i) improvements in the Multi Genome Viewer for exploring the genomes of multiple mouse strains, (ii) inclusion of many more mouse strains and new mouse strain pages with extended query options and (iii) integration of extensive data about mouse strain variants. We also describe improvements to the efficiency of literature curation processes and the implementation of an information portal focused on mouse models and genes for the study of COVID-19.

scholarly journals The Genetic Background Effect on Domesticated Species: A Mouse Evolutionary Perspective

2011 ◽  
Vol 11 ◽  
pp. 429-436 ◽  
Author(s):  
Eli Reuveni
Keyword(s):  
Genetic Background ◽  
Phenotypic Diversity ◽  
Association Studies ◽  
Laboratory Mouse ◽  
Mouse Strains ◽  
Sequencing Technologies ◽  
Genetic Background Effect ◽  
History Of ◽  
The Relationship ◽  
Careful Investigation

Laboratory mouse strains are known for their large phenotypic diversity and serve as a primary mammalian model in genotype-phenotype association studies. One possible attempt to understand the reason for this diversity could be addressed by careful investigation of the unique evolutionary history of their wild-derived founders and the consequence that it may have on the genetic makeup of the laboratory mouse strains during the history of human fancy breeding. This review will summarize recently published literature that endeavors to unravel the genetic background of laboratory mouse strains, as well as give new insights into novel evolutionary approaches. I will explain basic concepts of molecular evolution and the reason why it is important in order to infer function even among closely related wild and domesticated species. I will also discuss future frontiers in the field and how newly emerging sequencing technologies could help us to better understand the relationship between genotype and phenotype.

scholarly journals Common Inbred Strains of the Laboratory Mouse That Are Susceptible to Infection by Mouse Xenotropic Gammaretroviruses and the Human-Derived Retrovirus XMRV

2010 ◽  
Vol 84 (24) ◽  
pp. 12841-12849 ◽  
Author(s):  
Surendranath Baliji ◽  
Qingping Liu ◽  
Christine A. Kozak
Keyword(s):  
Germ Line ◽  
Expression Patterns ◽  
Laboratory Mouse ◽  
Wild Mouse ◽  
Inbred Strains ◽  
Mouse Strains ◽  
Laboratory Mice ◽  
Functional Variants ◽  
Mouse Species

ABSTRACT Laboratory mouse strains carry endogenous copies of the xenotropic mouse leukemia viruses (X-MLVs), named for their inability to infect cells of the laboratory mouse. This resistance to exogenous infection is due to a nonpermissive variant of the XPR1 gammaretrovirus receptor, a resistance that also limits in vivo expression of germ line X-MLV proviruses capable of producing infectious virus. Because laboratory mice vary widely in their proviral contents and in their virus expression patterns, we screened inbred strains for sequence and functional variants of the XPR1 receptor. We also typed inbred strains and wild mouse species for an endogenous provirus, Bxv1, that is capable of producing infectious X-MLV and that also contributes to the generation of pathogenic recombinant MLVs. We identified the active Bxv1 provirus in many common inbred strains and in some Japanese Mus molossinus mice but in none of the other wild mouse species that carry X-MLVs. Our screening for Xpr1 variants identified the permissive Xpr1sxv allele in 7 strains of laboratory mice, including a Bxv1-positive strain, F/St, which is characterized by lifelong X-MLV viremia. Cells from three strains carrying Xpr1sxv , namely, SWR, SJL, and SIM.R, were shown to be infectable by X-MLV and XMRV; these strains carry different alleles at Fv1 and vary in their sensitivities to specific X/P-MLV isolates and XMRV. Several strains with Xpr1sxv lack the active Bxv1 provirus or other endogenous X-MLVs and may provide a useful model system to evaluate the in vivo spread of these gammaretroviruses and their disease potential in their natural host.

scholarly journals Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation, and homozygous truncating mutations

2016 ◽  
Author(s):  
Anthony G. Doran ◽  
Kim Wong ◽  
Jonathan Flint ◽  
David J. Adams ◽  
Kent W. Hunter ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Cancer Susceptibility ◽  
Inbred Mouse ◽  
Laboratory Mouse ◽  
Inbred Strains ◽  
Mouse Strains ◽  
Missense Mutations ◽  
Age Related ◽  
Damage Repair ◽  
Unique Snps

AbstractBackgroundThe Mouse Genomes Project is an ongoing collaborative effort to sequence the genomes of the common laboratory mouse strains. In 2011, the initial analysis of sequence variation across 17 strains found 56.7M unique SNPs and 8.8M indels. We carry out deep sequencing of 13 additional inbred strains (BUB/BnJ, C57BL/10J, C57BR/cdJ, C58/J, DBA/1J, I/LnJ, KK/HiJ, MOLF/EiJ, NZB/B1NJ, NZW/LacJ, RF/J, SEA/GnJ and ST/bJ), cataloging molecular variation within and across the strains. These strains include important models for immune response, leukemia, age-related hearing loss and rheumatoid arthritis. We now have several examples of fully sequenced closely related strains that are divergent for several disease phenotypes.ResultsApproximately, 27.4M unique SNPs and 5M indels are identified across these strains compared to the C57BL/6J reference genome (GRCm38). The amount of variation found in the inbred laboratory mouse genome has increased to 71M SNPs and 12M indels. We investigate the genetic basis of highly penetrant cancer susceptibility in RF/J finding private novel missense mutations in DNA damage repair and highly cancer associated genes. We use two highly related strains (DBA/1J and DBA/2J) to investigate the genetic basis of collagen induced arthritis susceptibility.ConclusionThis paper significantly expands the catalog of fully sequenced laboratory mouse strains and now contains several examples of highly genetically similar strains with divergent phenotypes. We show how studying private missense mutations can lead to insights into the genetic mechanism for a highly penetrant phenotype.

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