Supplementary material for Integrative population and functional genomics of trypanotolerance in hybrid African cattle

SUPPLEMENTARY MATERIAL FOR INTEGRATIVE POPULATION AND FUNCTIONAL GENOMICS OF AFRICAN CATTLE Gillian P. McHugo Student Number: 15204236 Supplementary material for a thesis submitted to University College Dublin in fulfilment of the requirements for the degree of Doctor of Philosophy. UCD School of Agriculture and Food Science Head of School: Professor Frank J. Monahan Primary Supervisor: Professor David E. MacHugh Secondary Supervisor: Professor Stephen V. Gordon July, 2024 i Table of contents Table of contents ........................................................................................................................ i List of figures ............................................................................................................................ ii List of tables ............................................................................................................................. xi Appendix A. Supplementary material for Chapter 2 ............................................................ 1 Appendix B. Supplementary material for Chapter 3 .......................................................... 35 Appendix C. Supplementary material for Chapter 4 .......................................................... 77 Bibliography .......................................................................................................................... 117 ii List of figures Supplementary Figure A.1. Heatmap of mean identity-by-state values for the high-density SNP data set. ............................................................................................................................... 2 Supplementary Figure A.2. Tukey box plots showing the distribution of inbreeding values (F) for the high-density SNP data for each population. .................................................................... 3 Supplementary Figure A.3. Tukey box plots showing the distribution of inbreeding values (F) for the low-density SNP data for each population after inbreeding filters were applied. .......... 3 Supplementary Figure A.4. A. Principal component analysis (PCA) of the selected lowdensity SNP data set with cattle samples coloured according to population showing the first two principal components (PC1 and PC2), and B. bar chart of the proportion of variance for the top ten PCs. ....................................................................................................................................... 4 Supplementary Figure A.5. Hierarchical clustering of cattle samples using the high-density SNP data set. ............................................................................................................................... 5 Supplementary Figure A.6. Hierarchical clustering of cattle samples using the high-density SNP data set. ............................................................................................................................... 6 Supplementary Figure A.7. Hierarchical clustering of cattle samples using the low-density SNP data set. ............................................................................................................................... 7 Supplementary Figure A.8. Hierarchical clustering of cattle samples using the low-density SNP data set. ............................................................................................................................... 8 Supplementary Figure A.9. OptM results for the high-density SNP data set. ......................... 9 Supplementary Figure A.10. OptM results for the low-density SNP data set. ...................... 10 Supplementary Figure A.11. A. TreeMix phylogenetic tree for the high-density SNP data set with bootstrap values. B. a heatmap showing the standard error. ............................................ 11 Supplementary Figure A.12. A. TreeMix phylogenetic tree for the high-density SNP data set with bootstrap values and 12 migration edges. B. a heatmap showing standard error. ............ 11 Supplementary Figure A.13. A. TreeMix phylogenetic tree for the low-density SNP data set with bootstrap values. B. a heatmap showing the standard error. ............................................ 