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Supplementary Information for Comparative Analysis of Mammalian Y Chromosomes Illuminates Ancestral Structure and Lineage-Specific Evolution Supplementary Information for Comparative Analysis of Mammalian Y Chromosomes Illuminates Ancestral Structure and Lineage-Specific Evolution Gang Li, Brian W. Davis, Terje Raudsepp, Alison J. Pearks Wilkerson, Victor C. Mason, Malcolm Ferguson-Smith, Patricia C. O’Brien, Paul Waters and William J. Murphy. Figures 1-12 Pgs. 2-16 Tables 1-3 * Pgs. 17-19 Supplemental Methods Pgs. 20-24 *Supplementary Table 4 is attached as a separate Excel file 1 Figure 1. Copy number analysis of felid Y chromosome genes using qPCR and FISH A. Quantitative PCR analysis in three domestic cats 13 12 110 11 100 10 90 9 80 8 Number 70 7 60 6 Copy 50 5 40 4 30 3 Estimated Copy Number 20 2 Estimated 10 1 0 0 B. FISH mapping of domestic cat multicopy cDNA probes on snow leopard (Panthera uncia) Y chromosomes CUL4BY TETY1 TSPY FLJ36031Y 2 Figure 2. Summary of copy number and expression information for domestic cat and dog Y chromosome genes. Copy Expression Expression Copy number pattern pattern number biased biased 1 MC Testis specific Testis Ubiquitous Other tissue Testis Testis specific SHROOM2 Ubiquitous SHROOM2 1 MC Other tissue TETY2 TETY2 UTY UTY DDX3Y DDX3Y USP9Y USP9Y HSFY EIF1AY AMELY KDM5D ZFY EIF1AY EIF2S3Y BCORY1 ZFY CYorf15 UBE1Y KDM5D RBMYL DYNG Cat BCORY2 UBE1Y Dog HSFY OFD1 RPS4Y CYorf15-fusion SRY SRY family CYorf15 TSPY & TSPYL families CUL4BY1 CUL4BY2 3 Figure 3: Comparison of sequence conservation among 5 Y mammalian chromosomes (human, chimpanzee, rhesus, dog, and cat) using the sequenced cat (A) and dog (B, next page) Y chromosome sequence as a reference. Multispecies sequence conservation scores are shown by blue columns (bottom panel), and pairwise sequence identity between X and Y chromosome sequence is shown by red columns (top panel). Green circles with numbers indicate X-Y orthologous regions, the order of which is shown on a schematic of the X chromosome at the bottom. Gene and transcript information is listed below each panel. Functional genes are shown in black, while pseudogenes are shown in orange. Red bars at the bottom of each panel indicate known gene exons. A: 0 1 2 0.1 3 0.2 0.3 4 0.4 0.5mb 100% 60% 1 0.8 0.6 0.4 0.2 0 PAR CINPLP SHROOM2 TETY2 UTY DDX3Y USP9Y 0.5 5 0.6 6 0.7 7 8 0.8 9 0.9 10 11 1.0mb 100% 60% C/D/H/P 1 ZFY 5’ 0.8 0.6 0.4 0.2 0 MBTPS2P RPL12P SHROOM2P SHROOM2P AMELY EIF1AY EIF2S3Y ZFY UBE1Y enFeLV KDM5D 1.0 12 1.1 1.2 1.3 1.4 1.5mb 100% 60% 1 0.8 0.6 0.4 0.2 0 enFeLV HSFY EEF1A1P AP1S2P HSFY enFeLV HSFY RPS4YL HSFY EEF1A1P RPS4YL HSFY 1.5 1.6 14 1.7 13 1.8 1.86mb 100% 60% 20% 1 0.8 0.6 0.4 0.2 0 RPS4Y B NEK6P HSFY CYorf15P SRY CYorf15_fusion CYorf15 10 12 1 5 2 13 7 6 8 4 3 9 11 14 Cat X chromosome 4 B: 0 1 0.1 2 0.2 0.3 3 0.4 0.5mb 100% 60% 20% 1 0.8 0.6 0.4 0.2 0 PAR SHROOM2 TETY2 UTY DDX3Y CASP6P