AND/OR-Search by use of commas. Epub 2008 Sep 9. Nature 537, 508514 (2016). Thus, their identification is a powerful tool for finding errors in genome assemblies. Sci. In particular, the wild-derived strains represent a rich resource of novel target sites, resistance alleles, genes and isoforms not present in the reference strain, or indeed If you're looking for a strain that will help with your pain without making you feel high, this one is for you! Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. These divergent profiles suggest that Nlrp1c is not the sole mediator of anthrax lethal toxin resistance in the mouse but several other members may be involved. Several prominent examples include apolipoprotein L alleles, variants of which may confer resistance to Trypanosoma brucei, the primary cause of human sleeping sickness28,29; IFI16 (interferon gamma inducible protein 16, a member of AIM2-like receptors), a DNA sensor required for death of lymphoid CD4 T cells abortively infected with human immunovirus (HIV)30; NAIP (NLR family apoptosis inhibitory protein) in which functional copy number variation is linked to increased cell death upon Legionella pneumophila infection31; and secretoglobins (Scgb members), which may be involved in tumor formation and invasion in both human and mouse32,33. Diversity Outbred mice identify population-based exposure thresholds and genetic factors that influence benzene-induced genotoxicity. GENCODE: the reference human genome annotation for The ENCODE Project. For the first time, the underlying sequence at these loci is represented in strain-specific assemblies and gene predictions from across the inbred mouse lineage, which should facilitate increased dissection of complex traits. Careers. 1d). Physiol. 15). Bioinformatics 22, 14371439 (2006). This strain is an easy-to-grow photoperiod cultivar that will produce dense buds it's a great option for new growers. S.C., C.L., M.T., and B.Y. Mudge, J. M. & Harrow, J. 21, 12391248 (2011). Bioinformatics 31, 30783080 (2015). Assembly scaffolds are further joined into chromosomes so as to minimize the number of structural differences (such as inversions or chromosomal translocations) between references and a target genome. This makes it possible to exploit the combined evidence for gene finding and to discover genes that, for example, are only weakly expressed and partially supported in the reference strain but that have a high expression in other strains. This approach identified previously unannotated genes, including Efcab3-like, one of the largest known mouse genes (5,874 amino acids) that also appears conserved in mammals. Prostate Cancer 1, 118124 (2002). Your reply will be published soon after verification. Be mindful of the method of consumption (e.g., smoking, vaping, edibles) as it can impact the onset and duration of effects. 21, 15121528 (2011). Gene predictions from strain-specific RNA-Seq (Comparative Augustus24) added an average of 1,400 new isoforms to wild-derived and 1,207 new isoforms to classical strain gene annotation sets. The resulting AugustusCGP gene sets were quality filtered based on how well the exon-intron structure of a transcript was supported by the combined RNA-Seq evidence (80% of the introns with splice junction support and 80% of CDS exons with a read coverage of at least ten reads per kilobase of mRNA). The subsequent reads were used as input to SOAPdenovo273 r240 to produce genome scaffolds (parameters given in Supplementary Table 19). We used the presence of dense clusters of hSNPs on the C57BL/6J reference genome as a marker for extreme polymorphism and examined the de novo assembly to explore the underlying genomic architecture. You will find the link onto the strain-description pages, right below the short overview about the available hybrids. Metabolism of hexahydro-1,3,5-trinitro-1,3,5-triazine through initial reduction to hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine followed by denitration in Clostridium bifermentans HAW-1. We used the C57BL/6J GRCm38 sequence as a single reference and found that 95% adjacent synteny block pairs from the assemblies were also adjacent in C57BL/6J reference. Mamm. Mi, H., Muruganujan, A. The progressiveCactus whole genome alignments were used to project annotations from GENCODE VM860 onto each of the strain-specific assemblies using transMap75. All the information available on AskGrowers is only for educational purposes. Epub 2018 Nov 28. All samples were also systematically assessed for cellular ectopia (misplaced neurons). Lander, E. S. et al. Genesis 54, 7885 (2016). Interestingly, within this region, Cpsf3 (21.29 Mb) is located on an island of high conservation in all strains and a homozygous C57BL/6NJ knockout produces subviable offspring35. Curr. Planta. White coloring indicates a P value>0.05 and grey indicates that the brain region could not be confidently tested due to missing data. Further information on research design is available in the Nature Research Reporting Summary linked to this article. Genealogies of mouse inbred strains. Stremlau, M. et al. Genome Res. A single genotype-confirmed F1 mouse (Efcab3em1(IMPC)Wtsi) was used to generate mice for phenotyping. 