12 iii Supplementary Figure A.14. A. TreeMix phylogenetic tree for the low-density SNP data set with bootstrap values and three migration edges. B. a heatmap showing standard error. .............. 12 Supplementary Figure A.15. A. TreeMix phylogenetic tree for the high-density SNP data set with bootstrap values and 11 migration edges. B. a heatmap showing standard error. ............ 13 Supplementary Figure A.16. Local ancestry results for chromosome 23 (BTA23) for the European hybrid group calculated using MOSAIC with the high-density SNP data set. ........ 14 Supplementary Figure A.17. Local ancestry results for chromosome 23 (BTA23) for the African trypanotolerant hybrid group calculated using MOSAIC with the high-density SNP data set. ............................................................................................................................................. 15 Supplementary Figure A.18. Local ancestry results for chromosome 23 (BTA23) for the African trypanosusceptible hybrid group calculated using MOSAIC with the high-density SNP data set. ..................................................................................................................................... 16 Supplementary Figure A.19. Local ancestry results for chromosome 23 (BTA23) for the European hybrid group calculated using MOSAIC with the low-density SNP data set. ......... 17 Supplementary Figure A.20. Local ancestry results for chromosome 23 (BTA23) for the trypanotolerant African hybrid group calculated using MOSAIC with the low-density SNP data set. ............................................................................................................................................. 18 Supplementary Figure A.21. Local ancestry results for chromosome 23 (BTA23) for the trypanosusceptible African hybrid group calculated using MOSAIC with the low-density SNP data set. ..................................................................................................................................... 19 Supplementary Figure A.22. Local ancestry results for chromosome 23 (BTA23) for the European hybrid group calculated using ELAI with the high-density SNP data set. ............... 20 Supplementary Figure A.23. Local ancestry results for chromosome 23 (BTA23) for the trypanotolerant African hybrid group calculated using ELAI with the high-density SNP data set. ............................................................................................................................................. 21 Supplementary Figure A.24. Local ancestry results for chromosome 23 (BTA23) for the trypanosusceptible African hybrid group calculated using ELAI with the high-density SNP data set. ............................................................................................................................................. 22 iv Supplementary Figure A.25. Local ancestry results for chromosome 23 (BTA23) for the European hybrid group calculated using ELAI with the low-density SNP data set. ................ 23 Supplementary Figure A.26. Local ancestry results for chromosome 23 (BTA23) for the trypanotolerant African hybrid group calculated using ELAI with the low-density SNP data set. .................................................................................................................................................. 24 Supplementary Figure A.27. Local ancestry results for chromosome 23 (BTA23) for the trypanosusceptible African hybrid group calculated using ELAI with the low-density SNP data set. ............................................................................................................................................. 25 Supplementary Figure A.28. Correlation plots for the European hybrid local ancestry results (high-density SNP data set). ..................................................................................................... 26 Supplementary Figure A.29. Correlation plots for the trypanotolerant African hybrid local ancestry results (high-density SNP data set). ........................................................................... 27 Supplementary Figure A.30. Correlation plots for the trypanosusceptible African hybrid local ancestry results (high-density SNP data set). ........................................................................... 