Genome Build Versions/Data Sources Used for QTL Alignments 1

  • Btau_4.6: The Bos taurus/cattle genome assembly produced by the Human Genome Sequencing Center at Baylor College of Medicine. The genome was derived from a female and a male of the Hereford breed. The sequencing strategy produced a 7-fold mixed assembly that combines whole-genome shotgun (WGS) sequence and BAC sequence. Available from NCBI.
  • Reference 2
    Elsik Christine G, Tellam Ross L, Worley Kim C, Gibbs Richard A, Muzny Donna M, Weinstock George M, Adelson David L, Ei et al. (2009). The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (New York, N.Y.), 324 (5926): 522-8.
  • EC_2.0: A high-quality draft sequence of the genome of the horse (Equus caballus; 2009). Genomic DNA sequence released by the Broad Institute of MIT and Harvard as EquCab2.0 in September 2007 and used as the reference assembly for chromosome 1-31 and X (no sequence data was available for chromosome Y). The NCBI reference sequence for the mitochondrial genome was also included in the reference assembly. Available from Ensembl, NCBI.
  • Reference 2
    Wade C M, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear T L, Adelson D L, Bailey E, Bellone R R, Blcker et al. (2009). Genome sequence, comparative analysis, and population genetics of the domestic horse. Science (New York, N.Y.), 326 (5954): 865-7.
  • GG_4.0: The Gallus gallus/chicken genome assembly, includes improvements made by the Salzberg group at the U. of Maryland Center for Bioinformatics and Computational Biology and the near-finished Z sequence of Bellott et al. (Nature 466:612-616, 2010) as well as NGS sequence reads from the Washington University Genome Center. Available from Ensembl, NCBI.
  • Reference 2
    International Chicken Genome Sequencing Consortium. (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432 (7018): 695-716.
  • GG_5.0: This new draft assembly (GG_5.0) was generated as part of the USDA-approved sequence assembly improvement plan for the existing draft assembly (GG_4.0). At the McDonnell Genome Institute at Washington University, the previous red jungle fowl (used to create GG_4.0) and a female chicken "RJF #256" from an inbred line (UCD 001) were sequenced on the Pacific Biosciences RSII to roughly 70x genome coverage and assembled with the MHAP/PbCR algorithm, with varied sequencing technology, including Sanger, Illumina and 454. Available from NCBI.
  • Reference 2
    International Chicken Genome Sequencing Consortium. (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432 (7018): 695-716.
  • IpCoco_1.2: A doubled haploid channel catfish individual17 was used as template for sequencing. Illumina and PAC Bio technology were used to produce 8-10kb fragment libraries. Assembly was made using MaSuRCA-v2.2.0. AUGUSTUS and FGENESH were used for genome annotation. The genome sequence was validated by genetic mapping of 54,000 SNPs, and annotated with 26,661 predicted protein-coding genes. Available from NCBI.
  • Reference 2
    Liu Zhanjiang, Liu Shikai, Yao Jun, Bao Lisui, Zhang Jiaren, Li Yun, Jiang Chen, Sun Luyang, Wang Ruijia, Zhang Yu, Zho et al. (2016). The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nature communications, 7: 11757.
  • OAR_3.1: The Ovis_aries/sheep genome built was derived using next generation sequence derived from one female and one male Texel. The primary de novo assembly was performed using 75 fold Illumina GA sequence from the female, before the mate pair characteristics of the paired end reads were used to produce scaffolds spanning 2.71 Gb or approximately 91% of the sheep genome. A further 45 fold coverage of the male Texel was used for gap filling, before scaffolds are anchored onto the 27 sheep chromosomes. Available from Ensembl, NCBI.
  • Reference 2
    Jiang Yu, Xie Min, Chen Wenbin, Talbot Richard, Maddox Jillian F, Faraut Thomas, Wu Chunhua, Muzny Donna M, Li Yuxiang, et al. (2014). The sheep genome illuminates biology of the rumen and lipid metabolism. Science (New York, N.Y.), 344(6188): 1168-73.
