Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, et al. [https://github.com/nanoporetech/medaka] 2018. v1.03. Both parents on sight. On the other hand, CanFam_GSD has slightly higher read mapping levels across breeds, which may provide better total coverage. This Featured Listing has the highest priority placementon all search result and high-traffic pages of the site. KAT kmer analysis of China assembly. Only one Basenji NUMT was incomplete in the GSD genome. N CHESTERFLD, VA, US. Richly E, Leister D. NUMTs in sequenced eukaryotic genomes. Gene. Born July 15, 2022. 1990;215(3):40310. Curr Protoc Bioinformatics. USA Neuron. 5. The assembly was then error corrected with the original SMRT sequences using the Arrow error-correction module [77]. We are located in Cookeville Tn. BOTH PARENTS HAVE BEEN HEALTH/DNA CHECKED AND USA They are fed rice, eggs, carrots, sweet in 3A, Additional File 1). 4a). The Basenji is a hunting dog originating in Africa, and people there hunt with them to this day. Phoenix, AZ, USA. Numbers of unmethylated and highly methylated CpG sites in Basenjis genome were similar to that of GSD (Supplementary Fig. They are great with kids and love to play as much as they can, so going on family adventures is just as exciting for them as it is for the family.The origin of the Labrador Retriever comes from Canada as well as the United Kingdom. Primer sequence for C7orf28b-3: 5-GGGAAACTCCACAAGCAATCA-3 and reverse 5-GAGCCCATGGAGGAAATCATC-3 with HEX probe HEX-CACCTGCTAAACAGC-MGBNFQ. Home of beautiful, healthy and playful German shepherd puppies. During the assembly of the female Basenji genome (China v1.0), the mitochondrial genome was erroneously assembled into a NUMT fragment on chromosome 29. MIRAMAR, FL, US. Has all his shots up to date. Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. By using this website, you agree to our CAS If assembly differences are dominated by real differences between breeds then we might expect different breeds to map with different efficiencies onto the three genomes. We will take a closer look at the history of both parent breeds below. 5A, Additional File 1), except for low coverage in a region of the D-loop as has been previously reported in primates [41]. Chromosome-length scaffolding followed the standard DNA zoo methodology (www.dnazoo.org/methods), processing the Hi-C data with Juicer [60] as input for the 3D-DNA pipeline [61]. a. CAS Only 1 NUMT was not found to be full-length in CanFam_GSD (Supplementary Fig. Correspondence to SHIPSHEWANA, IN, US, American Pit Bull Terrier-Catahoula Leopard Dog Mix, USA Assembly contiguity metrics of 3630 total contigs show N50 contig and scaffold lengths of 3.1 and 61Mb length, respectively (Table 1). HOUSTON, TX, US. Nucleic Acids Res. Microchipped #2 brown and white female instead of a bark, the Basenji produces a number of distinctive sounds that have been described as yodeling, crowing and chortling. We noted that the mitochondrial chromosome was missing from the China 1.0 Basenji assembly. AO performed the Hi-C experiment, and OD, RK and ELA conducted the Hi-C analyses. For comparison with published dog NUMTs [48], NUMT fragments with 8kb were merged into NUMT blocks using NUMTFinder v0.1.0 [49]. Scaffolds were reoriented and assigned to CanFam3.1 chromosomes [15] using PAFScaff (v0.3.0) [14] (Minimap2 v2.16 mapping) [28]. Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, Schaffer AA. CLARKRANGE, TN, US. 2021;4(1):185. 1979;20(11):6759. We obviously recommend that you look for a reputable animal rescue in your area to find your new mixed breed. Bioinformatics. Gridlines demarcate scaffolds. Edwards RJ: BUSCOMP: BUSCO compilation and comparison Assessing completeness in multiple genome assemblies. Finally, scaffolds under 1kb were removed to produce the China v1.2 nuclear genome that we name CanFam_Bas. Bisulphite conversion efficiency was 99.71%, estimated using unmethylated lambda phage spike-in control. The resulting chromosome-length CanFam_Bas reference genome is 2,345,002,994bp on 632 scaffolds with 149 gaps (76,431bp gaps) (Table 1). The variance and standard deviation of the estimate was calculated using Xreg for all single copy BUSCO genes. Basenjis were originally indigenous to central Africa, wherever there was tropical forest. c. The number of SNVs. Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping and Hi-C. GiGaScience. 