28 Supplementary Figure A.31. Correlation plots for the European hybrid local ancestry results (low-density SNP data set). ...................................................................................................... 29 Supplementary Figure A.32. Correlation plots for the trypanotolerant African hybrid local ancestry results (low-density SNP data set). ............................................................................. 30 Supplementary Figure A.33. Correlation plots for the trypanosusceptible African hybrid local ancestry results (low-density SNP data set). ............................................................................. 31 Supplementary Figure A.34. g:Profiler functional enrichment of introgressed regions in European, and trypanotolerant and trypanosusceptible African hybrid populations detected with MOSAIC and low-density SNP data. ....................................................................................... 32 Supplementary Figure A.35. g:Profiler functional enrichment of introgressed regions in European, and trypanotolerant and trypanosusceptible African hybrid populations detected with ELAI and high-density SNP data. ............................................................................................ 33 Supplementary Figure A.36. g:Profiler functional enrichment of introgressed regions in European, and trypanotolerant and trypanosusceptible African hybrid populations detected with ELAI and low-density SNP data. .............................................................................................. 34 v Supplementary Figure B.1. Boxplots showing the log2 expression intensity of the probe sets for each sample of the A. raw and B. normalised data after quality control filtering separated into NDAM and BORA populations and coloured according to tissue. ................................... 43 Supplementary Figure B.2. A. Principal component analysis (PCA) of the microarray data set with samples coloured according to days post infection (dpi) with the outer colour representing the tissue and shape indicating the population showing the first and third principal components (PC1 and PC3), and B. bar chart of proportion of variance of the top ten PCs. ....................... 44 Supplementary Figure B.3. A. Principal component analysis (PCA) of the microarray data set with samples coloured according to days post infection (dpi) with the outer colour representing the tissue and shape indicating the population showing the first and fourth principal components (PC1 and PC4), and B. bar chart of proportion of variance of the top ten PCs. ....................... 45 Supplementary Figure B.4. A. Principal component analysis (PCA) of the microarray data set with samples coloured according to tissue and shape indicating the population showing the first and fifth principal components (PC1 and PC5), and B. bar chart of proportion of variance of the top ten PCs. ......................................................................................................................... 46 Supplementary Figure B.5. Bar chart showing the numbers of significantly differentially expressed genes for the RESP contrasts. .................................................................................. 47 Supplementary Figure B.6. Bar chart showing the numbers of significantly differentially expressed genes for the DIRE contrasts. .................................................................................. 48 Supplementary Figure B.7. Bar chart showing the numbers of significantly differentially expressed genes for the NDAM contrasts. ............................................................................... 49 Supplementary Figure B.8. Bar chart showing the numbers of significantly differentially expressed genes for the BORA contrasts. ................................................................................. 50 Supplementary Figure B.9. UpSet plot showing the top 20 intersections among all 64 contrasts. ................................................................................................................................... 