USP9Y HSFY 4 0.6 5 6 0.7 0.8 7 0.9 0.5 8 1.0mb 100% 60% 20% 1 0.8 0.6 0.4 0.2 0 RPL23LP EIF1AY KDM5D ZFY BCORY1 CYorf15 RBMYL DYNG 8 1.1 9 1.2 10 1.3 1.4 1.0 11 1.5mb 100% 60% 20% 1 0.8 0.6 0.4 0.2 0 SRY SRY TRAPPC2P BCORY2 UBE1Y OFD1 Hnrpa1P 1.5 1.6 1.7 1.8 1.9 2.0mb 100% 60% 20% 1 0.8 0.6 0.4 0.2 0 SRY SRY SRY SRY SRY 2.0 2.1 2.2 2.3 2.4 2.5mb 100% 60% 20% 1 0.8 0.6 0.4 0.2 0 TSPY & TSPYL CUL4BY1 CUL4BY2 1 10 7 4 6 8 3 2 9 5 family Dog X chromosome 11 5 Figure 4. Triangular self dot plots of self-self DNA sequence identities within the dog and cat MSY sequences. The horizontal panel below each figure displays the average % self-self identity, based on a sliding window analysis (window size=50 nucleotides, distance between each window step=5 nucleotides). Sequences with 100 percent identity present a dot in the triangular dot plot. Horizontal and vertical lines represent direct and inverted repeats. The MSY schematic with scale is shown below the triangular plot with colored background representing the different gene regions. Gene bodies are represented within the colored blocks as directional arrows, drawn to scale. dog 100% 80% 60% 40% 20% 0% 0 0.5 1.0 1.5 2.0 2.5(mb) cat Pseudoautosomal region 100% Single copy region 80% 60% 40% Ampliconic region 20% X-transposed 0% 0 0.5 1.0 1.5 1.9(mb) 6 Figure 5. A) Gene structure and expression profile (RNASeq) of the novel coding gene, DYNG, found on the domestic dog Y chromosome. B) Self-self blast result of the transcript identifies the internal repeats within the open reading frame. Expression of dog Y chromosome novel gene (DYNG) A: 0 2 4 6 8 10 12 14 16 20 22kb 100 testis 50 0 brain 50 0 liver 50 0 lung 50 0 heart 50 0 blood 50 0 muscle 50 0 ATG TAA Gene structure 1 2 3 4 5 6 7 8 9 10 7 Figure 6. Evolution of the CYorf15 gene family in select mammals. A) Structural comparison of human CYorf15 gene family, with B) dog CYorf15 gene, cat CYorf15 fusion gene and the X chromosome gene Gamma taxilin, (TXLNG). Dashed arrows and boxes indicate regions of sequence homology between the different gene family members, based on pairwise sequence comparisons. Chromosome X Human TXLNG gene exon 1 2 3 4 5 6 7 8 9 10 A: human CYorf15A gene human CYorf15B gene 1 2 3 4 5 6 7 8 9 Dog CYorf15 gene Chromosome X exon 1 Ancestral carnivore TXLNG gene 2 3 4 5 6 7 8 9 10 cat CYorf15-fusion gene 1 2 3 4 5 6 de novo X degenerate gene fusion origination region region B: 1 2 3 4 5 6 7 cat EIF1AY gene 8 Figure 7. OFD1 gene tree estimated using maximum likelihood method under a GTR+G+I model. Numbers near each node on the tree are bootstrap values (500 pseudoreplicates: only values higher than 80 have been shown). Taxon names are denoted by (species common name)/(ENSEMBL transcript name or NCBI accession number)/(available chromosome information). The chimpanzee Y chromosome OFD1 pseudogene is denoted by the start and end locations within the published Y chromosome sequence. Chimp pseudogene Y 