14, R22 (2013). We examined three immunity-related loci on chromosome 11, IRG (GRCm38: 48.8549.10 Mb), Nlrp1 (71.0571.30 Mb), and Slfn (82.983.3 Mb) because of their polymorphic complexity and importance for mouse survival48,49,50. Nature 474, 337342 (2011). Strain-specific consensus gene sets were produced using the GENCODE C57BL/6J annotation and strain-specific RNA sequencing (RNA-Seq) from multiple tissues23 (Supplementary Table 8 and Supplementary Fig. The cytoplasmic body component TRIM5alpha restricts HIV-1 infection in Old World monkeys. Google Scholar. We identify and characterize 2,567 regions on the current mouse reference genome exhibiting the greatest sequence diversity. was supported by a research grant from CONICYT/FONDECYT/REGULAR No.1171004 and the European Commission (EUFP7 BLUEPRINT grant HEALTH-F5-2011-282510). nov., a strictly anaerobic bacterium that grows via fermentation and reduces the cyclic nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Comparative Annotation Toolkit (CAT) simultaneous clade and personal genome annotation. WebAlthough its exact genetics and breeder arent documented, this bud may have a connection to an Afghani indica landrace. Learn about its many uses, its cultural significance, and its ongoing evolution as a natural medicine. A novel start codon upstream of Slfn4, which causes a 25 amino acid N-terminal extension, was identified in PWK/PhJ and WSB/EiJ. The 16S rRNA gene sequence for strain HAAP-1, consisting of 1485 base pairs, 2017 Apr;6(2):e00423. Indoors, you can expect to harvest 1-2 Oz/Ft (~ 400 g/m) of weed. Zhang, Z. et al. Despite this, previous SNP variation catalogs have identified high-quality heterozygous SNPs (hSNPs) when reads were aligned to the C57BL/6J reference genome12. Based on these results, samples were selected for odor evaluation by 55 sensory panelists in work carried out by Headspace Sensorys Gilbert. We observed several innate immunity gene families in mice with a high density of retrotransposons, which is the likely mechanism for diversification at these loci (for example, Nlrp1, Fig. Modeling host genetic regulation of influenza pathogenesis in the collaborative cross. Both loci have been targeted using a conditional approach as part of the International Knockout Mouse Consortium (IKMC) resource. AND We used CRISPR (clustered regularly interspaced short palindromic repeats) to create Efcab3-like mutant mice (Efcab3em1(IMPC)Wtsi, see Methods) and recorded 188 primary phenotyping measures (Supplementary Data 9). This represented the density at which the interval content and total unique overlapping base pairs was observed to be clustered around distinct loci (Supplementary Fig. Boroviak, K., Doe, B., Banerjee, R., Yang, F. & Bradley, A. Chromosome engineering in zygotes with CRISPR/Cas9. Also, if you've been struggling with weight loss and don't know how to get out of the slump that comes with losing motivation to eat healthily, try this strain. AugustusPB transcripts that could not be confidently assigned to parent transcripts were discarded and not evaluated for novel contribution. 9, e1003196 (2013). The resulting read alignments were quality filtered by coverage (80%), identity (90%) and uniqueness; that is, when a read mapped to multiple loci, the best alignment for that read was only kept if the alignment score of the second best was considerably worse. Here we generate the first chromosome-scale genome assemblies for 12 classical and 4 wild-derived inbred strains, thus revealing at unprecedented resolution the striking strain-specific allelic diversity that encompasses 0.52.8% (14.475.5 Mb, excluding C57BL/6NJ) of the mouse genome. Nat. Immunol. The authors declare no competing interests. CAS Thanks a lot for sharing your opinion! David Downs. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. Second, C57BL/6J reads aligned to the regions of interest in the C57BL/6NJ assembly were extracted for targeted assembly, leading to the generation of contigs covering sequences currently missing from the reference. The transcripts resulting from transMap as well as AUGUSTUS were evaluated by a consensus-finding algorithm that attempts to use a combination of fidelity to the reference and a series of binary classifiers to construct a consensus gene set. WebHeadspace is a relatively new hybrid marijuana strain. For non-coding transcripts, the fewest number of transcripts to keep at least 80% of present non-coding splice junctions were retained. B.P., I.T.F., M.A., J.A., M.Di., D.D.D., D.E., A.F., M.G., J.G., J.H., S.N., P.M., F.C.P.N., L.Ro., M.S., C.Si., C.St., G.T., R.B., J.Lo., M.S.H., D.T., and J.Li. The representation of known mouse repeat families in the assemblies shows that the short repeat (<200 base pairs (bp)) content was comparable to GRCm38 (Supplementary Fig. Am. J. Physiol. Uteroglobin: a potential novel tumor suppressor and molecular therapeutic for prostate cancer. Medical patients choose Head space to relieve symptoms of stress, pain and anxiety according the growers who claim this produces dark green