51 Supplementary Figure B.10. UpSet plot showing the top 20 intersections among the RESP contrasts. ................................................................................................................................... 52 Supplementary Figure B.11. UpSet plot showing the top 20 intersections among the DIRE contrasts. ................................................................................................................................... 53 vi Supplementary Figure B.12. UpSet plot showing the top 20 intersections among the NDAM contrasts. ................................................................................................................................... 54 Supplementary Figure B.13. UpSet plot showing the top 20 intersections among the BORA contrasts. ................................................................................................................................... 55 Supplementary Figure B.14. Volcano plot showing the results of the RESP contrast for the peripheral blood mononuclear cell (PBMC) samples at 14 days post infection (dpi). ............. 56 Supplementary Figure B.15. Volcano plot showing the results of the RESP contrast for the peripheral blood mononuclear cell (PBMC) samples at 25 days post infection (dpi). ............. 57 Supplementary Figure B.16. Volcano plot showing the results of the RESP contrast for the liver samples at 12 days post infection (dpi). ........................................................................... 58 Supplementary Figure B.17. Volcano plot showing the results of the RESP contrast for the liver samples at 15 days post infection (dpi). ........................................................................... 59 Supplementary Figure B.18. Volcano plot showing the results of the RESP contrast for the liver samples at 18 days post infection (dpi). ........................................................................... 60 Supplementary Figure B.19. Volcano plot showing the results of the RESP contrast for the liver samples at 21 days post infection (dpi). ........................................................................... 61 Supplementary Figure B.20. Volcano plot showing the results of the RESP contrast for the liver samples at 26 days post infection (dpi). ........................................................................... 62 Supplementary Figure B.21. Volcano plot showing the results of the RESP contrast for the liver samples at 29 days post infection (dpi). ........................................................................... 63 Supplementary Figure B.22. Volcano plot showing the results of the RESP contrast for the liver samples at 32 days post infection (dpi). ........................................................................... 64 Supplementary Figure B.23. Volcano plot showing the results of the RESP contrast for the liver samples at 35 days post infection (dpi). ........................................................................... 65 Supplementary Figure B.24. Volcano plot showing the results of the RESP contrast for the lymph node samples at 21 days post infection (dpi). ............................................................... 66 vii Supplementary Figure B.25. Volcano plot showing the results of the RESP contrast for the lymph node samples at 35 days post infection (dpi). ............................................................... 67 Supplementary Figure B.26. Volcano plot showing the results of the RESP contrast for the spleen samples at 21 days post infection (dpi). ........................................................................ 68 Supplementary Figure B.27. Volcano plot showing the results of the RESP contrast for the spleen samples at 35 days post infection (dpi). ........................................................................ 69 Supplementary Figure B.28. g:Profiler functional enrichment of significantly differentially expressed genes (DEGs) in the peripheral blood mononuclear cell (PBMC) sample RESP contrasts. ................................................................................................................................... 70 Supplementary Figure B.29. g:Profiler functional enrichment of significantly differentially expressed genes (DEGs) in the liver sample RESP contrasts. .................................................. 