2158661-2174171 99 Chimp pseudogene Y 12093450-12108956 100 Chimp pseudogene Y 1875170-1888918 100 Chimp pseudogene Y 5539194-5552933 Human ENSG00000226011 pseudogene 1 Y 100 Human ENSG00000226611 pseudogene 2 Y 100 Human ENSG00000232585 pseudogene 12 Y Human ENSG00000225287 pseudogene 13 Y 100 100 Human ENSG00000235511 pseudogene 18 Y Human Human ENSG00000237302 pseudogene 11 Y human and chimpanzee 100 Human ENSG00000238088 pseudogene 7 Y OFD1 pesudogenes on Y Human ENSG00000229406 pseudogene 4 Y chromosome Human ENSG00000231988 pseudogene 3 Y Human ENSG00000231159 pseudogene 8 Y 76 85 Human ENSG00000230476 pseudogene 9 Y 100 Human ENSG00000234888 pseudogene 15 Y 100 Human ENSG00000225466 pseudogene 10 Y 100 Human ENSG00000242153 pseudogene 6 Y Human ENSG00000240438 pseudogene 5 Y 100 Chimp pseudogene Y 7184466-7201836 Human ENST00000340096 chrX 98 99 Chimp ENSPTRT00000040191 chrX 88 Gorilla ENSGGOT00000006486 chrX Old and New World 96 100 Orangutan XM 002831405 chrX monkey OFD1 genes on Gibbon XM 003261047 chrX 95 Macaque ENSMMUT00000027270 chrX X chromosome 93 Marmoset ENSCJAT00000007661 Tarsier ENSTSYT00000010650 Bushbaby ENSOGAT00000002877 99 Mouse Lemur ENSMICT00000006746 Tree Shrew ENSTBET00000004188 95 Pika ENSOPRT00000015058 Guinea Pig ENSCPOT00000015451 Mouse AJ438159 ChrX 98 Squirrel ENSSTOT00000003307 Cow NM 001192637 chrX 100 cattle OFD1 genes Cow JN193532 chrY 100 100 Dolphin ENSTTRT00000006504 100 100 Pig XM 003134936 chrX Alpaca ENSVPAT00000004619 Shrew ENSSART00000006423 Hedgehog ENSEEUT00000009611 Dog XM 537958 chrX 100 Dog JX964865 chrY dog OFD1 genes 98 Panda XM 002927445 OFD1 100 97 Cat ENSFCAT00000014879 chrX Megabat ENSPVAT00000011753 99 Microbat ENSMLUT00000012689 100 Horse XM 001917181 chrX Armadillo ENSDNOT00000002102 100 Sloth ENSCHOT00000009231 99 Hyrax ENSPCAT00000000091 85 Elephant ENSLAFT00000014407 100 100 Lesser hedgehog ENSETET00000004345 100 Opossum ENSMODT00000021978 chr7 Platypus ENSOANT00000004149 Anole Lizard XM 003218852 chr3 Chicken XM 416831 chr1 Zebra Finch ENSTGUT00000008548 chr1 0.1 9 Figure 8. Results of positive selection test for the branch leading to domestic dog OFD1Y gene. A) OFD1 gene tree, with branch lengths based on non-synonymous substitution rates. B) Bayesian posterior probabilities for protein sites under positive natural selection (branch-site models comparison). Colored bars underneath indicate different structural domains. C) Results of likelihood ratio tests for two pairs of model comparisons. dog OFD1 Y A: cow OFD1 Y dog OFD1 X pig OFD1 X cow OFD1 X panda OFD1 X cat OFD1 X horse OFD1 X elephant OFD1 X chimpanzee OFD1 X rhesus OFD1 X human OFD1 X 0.1 mouse OFD1 X C: B: Bayesian posterior probabilities of positive selection Results of likelihood ratio tests for dog OFD1Y branch 1 Models Significance 0.8 Two ratio/One ratio P<0.001 0.6 Branch-site models P<0.001 0.4 0.2 0 LisH domain Coiled coil 10 Figure 9.
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