Daniel Winston Bellott

Supplementary Information for:

Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes

Jan E Janečka, Brian W Davis, Sharmila Ghosh, Nandina Paria, Pranab J Das, Ludovic Orlando, Mikkel Schubert, Martin K Nielsen, Tom A E Stout, Wesley Brashear, Gang Li, Charles D Johnson, Richard P Metz, Al Muatasim Al Zadjali, Charles C Love, Dickson D Varner, Daniel W Bellott, William J Murphy, Bhanu P Chowdhary, Terje Raudsepp

Nature Communications 9, 2945 (2018)

Notes:

Supplementary Information: (PDF)

Includes:

• Supplementary Note 1: BAC tiling path of horse MSY
• Supplementary Note 2: Horse MSY sequencing and assembly
• Supplementary Note 3: Horse MSY sequence annotation
• Supplementary Note 4: Transcriptional profiling of horse MSY genes
• Supplementary Note 5: MSY testis transcripts in horse, donkey and mule
• Supplementary Note 6: Horizontal transfer
• Supplementary Table 1: Metrics of horse MSY sequence assembly
• Supplementary Table 2: Horse MSY repeat content
• Supplementary Table 3: Divergence times and phylogenetic topologies of eMSY genes
• Supplementary Table 4: Horse, donkey and mule testis RNAseq statistics
• Supplementary Table 5: Evolutionary strata and divergence estimates of horse gametologs
• Supplementary Table 6: Details of the Parascaris samples
• Supplementary Figure 1: BAC tiling path map for horse MSY sequencing and assembly
• Supplementary Figure 2: Validation of tiling path BACs by FISH
• Supplementary Figure 3: Estimation the size of gaps in eMSY tiling path by FISH
• Supplementary Figure 4: Intra-chromosomal sequence similarity
• Supplementary Figure 5: Expression profiles of eMSY genes by reverse transcriptase PCR
• Supplementary Figure 6: MSY gene expression in horse, donkey and mule testis
• Supplementary Figure 7: ETSTY7 FISH analysis in equids and the rhino
• Supplementary Figure 8: Validation of horizontal transfer
• Supplementary Figure 9: Time trees
• Supplementary Figure 10: Maximum likelihood trees for 41 eMSY genes
• Supplementary References

Peer Review File: (PDF)

Peer Review File

Description of Additional Supplementary Files: (PDF)

Description of Additional Supplementary Files

Data:

Supplementary Data 1: (XLS)

a) Genome-wide testis RNAseq read coverage per gene per individual; b) Genes significantly down-regulated in mules compared to both horse and donkey, and c) GO enrichment for genes with 30X greater read depth in horse and donkey compared to mule.

Supplementary Data 2: (TXT)

The eMSYv3.1 draft that is deposited in GenBank has two locations where two vector sequences were removed relative to eMSYv3.0 used for analysis in this manuscript. Therefore, in order for the coordinates in the GTF file to correspond to the correct positions, you must insert a 1,396-bp gap sequence (Ns) after position 8,048,430 and another 18,381-bp gap sequence (Ns) after position 2,506,950 into the eMSYv3.1 sequence. The total sequence length after making these two insertions should be 9,497,449 bp.

Supplementary Data 3: (TXT)

SM file of all GENECONV results.

Supplementary Data 4: (XLS)

Details for Sequence Tagged Sites (STSs) in eMSY tiling path.

Supplementary Data 5: (XLS)

Details for BACs in eMSY tiling path and sequence assembly.

Supplementary Data 6: (XLS)

Composite information on horse MSY genes and transcripts.

Supplementary Data 7: (XLS)

Information on MSY gene paralogs and orthologs for time trees.

Supplementary Data 8: (XLS)

Horse, donkey and mule Testis RNAseq read coverage per individual eMSY genes/transcripts.

Supplementary Data 9: (XLS)

Samples for MSY comparison in equids and ancient and modern horses.

Supplementary Data 10: (XLS)

Comparative data on MSY gene content in eutherian mammals (for Figure 8).

Supplementary Data 11: (XLS)

Primers for RT-PCR and to validate eMSY assembly and HT.

Supplementary Data 12: (XLS)

RNAseq GFF.

Supplementary Data 13: (XLS)

Time tree constraints. Node constraints used to estimate divergence time for Y homologs are shown for each constrained node in the format used by the mcmctree program. For each gene, the best scoring maximum likelihood tree was obtained using RAxML. The time estimates are the confidence interval from TimeTree (www.timetree.org).

Supplementary Data 14: (XLS)

MSY sequence coverage in equids and ancient and modern horses.