71 Supplementary Figure B.30. g:Profiler functional enrichment of significantly differentially expressed genes (DEGs) in the lymph node sample RESP contrasts. Each circle represents a significantly enriched GO term with the size indicating the ratio of the intersection between the term and the DEGs. .................................................................................................................. 72 Supplementary Figure B.31. g:Profiler functional enrichment of significantly differentially expressed genes (DEGs) in the spleen sample RESP contrasts. ............................................... 73 Supplementary Figure B.32. EnrichmentMap network of significantly enriched GO terms identified from g:Profiler functional enrichment of significant differentially expressed genes (DEGs) for the DIRE contrasts. ................................................................................................ 74 Supplementary Figure B.33. EnrichmentMap network of significantly enriched GO terms identified from g:Profiler functional enrichment of significant differentially expressed genes (DEGs) for the NDAM contrasts. ............................................................................................. 75 Supplementary Figure B.34. EnrichmentMap network of significantly enriched GO terms identified from g:Profiler functional enrichment of significant differentially expressed genes (DEGs) for the BORA contrasts. .............................................................................................. 76 Supplementary Figure C.1. Heatmap of mean identity by state values for SNP data in European, African, and Asian cattle populations. ..................................................................... 87 viii Supplementary Figure C.2. Tukey box plots showing the distribution of inbreeding values (F) for SNP data for each population of European, African, and Asian cattle. .............................. 88 Supplementary Figure C.3. A. Principal component analysis (PCA) of SNP data for cattle coloured according to population showing the first two principal components and B. bar chart of proportion of variance of the top ten principal components. ............................................... 89 Supplementary Figure C.4. A. Principal component analysis (PCA) of the high-density SNP data for the cattle samples from Chapter 2 coloured according to population showing the first two principal components and B. bar chart of proportion of variance of the top ten principal components. .............................................................................................................................. 90 Supplementary Figure C.5. A. Principal component analysis (PCA) of the low-density SNP data for the cattle samples from Chapter 2 coloured according to population showing the first two principal components and B. bar chart of proportion of variance of the top ten principal components. .............................................................................................................................. 91 Supplementary Figure C.6. Hierarchical clustering of the SNP data for European, African, and Asian cattle populations. .................................................................................................... 92 Supplementary Figure C.7. Hierarchical clustering of the SNP data for European, African, and Asian cattle populations. .................................................................................................... 93 Supplementary Figure C.8. Hierarchical clustering of the high-density SNP data from Chapter 2 for European, African, and Asian cattle populations. ............................................. 94 Supplementary Figure C.9. Hierarchical clustering of the low-density SNP data from Chapter 2 for European, African, and Asian cattle populations. ............................................................ 95 Supplementary Figure C.10. g:Profiler functional enrichment of introgressed regions in the African B. taurus cattle populations with gene expression data available according to local ancestry analysis of SNP data. .................................................................................................. 