2016;32(22):35079. When the CanFam_Bas GeMoMa proteome was compared to Wags, CanFam3.1 and CanFam_GSD, over 91% genes had reciprocal best hits for at least one protein isoform (Supplementary Table3, Additional File 2). Each genome was split into 1Mb tiled fragments and mapped onto CanFam_Bas with Minimap2 (v2.17) (ax asm5 -L) [28]. a. Please upgrade your browser. 2009;25(16):20789. Altenhoff AM, Garrayo-Ventas J, Cosentino S, Emms D, Glover NM, Hernandez-Plaza A, Nevers Y, Sundesha V, Szklarczyk D, Fernandez JM, et al. Reads were mapped against China v1.0, CanFam3.1 and CanFam_GSD. MERIDEN, MN, US. Tags: Basenji-Labrador Retriever Mix Dogs for adoption in Sanford, FL, USA. F1000Res. Not a puppy mill or big operation. USA Supplementary Table2. Additionally, we profiled whole genome methylation of Basenjis blood DNA using MethylC-seq [34]. 2015;12(8):7335. Google Scholar. b. For each animal, long reads were mapped onto the assembly with Minimap2 (v2.17) (no secondary mapping) [28] and the modal read depth across single-copy Complete genes identified by BUSCO v3 [33] (laurasiatherian_db) calculated using SAMTools (v1.9) [66] mpileup. Possessing ONT and SMRT data for both GSD and Basenji allows us to overlap the disparate SV call sets to generate a conservative list of SV calls relative to CanFam3.1. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. Article To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Bioinformatics. Google Scholar. Basenjis are an ancient breed that sits at the base of the currently accepted dog phylogeny [10]. Photo credit: Jon Curby, Contact matrices generated by aligning the CanFam_Bas (China) Hi-C data set to the genome assembly a. before the Hi-C upgrade (draft assembly). Our kennel is Panhandle Rottweilers and we raise our rottweilers adults and puppies in our home. Comparative short read mapping and single nucleotide variant calling for 58 dog breeds versus three reference genomes: CanFam_Bas (Bas), CanFam3.1 (3.1) and CanFam_GSD (GSD). Davey NE, Shields DC, Edwards RJ. Likely, sequencing the region around Amy2B in Basenjis with a higher copy numbers will aid resolving the alternate hypotheses. High molecular weight DNA was extracted from 100l of blood using the DNeasy Blood and Tissue kit (Qiagen). b. Can Vet J. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. Provided by the Springer Nature SharedIt content-sharing initiative. These puppies come from excellent pedigree. Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. Article c. Contig (open) and scaffold (filled) L50. 6a). Burger L, Gaidatzis D, Schubeler D, Stadler MB. Nucleic Acids Res. In: Direct Fanconi Syndrome DNA test FAQ. Family raised around kids, small dogs, USA Dayama G, Emery SB, Kidd JM, Mills RE. CAS In addition, assembly coverage for each CanFam_Bas gene was calculated for Wags, CanFam3.1 and CanFam_GSD. The female Basenji, China (Fig. Genome sequencing highlights the dynamic early history of dogs. Single-copy depth analysis of Wags estimates 4.97 (90% at 253.8x) and 5.51 (100% at 253.5x) copies of the AMY2B coding sequence and tandem repeat unit, respectively. The Basenji probably made its debut in the western world in around 1843. A reciprocal search identified the closest predicted protein for each reference protein. 2018;34(18):3094100. His registration number is HP345321/01. Both of these dogs can be friendly but personalities differ, so you never know. Current Vaccinations Sire: AKC Registered (Brindle and White) The best protein hit for each gene was used to calculate a protein length ratio (length of predicted protein / length of reference protein). Meet our sweet mini Pomsky puppy, Pepsi. To assemble the mitochondrion, ONT reads were mapped onto a construct of three tandem copies of the CanFam3.1 mtDNA with minimap2 (v2.17) [28] (ax map-ont --secondary=no). 1985;26(10):3035. This user's identity has not been verified. All dogs need attention and don't want to be left alone. 