  • OAR_4.0: The Ovis aries genome is distributed over 26 autosomes and two sex chromosomes. The annotation produced for this release (102) was compared to the annotation in the previous release (101) for each assembly annotated in both releases. Scores for current and previous gene and transcript features were calculated based on overlap in exon sequence and matches in exon boundaries. Pairs of current and previous features were categorized based on these scores, whether they are reciprocal best matches, and changes in attributes (gene biotype, completeness, etc.). Available from NCBI.
  • Reference 2
    Archibald A L, Cockett N E, Dalrymple B P, Faraut T, Kijas J W, Maddox J F, McEwan J C, Hutton Oddy V, Raadsma H W, Wad et al. (2010). The sheep genome reference sequence: a work in progress. Animal genetics, 41(5): 449-53.
  • OM_v1: The 454 genomic libraries were prepared using genomic DNA from a single homozygous doubled haploid YY male. Each library was sequenced using Pico Titer Plates on a 454 GSFlx instrument with Titanium or long read chemistry and were assembled together with Newbler. The resulting assembly was 1.9 Gb in leangth. Available from NCBI.
  • Reference 2
    Berthelot Camille, Brunet Fr�d�ric, Chalopin Domitille, Juanchich Am�lie, Bernard Maria, No�l Benjamin, Bento P et al. (2014). The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nature communications, 5: 3657.
  • SS_10.2: The Sus scrofa/pig genome was produced in August 2011 by the Swine Genome Sequencing Consortium (SGSC). It consists of 20 chromosomes (1-18, X and Y) and 4562 unplaced scaffolds. This genome assembly has GCA_000003025.4 as its GenBank assembly accession. Available from Ensembl, NCBI.
  • Reference 2
    Groenen Martien A M, Archibald Alan L, Uenishi Hirohide, Tuggle Christopher K, Takeuchi Yasuhiro, Rothschild Max F, Rog et al. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491 (7424): 393-8.
  • SS_11.1: The sequence data from which this assembly was constructed largely comprise 65x genome coverage in whole genome shotgun (WGS) Pacific Biosciences long reads (Pacific Biosciences RSII, with P6/C4 chemistry). Illumina HiSeq2500 WGS paired-end and mate pair reads were used for final error correction using PILON. Sanger and Oxford Nanopore sequence data from a few CHORI-242 BAC clones were used to fill gaps. All the WGS data were generated from a single Duroc female (TJ Tabasco, also known as Duroc 2-14) which was also the source of DNA for the CHORI-BAC library. Sscrofa11 replaces the previous assembly, Sscrofa10.2, which was largely established from the same Duroc 2-14 DNA source. Available from NCBI.
  • Reference 2
    Groenen Martien A M, Archibald Alan L, Uenishi Hirohide, Tuggle Christopher K, Takeuchi Yasuhiro, Rothschild Max F, Rog et al. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491 (7424): 393-8.
  • UMD_3.1: The Bos taurus/cattle genome build were assembled by the Center for Bioinformatics and Computational Biology at University of Maryland (CBCB) using the Celera Assembler. This assembly used sequences from a mixture of hierarchical and whole-genome shotgun sequencing methods. The UMD3.1 has been made available to the public in December 2009. All contigs and chromosomes are unchanged. Available from Ensembl, NCBI, UMD.
  • Reference 2
    Zimin Aleksey V, Delcher Arthur L, Florea Liliana, Kelley David R, Schatz Michael C, Puiu Daniela, Hanrahan Finnian, Pe et al. (2009). A whole-genome assembly of the domestic cow, Bos taurus. Genome biology, 10 (4): R42.

NOTE:
  1. The QTL alignments are implemented in GBrowse and accessible by dynamic links within the QTLdb.
  2. The references represent major milestones in sequencing a genome. The citatation of a reference may or may not exactly represent the most recent version of a genome assembly which is often a result of continued improvement.
Last updated: November 16, 2016 10:35:39

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