96 Supplementary Figure C.11. g:Profiler functional enrichment of introgressed regions in the trypanotolerant African hybrid cattle populations with gene expression data available according to local ancestry analysis of SNP data. ..................................................................................... 97 3 Supplementary Figure A.2. Tukey box plots showing the distribution of inbreeding values (F) for the high-density SNP data for each population. Outliers are indicated with a black outline. Supplementary Figure A.3. Tukey box plots showing the distribution of inbreeding values (F) for the low-density SNP data for each population after inbreeding filters were applied. Outliers are indicated with a black outline. 4 Supplementary Figure A.4. A. Principal component analysis (PCA) of the selected lowdensity SNP data set with cattle samples coloured according to population showing the first two principal components (PC1 and PC2), and B. bar chart of the proportion of variance for the top ten PCs. 5 Supplementary Figure A.5. Hierarchical clustering of cattle samples using the high-density SNP data set. Results are shown for a range of assumed values for the number of ancestral populations (K = 2‒9). 6 Supplementary Figure A.6. Hierarchical clustering of cattle samples using the high-density SNP data set. Results are shown for a range of assumed values for the number of ancestral populations (K = 10‒17). 7 Supplementary Figure A.7. Hierarchical clustering of cattle samples using the low-density SNP data set. Results are shown for a range of assumed values for the number of ancestral populations (K = 2‒9). 8 Supplementary Figure A.8. Hierarchical clustering of cattle samples using the low-density SNP data set. Results are shown for a range of assumed values for the number of ancestral populations (K = 10‒17). 9 Supplementary Figure A.9. OptM results for the high-density SNP data set. A. the mean and standard deviation (SD) across 10 iterations for the composite likelihood (L(m)). B. the proportion of variance explained showing the 99.8% threshold (horizontal dotted line) recommended by Pickrell and Pritchard (2012). C. the second-order rate of change (Δm) across migration edges (m). 10 Supplementary Figure A.10. OptM results for the low-density SNP data set. A. the mean and standard deviation (SD) across 10 iterations for the composite likelihood (L(m)). B. the proportion of variance explained showing the 99.8% threshold (horizontal dotted line) recommended by Pickrell and Pritchard (2012). C. the second-order rate of change (Δm) across migration edges (m). 11 Supplementary Figure A.11. A. TreeMix phylogenetic tree for the high-density SNP data set with bootstrap values. B. a heatmap showing the standard error. Supplementary Figure A.12. A. TreeMix phylogenetic tree for the high-density SNP data set with bootstrap values and 12 migration edges. B. a heatmap showing standard error. 12 Supplementary Figure A.13. A. TreeMix phylogenetic tree for the low-density SNP data set with bootstrap values. B. a heatmap showing the standard error. Supplementary Figure A.14. A. TreeMix phylogenetic tree for the low-density SNP data set with bootstrap values and three migration edges. B. a heatmap showing standard error. 19 Supplementary Figure A.21. Local ancestry results for chromosome 23 (BTA23) for the trypanosusceptible African hybrid group calculated using MOSAIC with the low-density SNP data set. Each vertical line on the chromosome plot represents a SNP and is coloured according to the ancestry results. 20 Supplementary Figure A.22. Local ancestry results for chromosome 23 (BTA23) for the European hybrid group calculated using ELAI with the high-density SNP data set. Each vertical line on the chromosome plot represents a SNP and is coloured according to the ancestry results. 21 Supplementary Figure A.23. Local ancestry results for chromosome 23 (BTA23) for the trypanotolerant African hybrid group calculated using ELAI with the high-density SNP data set. Each vertical line on the chromosome plot represents a SNP and is coloured according to the ancestry results. 22 Supplementary Figure A.24. Local ancestry results for chromosome 23 (BTA23) for the trypanosusceptible African hybrid group calculated using ELAI with the high-density SNP data set. Each vertical line on the chromosome plot represents a SNP and is coloured according to the ancestry results. 