leaves dotted with trichomes while burnt orange hairs on them as well! If you're looking for something that will help you focus on a project or creative endeavor, this is the strain for you! Of the 785 predictions investigated, 62 led to the annotation of new loci, including 19 protein-coding genes and 6 pseudogenes (Supplementary Table 14 and Supplementary Data 8). We found an 18 amino acid mismatch in the nucleotide-binding domain (NBD) between Nlrp1b_CAST and Nlrp1b_PWK. eLife 6, (2017). Each input genome assembly, along with its associated Chicago library read pairs in FASTQ format, were used as input data for HiRise, a software pipeline designed specifically to scaffold genomes using Chicago library data2. Inbred laboratory mouse strains are characterized by at least 20 generations of inbreeding and are genetically homozygous at almost all loci 1. Despite this, previous SNP variation catalogs have identified high-quality heterozygous SNPs (hSNPs) when reads were aligned to the C57BL/6J reference genome 12. Headspace has a modest amount of 19% THC on average although this number could vary from one grower to another. 2009 Feb;20(1):15-26. doi: 10.1007/s10532-008-9195-1. Headspace potency is higher THC than average. To this end, we have characterized the CAST/EiJ olfactory receptor repertoire using our de novo assembly and identified 1,249 candidate olfactory receptor genes (Supplementary Data 5). These comparative transcripts were given to the gene-finding tool AUGUSTUS13 as strong hints (external evidence) in conjunction with weaker hints derived from all available RNA-Seq data for the given strain. Rev. We are here to help! The origin of the strain is very controversial, but, in both instances, its genealogy includes OG Kush and Durban Poison, which gives it a minty and pungent punch with a sweet after-burst. We also created a de novo set of strain-specific genes and isoforms from Comparative Augustus (AugustusCGP)24 using the strain-specific RNA-Seq and the progressive Cactus alignment. Windows were grouped according to the number of hSNPs they contained. A subsequent round of consensus finding was employed to incorporate these transcripts into the final consensus annotation set. The data about strains, products and their effects, contained on the website is based on the consumer reviews. Internet Explorer). 38, 21682171 (2006). a, Summary of the strain-specific gene sets showing the number of genes broken down by GENCODE biotype. Hum. Consult with a cannabis healthcare professional for specific medical concerns, and always verify the legality of cannabis in your location. a, Comparative Augustus identified an unannotated 188 exon gene (Efcab3-like, red tracks). Nat. We're still trying figure out what flavors or effects you've experienced - if it was good leave us an review below so other users know too 17, 167 (2016). J. Appl. Dummer, P. D. et al. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK, Jingtao Lilue,Anthony G. Doran,Ruth Bennett,Paul Flicek,Adam Frankish,Jane Loveland,David Thybert&Thomas M. Keane, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK, Jingtao Lilue,Anthony G. Doran,Monica Abrudan,William Chow,Joanna Collins,Petr Danecek,Dirk-Dominik Dolle,Matt Dunn,Richard Durbin,Paul Flicek,Adam Frankish,Beiyuan Fu,James Gilbert,Jennifer Harrow,Kerstin Howe,Ximena Ibarra-Soria,Chris J. Lelliott,Darren W. Logan,Jane Loveland,Naomi Park,Sarah Pelan,Mike Quail,Lesley Shirley,Charles Steward,Mark Thomas,Glen Threadgold,James Torrance,Kim Wong,Jonathan Wood,Fengtang Yang,David J. Adams&Thomas M. Keane, Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA, USA, Ian T. Fiddes,Joel Armstrong,Mark Diekhans,Dent Earl&Benedict Paten, Institut de Gntique et de Biologie Molculaire et Cellulaire, Centre National de la Recherche Scientifique UMR7104, Institut National de la Sant et de la Recherche Mdicale U964, Universit de Strasbourg, Illkirch, France, Centre des Sciences du Got et de lAlimentation, University of Bourgogne Franche-Comt, Dijon, France, The Jackson Laboratory, Bar Harbor, ME, USA, Department of Genetics, University of Cambridge, Cambridge, UK, Brain Research Institute, University of California, Los Angeles, CA, USA, Yale Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA, Mark Gerstein,Paul Muir,Fabio C. P. Navarro&Cristina Sisu, OxFORD Asset Management, OxAM House, Oxford, UK, Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA, Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA, Genetics Institute, University College London, London, UK, Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany, Stefanie Nachtweide,Lars Romoth&Mario Stanke, Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK, German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics, Heidelberg, Germany, Department of Bioscience, Brunel University London, Uxbridge, UK, Departamento de Biologa Celular y Molecular, Facultad de Ciencias Biolgicas, Pontificia Universidad Catlica de Chile, Santiago, Chile, Earlham Institute, Norwich Research Park, Norwich, UK, School of Life Sciences, University of Nottingham, Nottingham, UK, You can also search for this author in