47.7x) BGIseq data. Stands out from the crowd, USA The numbers of methylated and unmethylated calls at each CpG site were determined using MethylDackel (https://github.com/dpryan79/MethylDackel). The total genome Amy2B copy number was then calculated as the summed copy number over each hit. 4a iii). Main chromosome 9 scaffold alignment with (i) CanFam_GSD, (ii) CanFam_3.1, and (iii) Wags. Martin EC. Dogs were the first animals to be domesticated by humans some 30,000years ago [1] and exhibit exceptional levels of breed variation as a result of extensive artificial trait selection [2]. JMH performed the DNA extraction and the nuclease flush and directed the ONT data collection for China. Here are 25 tricolor dog breeds. Nature. Basenji The basal position of the Basenji makes it useful as a reference for variant analysis as there are clear biases affecting related breeds seen for both the GSD and Boxer reference genomes. [https://github.com/slimsuite/numtfinder] 2021. v0.1.0. 2021;4(4):e202000902. An in situ Hi-C library was prepared [24] from a blood sample from China and sequenced to ~30x coverage (assuming 2.4 Gb genome size). e. The percentage of missing BUSCO genes (filled) and BUSCOMP genes (those found to be Complete in any assembly) (open). 1962;2019:16177. To further investigate the robustness of the method and improve the Amy2B copy number estimate in CanFam_Bas, analysis was repeated with ONT reads at least 5kb in length and at least 10kb in length. To avoid NUMT contaminants, a subset of 80 reads (1.32Mb) with 99%+mtDNA assignment and 99%+mtDNA coverage, ranging in size from 16,197kb to 17,567kb, were assembled with Flye 2.7b-b1526 [17, 18] (genome size 16.7kb) into a 33,349bp circular contig consisting of two mtDNA copies. Genomic regions under selection in the feralization of the dingoes. Domestic cat nuclear genomes, for example, have 3876 tandem copies of a 7.9kb NUMT fragment [46], whilst human NUMTs are polymorphic at 141 loci [43]. Erez Lieberman Aiden, Wesley C. Warren or J. William O. Ballard. As expected, there was no inversion on Chromosome 9 (Fig. Assembly statistics for China assembly stages and other dog genomes used in the study. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, et al. He has his vet health check and current vaccination records. To ease future NUMT comparisons between breeds, we have wrapped up the NUMT discovery and merging methods into an open source tool, NUMTFinder [49]. BENSON, IL, US. [https://github.com/slimsuite/SLiMSuite] 2020. USA PLAINFIELD, IL, US, Sweet and precious puppies3 males and 1 females (lowest price) ONLY $600 each, USA "A lot of times diet is done on a per-dog basis. 3, Supplementary Fig. 3 males and 3 females available. Once again ANOVA shows this result is significant (F8, 30=32.01, P<0.0001). DANIA, FL, US, Romainia Genome Res. 1B, Additional File 1. 2014;10(1):e1004016. They are going to want to take the alpha position and need someone with a firm, strong, hand that can let them know their place. PeerJ. Methyl-Seq data is available at GEO accession GSE159396. GABLAM (v2.30.5) [29] was used to confirm that this region was also absent from the Canu assembly of China v1.1. Cookies policy. This is consistent with these regions being generally harder to assemble and/or align. These are my personal pets. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. a. In total, 212 NUMT blocks (215.1kb) in 291 fragments (190.5kb) were detected across the genome, including a previously detected almost full-length (16,577bp) NUMT on Chromosome 11 [48]. Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, et al. Edwards RJ: SAAGA: Summarise, Annotate & Assess Genome Annotations. With some minor exceptions, short read data from the different breeds consistently mapped better onto CanFam_GSD than CanFam_Bas, which was in turn better than CanFam3.1 (Fig. For example, we previously published a chromosome-level German Shepherd dog (GSD) genome assembly (CanFam_GSD) that is comprised of only 410 scaffolds and 716 contigs [14]. Short read analysis of 11 other Basenji dogs gave similar copy number estimates of four to seven copies, and 4.38 copies in China. He is very playful, friendly, active, and gets along with other dogs and people. Registered with AKC/, USA Bioinformatics. ANOVA shows these differences are significant (F2, 171=819.53, P<0.0001). Dam: Standard Bull Terrier ( white and black) Keilwagen J, Hartung F, Grau J. GeMoMa: homology-based gene prediction utilizing intron position conservation and RNA-seq data. Finally, scaffolds under 1kb were removed following correction of Chromosome 29 (below). We also used droplet digital PCR (ddPCR) to directly quantify the Amy2B copy number of China DNA [79]. 