23 Supplementary Figure A.25. Local ancestry results for chromosome 23 (BTA23) for the European hybrid group calculated using ELAI with the low-density SNP data set. Each vertical line on the chromosome plot represents a SNP and is coloured according to the ancestry results. 24 Supplementary Figure A.26. Local ancestry results for chromosome 23 (BTA23) for the trypanotolerant African hybrid group calculated using ELAI with the low-density SNP data set. Each vertical line on the chromosome plot represents a SNP and is coloured according to the ancestry results. 25 Supplementary Figure A.27. Local ancestry results for chromosome 23 (BTA23) for the trypanosusceptible African hybrid group calculated using ELAI with the low-density SNP data set. Each vertical line on the chromosome plot represents a SNP and is coloured according to the ancestry results. 26 Supplementary Figure A.28. Correlation plots for the European hybrid local ancestry results (high-density SNP data set). Each dot represents a SNP coloured according to chromosome. The positions on the xand y-axes indicate the weighted mean ancestry proportions for that SNP according to MOSAIC and ELAI, respectively. A. European B. taurus, B. African B. taurus, and C. B. indicus ancestry components. The lines represent linear models for each chromosome, coloured accordingly. 27 Supplementary Figure A.29. Correlation plots for the trypanotolerant African hybrid local ancestry results (high-density SNP data set). Each dot represents a SNP coloured according to chromosome. The positions on the xand y-axes indicate the weighted mean ancestry proportions for that SNP according to MOSAIC and ELAI, respectively. A. European B. taurus, B. African B. taurus, and C. B. indicus ancestry components. The lines represent linear models for each chromosome, coloured accordingly. 28 Supplementary Figure A.30. Correlation plots for the trypanosusceptible African hybrid local ancestry results (high-density SNP data set). Each dot represents a SNP coloured according to chromosome. The positions on the xand y-axes indicate the weighted mean ancestry proportions for that SNP according to MOSAIC and ELAI, respectively. A. European B. taurus, B. African B. taurus, and C. B. indicus ancestry components. The lines represent linear models for each chromosome, coloured accordingly. 35 Appendix B. Supplementary material for Chapter 3 Supplementary Table B.1. Contrast ID, contrast type, tissue, days post infection (dpi), and formula for each of the 64 contrasts. Contrast ID Contrast Tissue dpi Contrast formula RESP BL 14 RESP BL 14 (NDAM BL 14 - NDAM BL 00) - (BORA BL 14 - BORA BL 00) RESP BL 25 RESP BL 25 (NDAM BL 25 - NDAM BL 00) - (BORA BL 25 - BORA BL 00) RESP BL 34 RESP BL 34 (NDAM BL 34 - NDAM BL 00) - (BORA BL 34 - BORA BL 00) RESP LI 12 RESP LI 12 (NDAM LI 12 - NDAM LI 00) - (BORA LI 12 - BORA LI 00) RESP LI 15 RESP LI 15 (NDAM LI 15 - NDAM LI 00) - (BORA LI 15 - BORA LI 00) RESP LI 18 RESP LI 18 (NDAM LI 18 - NDAM LI 00) - (BORA LI 18 - BORA LI 00) RESP LI 21 RESP LI 21 (NDAM LI 21 - NDAM LI 00) - (BORA LI 21 - BORA LI 00) RESP LI 26 RESP LI 26 (NDAM LI 26 - NDAM LI 00) - (BORA LI 26 - BORA LI 00) RESP LI 29 RESP LI 29 (NDAM LI 29 - NDAM LI 00) - (BORA LI 29 - BORA LI 00) RESP LI 32 RESP LI 32 (NDAM LI 32 - NDAM LI 00) - (BORA LI 32 - BORA LI 00) RESP LI 35 RESP LI 35 (NDAM LI 35 - NDAM LI 00) - (BORA LI 35 - BORA LI 00) RESP LN 21 RESP LN 21 (NDAM LN 21 - NDAM LN 00) - (BORA LN 21 - BORA LN 00) RESP LN 35 RESP LN 35 (NDAM LN 35 - NDAM LN 00) - (BORA LN 35 - BORA LN 00) RESP SP 21 RESP SP 21 (NDAM SP 21 - NDAM SP 00) - (BORA SP 21 - BORA SP 00) RESP SP 35 RESP SP 35 (NDAM SP 35 - NDAM SP 00) - (BORA SP 35 - BORA SP 00) DIRE BL 00 DIRE BL 0 NDAM BL 00 - BORA BL 00 DIRE BL 14 DIRE BL 14 NDAM BL 14 - BORA BL 14 DIRE BL 25 DIRE BL 25 NDAM BL 25 - BORA BL 25 DIRE BL 34 DIRE BL 34 NDAM BL 34 - BORA BL 34 DIRE LI 00 DIRE LI 0 NDAM LI 00 - BORA LI 00 DIRE LI 12 DIRE LI 12 NDAM LI 12 - BORA LI 12 DIRE LI 15 DIRE LI 15 NDAM LI 15 - BORA LI 15 DIRE LI 18 DIRE LI 18 NDAM LI 18 - BORA LI 18 DIRE LI 21 DIRE LI 21 NDAM LI 21 - BORA LI 21 DIRE LI 26 DIRE LI 26 NDAM LI 26 - BORA LI 26 DIRE LI 29 DIRE LI 29 NDAM LI 29 - BORA LI 29 DIRE LI 32 DIRE LI 32 NDAM LI 32 - BORA LI 32 DIRE LI 35 DIRE LI 35 