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.
- 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.
Wade C M, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear T L, Adelson D L, Bailey E, Bellone R R, Blöcker 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.
- 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.
- 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.
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
- 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, ECBI.
- 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.
- The QTL alignments are implemented in GBrowse and
accessible by dynamic links within the QTLdb.
- 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.