Supplemental Information. Y Chromosome Uncovers the Recent. Oriental Origin of Modern Stallions

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1 urrent iology, Volume 27 Supplemental Information Y hromosome Uncovers the Recent Oriental Origin of Modern Stallions arbara Wallner, Nicola Palmieri, laus Vogl, Doris Rigler, Elif ozlak, Thomas Druml, Vidhya Jagannathan, Tosso Leeb, Ruedi Fries, Jens Tetens, Georg Thaller, Julia Metzger, Ottmar Distl, Gabriella Lindgren, arl-johan Rubin, Leif Andersson, Robert Schaefer, Molly Mcue, Markus Neuditschko, Stefan Rieder, hristian Schlötterer, and Gottfried rem

2 A Frequency ontig length scpy Number of contigs Number of contigs mcpy Proportion of the contig covered MNA (Mean Normalised Average overage ) D m m m f f f f ntc E male male male female F Figure S1. Reference work results. Related to Figure 1. (A) ontig length distribution of the de novo contigs and 2794 nonrepmsy contigs (blue). () Proportion of the nonrepmsy contigs covered by female (red) and male (blue) reads. Abscissa: proportion of contig sequence matched by short reads, ordinate: number of contigs. () The mean normalised average coverage (MNA) treshold of 1.5 (red line) separates 2491 single copy MSY contigs (scpmsy) from 303 mulit copy MSY contigs. (D) Y specificity of a contig was confirmed by comparatively amplifying male (m) and female (f) genomic DNA and a no-template-control (-). The expected PR amplicon is indicated by the red arrow. Primers are listed in Data S1. IGV screenshot of whole genome NGS (three males and one female) data mapped to a scpmsy (E) and a mcpmsy (F) contig.

3 Figure S2 Average mapping coverage A males' D females'

4 Figure S2. MSY variant ascertainment and validation. Related to Figure 2. (A) Average mapping coverage of males (blue) and females (red) to scpmsy contigs. () Results of MSY variant validation. Total number of variants in respective categories (related to Data S2), number of variants selected for validation in each category and number of successfully confirmed variants is shown. (, D) Validation of six MSY variants is shown as example. ) IGV screenshot of three true_variants and successful validation. The two domestic variants were validated with LG KASP technology, the Przewalski s variant with Sanger sequencing. D) Three not_true_variants (two from category false_positives and one false_positive_icel_orl_only ) and validation failure. The corresponding regions in IGV image and the Sanger electropherogramm are marked with coloured boxes. Abbrevations: male (m), female (f), no template control (ntc), domestic horse (dom), Przewalski s horse (prz)

5 A DARLEY ARAIAN,1700 Mutations 1 Meioses 18 Years 237 ST. SIMON,1881, ro PRINE IO,1941, THE LAST ORANGE,1941, SELLE FRANAIS OLD02 Tb P1 Tb-k Mutations 2 Meioses 56 Years 750 DARLEY ARAIAN,1700 WHALEONE,1807, TOUHSTONE, 1831, STOKWELL,1849, WF01 DARK RONALD,1905, SON-IN-LAW,1911, re OR DE LA RYERE, 1968,SELLE FRANAIS HOL02 ORPORAL,1963, HOLSTEINER HOL01 Tb-dW2 GOLDSHAUM, 1891, DEFILANT,1896, GRAF,1941, W01 FLYING FOX,1896, rf DISKANT,1957, OLD01 OLIVERI, 1953, RAO310 Tb-dW3 Godolphin Arabian, 1724 Mutations 1 Meioses 27 Years 352 OMUS,1809, FLENHEIM,1886, ARALDINE,1878, rl FLUEGELADJUTANT,1938, FURIOSO,1939, HAN01 Tb-g3 WF02 Tb-g2 Figure S3. De novo mutation rate and TMRA estimates. Related to Figure 3. (A-) Pedigree reconstruction of three genealogies harbouring four de novo mutations (ro, re, rf, rl). Sequenced samples are on the bottom. Ancestors are represented by dots (black dots no name, red dots ancestor identity provided). Number of mutations, meioses and total years covered in the genealogy are given.

6 A YOUNG MARSKE,1771,T Tb-d AMEL,1822T Tb-dW2 ARTLETS HILDERS,1716,T SIR HERULES,1826,T Tb-dW3 WHALEONE,1807,T DARLEY ARAIAN,1700 HT: Tb-d ELIPSE,1764,T DEFENE,1824,T KING FERGUS,1775,T OLD SHALES,1755,HAKNEY FLYING HILDERS,1715,T PERSIMMON,1893,T ST FRUSQUIN,1893,T Tb-k Tb MAMRINO,1806,STANDARDRED Tb-dM PRIVATEER,1825,T WALTON,1799,T FURIOSO XIII,1931,FUR FOURIRE,1896,T JAMAIS,1931,SF PHANTOM,1808,T SIR PETER TEAZLE,1784,T NORMANN,1868,SF EDELKNAE II,1942,OLD WASHINGTON DENMARK,1855,S STONEWALL KING,1920,S HAPHAZARD,1797,T DENMARK,1858,S VANITYS SENSATION OF REILLY,1947,S Tb DIAMOND DENMARK,1858,S INDIANA AE,1944,S DJEE,1945,T SELIM,1802,T AMYSE,1884,T DJEEL,1937,T yerley Turk,1680 HT: Tb EX VOTO,1900,T MARDOHEE,1941,AA LARION,1944,T ASTREL,1801,T LE SANY,1884,T SAINT SAULGE,1899,T RAMZES,1937, AA Tb-r DOULE DIAMOND,1947,QH FLORIZEL,1768,T VAN TROMP,1832,QH PETER MUE,1895,QH OLD SORREL,1915,QH SHEIK,1918,QH Tb-d Tb-g1 FERDINAND,1941,HAN Tb4dW PROTETOR,1831,T FLENHEIM,1886,HAN Godolphin)Arabian,1724) OMUS,1809,T FLUEGELADJUTANT,1938,HAN Tb4g3) PRZEDSWIT,1872,T Tb4g2) HUMPHREY LINKER,1822,T WEST AUSTRALIAN,1850,T FURIOSO,1939,T Figure S4. Pedigree reconstruction. Related to Figure 4. Paternal genealogy and HTs of descendants of Darley Arabian (A), yerley Turk () and Godolphin Arabian (). oloured circles are the HTs of individual samples and the colour-code is synchronized to Figure 2 and 4. Respective HTs of lineages are given in brackets and within lineage de novo HTs are underlined. Pedigree errors are indicated by arterisks. Abbrevations: Angloarabian (AA), English Thoroughbred (T), Furioso (FUR), Hanoverian (HAN), Oldenburger (OLD), Quarter Horse(QH), Saddlebred (S), Selle Francais (SF)

7 Supplemental Data S1 S4 uploaded as separate spreadsheets.