Daniel Winston Bellott

Supplementary Information for:

Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages

Jennifer F Hughes, Helen Skaletsky, Tatyana Pyntikova, Natalia Koutseva, Terje Raudsepp, Laura G Brown, Daniel W Bellott, Ting-Jan Cho, Shannon Dugan-Rocha, Ziad Khan, Colin Kremitzki, Catrina Fronick, Tina A Graves-Lindsay, Lucinda Fulton, Wesley C Warren, Richard K Wilson, Elaine Owens, James E Womack, William J Murphy, Donna M Muzny, Kim C Worley, Bhanu P Chowdhary, Richard A Gibbs, David C Page

Genome Research 30, 1726-1716 (2020)

Figures:

Supplemental Figures and Methods: (PDF)

Includes:

• Supplemental Figure S1: Annotated sequence of the bull MSY
• Supplemental Figure S2: Extended metaphase FISH analysis to determine relative positions of tandem arrays
• Supplemental Figure S3: Extended metaphase FISH analysis to determine range of long-arm amplicon and interphase and fiber FISH analysis to estimate gap sizes
• Supplemental Figure S4: Long-arm amplicon substructure in bull MSY
• Supplemental Figure S5: Map of bull MSY genes in relation to ampliconic repeat architecture
• Supplemental Figure S6: Copy number variability within MSY amplicons and HSFX among 234 bulls representing four different breeds
• Supplemental Figure S7: Gene expression analysis in purified male germ cells
• Supplemental Methods
• Supplemental References

Tables:

Supplemental Table S1: (XLS)

GenBank Accession Numbers for BACs in Bull MSY Assembly and Bull MSY AGP

Supplemental Table S2: (XLS)

Radiation hybrid panel mapping results

Supplemental Table S3: (XLS)

GenBank accession numbers and references for bull MSY genes

Supplemental Table S4: (XLS)

GenBank Accession Numbers for Bull HSFX-containing BACs

Files:

Supplemental File S1: (RTF)

Model bull MSY sequence, spanning 44 Mb, that incorporates estimated gaps sizes

Supplemental File S2: (RTF)

Long-range PCR products specific for each satellite class used as FISH probes

Supplemental File S3: (RTF)

HSFY/HSFX sequences used in phylogenetic analysis

Supplemental Code S1: (RTF)

Triangular Dotplot

Supplemental Code S2: (RTF)

Square Dotplot