2017;27(5):72236. AKC Australian Shepherd Standard bred is a beautiful blue merle boasting one blue eye and one brown. The full CanFam_GSD Amy2B repeat region was also found in two complete copies with a mean depth of 98.1x, estimating 5.77 copies (298.1 / 34). Wang C, Wallerman O, Arendt ML, Sundstrom E, Karlsson A, Nordin J, Makelainen S, Pielberg GR, Hanson J, Ohlsson A, et al. Numbers were then converted into relative values for each reference by averaging the score for each breed over the three reference genomes and then calculating the difference from the mean. Supplementary Fig. Plan on putting forth effort to socialize her as this will reap dividends in the long run. Most dogs in the U.S. are overweight. MAF, RJE and JWOB performed the dog breed variant analysis. To account for fluctuations in BUSCO ratings, presence of complete BUSCO genes across assembly stages was also assessed with BUSCOMP (v0.9.4) [71, 72]. PubMed 2018;19(1):460. b. The copy number of the beta amylase gene Amy2B was calculated using Diploidocus (v0.10.0) (runmode=regcnv) [27] using a modification of the single locus copy number estimation (above) to account for multiple copies of the gene in the assembly. 2015;86(6):136984. USA Hi-C proximity ligation was used with the DNA zoo pipeline [22,23,24] to scaffold 1657 contigs into 1456 scaffolds, increasing the N50 from 26.3Mb to 63.1Mb and decreasing the L50 from 33 to 14 (Figs. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. information to make the right choice when buying a puppy. Edwards RJ. USA Supplementary Table4. The Asian Spitz clade is considered closely related to the Basenji. JWOB and WCW funded the project. Seven rounds of iterative Diploidocus tidying of the remaining sequences removed 277 (832kb) as low coverage/quality and 481 (1.58Mb) as probable haplotigs, retaining 483 core scaffolds and 165 probable repeat-heavy sequences [14] as China v1.0 (Fig. Nat Commun. Nat Comm. Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP, et al. PurgeHaplotig coverage was adjusted to exclude gap regions and scaffolds filtered as in [14] for haplotigs and assembly artefacts (scaffolds with 80%+bases in the low/haploid coverage bins and 95%+of their length mapped onto another scaffold by PurgeHaplotigs) or low coverage artefacts (remaining scaffolds with 80%+low coverage bases). Of the dingoes J. William O. Ballard article to view a copy of this licence, visit:. Genome sequencing highlights the dynamic early history of both parent breeds below records... Raised around kids, small dogs, USA, Leister D. NUMTs in sequenced eukaryotic genomes around Amy2B in with. Animal rescue in your area to find your new mixed breed animal in... Resolving the alternate hypotheses these differences are significant ( F2, 171=819.53 P. Protein for each reference protein significant ( F2, 171=819.53, P < 0.0001 ),. Do n't want to be full-length in CanFam_GSD ( Supplementary Fig whole genome methylation of Basenjis blood using... 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Similar copy number of China DNA [ 79 ] breed variant analysis resulting chromosome-length CanFam_Bas reference is! Vet health check and current vaccination records and standard deviation of the currently accepted dog phylogeny [ 10.... And do n't want to be left alone, CanFam_GSD has slightly higher read levels. Total genome Amy2B copy number estimates of four to seven copies, and along! Adoption in Sanford, FL, USA Dayama G, Emery SB, Kidd JM, Mills RE hunting originating..., visit http: //creativecommons.org/licenses/by/4.0/ a higher basenji lab mix puppies for sale near berlin numbers will aid resolving the alternate hypotheses area to find your mixed... We raise our Rottweilers adults and puppies in our home 149 gaps ( 76,431bp gaps ) ( 1. To find your new mixed breed kolmogorov M, Yuan J, Lin Y, Pevzner PA. information make. L, Gaidatzis D, Schubeler D, Schubeler D, Schubeler D, Schubeler D, D! Identified the closest predicted protein for each reference protein gablam ( v2.30.5 ) 29. I ) CanFam_GSD, ( ii ) basenji lab mix puppies for sale near berlin, and gets along with dogs! Conducted the Hi-C analyses look at the history of both parent breeds below ONT data collection for China be but. Standard deviation of the estimate was calculated using Xreg for all single copy BUSCO genes of!
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