NDAM LI 35 - BORA LI 35 36 Supplementary Table B.1 continued. Contrast ID Contrast Tissue dpi Contrast formula DIRE LN 00 DIRE LN 0 NDAM LN 00 - BORA LN 00 DIRE LN 21 DIRE LN 21 NDAM LN 21 - BORA LN 21 DIRE LN 35 DIRE LN 35 NDAM LN 35 - BORA LN 35 DIRE SP 21 DIRE SP 21 NDAM SP 21 - BORA SP 21 DIRE SP 35 DIRE SP 35 NDAM SP 35 - BORA SP 35 NDAM BL 14 NDAM BL 14 NDAM BL 14 - NDAM BL 00 NDAM BL 25 NDAM BL 25 NDAM BL 25 - NDAM BL 00 NDAM BL 34 NDAM BL 34 NDAM BL 34 - NDAM BL 00 NDAM LI 12 NDAM LI 12 NDAM LI 12 - NDAM LI 00 NDAM LI 15 NDAM LI 15 NDAM LI 15 - NDAM LI 00 NDAM LI 18 NDAM LI 18 NDAM LI 18 - NDAM LI 00 NDAM LI 21 NDAM LI 21 NDAM LI 21 - NDAM LI 00 NDAM LI 26 NDAM LI 26 NDAM LI 26 - NDAM LI 00 NDAM LI 29 NDAM LI 29 NDAM LI 29 - NDAM LI 00 NDAM LI 32 NDAM LI 32 NDAM LI 32 - NDAM LI 00 NDAM LI 35 NDAM LI 35 NDAM LI 35 - NDAM LI 00 NDAM LN 21 NDAM LN 21 NDAM LN 21 - NDAM LN 00 NDAM LN 35 NDAM LN 35 NDAM LN 35 - NDAM LN 00 NDAM SP 21 NDAM SP 21 NDAM SP 21 - NDAM SP 00 NDAM SP 35 NDAM SP 35 NDAM SP 35 - NDAM SP 00 BORA BL 14 BORA BL 14 BORA BL 14 - BORA BL 00 BORA BL 25 BORA BL 25 BORA BL 25 - BORA BL 00 BORA BL 34 BORA BL 34 BORA BL 34 - BORA BL 00 BORA LI 12 BORA LI 12 BORA LI 12 - BORA LI 00 BORA LI 15 BORA LI 15 BORA LI 15 - BORA LI 00 BORA LI 18 BORA LI 18 BORA LI 18 - BORA LI 00 BORA LI 21 BORA LI 21 BORA LI 21 - BORA LI 00 BORA LI 26 BORA LI 26 BORA LI 26 - BORA LI 00 BORA LI 29 BORA LI 29 BORA LI 29 - BORA LI 00 BORA LI 32 BORA LI 32 BORA LI 32 - BORA LI 00 BORA LI 35 BORA LI 35 BORA LI 35 - BORA LI 00 BORA LN 21 BORA LN 21 BORA LN 21 - BORA LN 00 BORA LN 35 BORA LN 35 BORA LN 35 - BORA LN 00 BORA SP 21 BORA SP 21 BORA SP 21 - BORA SP 00 BORA SP 35 BORA SP 35 BORA SP 35 - BORA SP 00 37 Supplementary Table B.2. Tissue, days post infection (dpi), and the top 10 most significant genes with increased and decreased expression with valid gene symbols for the direct contrasts. Tissue dpi Genes with increased expression BL 0 TTLL1, PGA5, USP42, OLFM4, GPR132, MED27, WLS, SH3GLB2, PMF1, EIF2B2 BL 14 TTLL1, USP42, GPR132, UPK3B, TM9SF5, WLS, KLC1, MRPS6, TIPIN, BLK BL 25 TTLL1, TM9SF5, TBXA2R, ADRA2A, RUM1, DHPS, ARL6IP4, ZNF318, KLHDC8A, APOL3 BL 34 TTLL1, SPDEF, KLHDC8A, TM9SF5, DHPS, KCNN4, RUM1, ARL6IP4, CDK20, FCRL3 LI 0 DOCK11, MAGIX, AGA, MEP1B, TMLHE, TCIRG1, SETD9, IRAK4, TRIM13, GSTM1 LI 12 DOCK11, AGA, MAGIX, CYP4F47, SETD9, IRAK4, IL18BP, TCIRG1, CHIA, TMEM41A LI 15 MAGIX, DOCK11, ALDH7A1, AGA, TMLHE, CYP4A59, CYP4A11, INTS8, PON3, CYP4F47 LI 18 DOCK11, MAGIX, AGA, EPCAM, PDLIM4, ARL4D, ADTRP, TTLL1, SETD9, LTF LI 21 AGA, CYP2D43, CYP2D14, COL12A1, EPPK1, DOCK11, MAGIX, TRIM13, IRAK4, ALDH7A1 LI 26 UGT2B10, DOCK11, TSPAN6, CCDC191, MAGIX, RTN2, SETD9, AGA, MMAA, DBI LI 29 UGT2B10, DOCK11, CYP4A59, CYP4A11, AGA, DPYS, ATPAF1, QPRT, CYP4F47, MAGIX LI 32 DOCK11, AGA, ADTRP, LTF, MAGIX, UGT2B10, APLNR, bta-mir-30f, GSTM1, EPCAM LI 35 DOCK11, AGA, CYP2D43, CYP2D14, CYP4F47, CHIA, TSPAN6, PTPRM, RETSAT, CTDSP2 LN 0 CLDN11, TTLL1, BRB, CYP4B1, STAB1, PROS1, HEPH, CTSK, C1QTNF5, MT3 LN 21 TTLL1, SLC38A11, SUCLG1, SNORA73, EIF2B2, TXNDC11, MZB1, SLC25A26, PDIA5, ORC1 LN 35 TTLL1, SNORA73, LXN, MYB, DEFB4A, SLC38A11, CHD1L, TRNAU1AP, bta-mir-221, ORC1 SP 0 TTLL1, F2RL2, FABP3, RGS5, KIF3A, BMP2, TNFAIP6, NDN, SYT1, ITGA8 SP 21 TTLL1, ECRG4, TRMT10B, PTGDS, STMN2, KCNA3, CD38, CD2, CFI, MSN SP 35 TTLL1, SNCA, LXN, RNASE4, MSN, ECRG4, STMN2, MAB21L1, TIPIN, TM9SF5 Tissue dpi Genes with decreased expression BL 0 PHF12, VCAN, S100A7, PPP1R15A, CXCL5, ADAMDEC1, PLAU, CLECL1P, SAP18, CRYGS BL 14 PHF12, GABARAPL2, OASL, MORN4, CRYGS, UCHL3, SEL1L3, MED16, SAP18, ERAP1 BL 25 VCAN, PFKFB4, PROCR, MORN4, JAM3, SELENOP, PHF12, DHRS7, SLC25A17, MTURN BL 34 PROCR, MTURN, SLC25A17, MORN4, DHRS7, SMOX, TUBB1, ISCU, MFSD2B, ITGA2 LI 0 RFTN1, CYP4F2, TMEM45B, TPD52L1, MANEA, SPTSSB, PSMC5, PLBD1, SAP18, MED16 38 Supplementary Table B.2 continued. Tissue dpi Genes with decreased expression LI 12 SPTSSB, RFTN1, CYP4F2, MANEA, DNAJC22, TPD52L1, TMEM45B, TMLHE, BAMBI, TBC1D7 LI 15 SPTSSB, CYP4F2, RFTN1, PLBD1, TMEM45B, RAC1, TPD52L1, MANEA, ERAP1, GPX1 LI 18 CYP4F2, BAMBI, TPD52L1, RFTN1, SPTSSB, DNAJC22, PTER, MANEA, DNASE1L3, DCXR LI 21 TPD52L1, PTER, KBTBD6, CYP4F2, MANEA, CRCP, RCBTB2, SLC5A6, TMLHE, JSP.1 LI 26 RFTN1, CYP4F2, ARSB, COX10, MANEA, ARPC1B, PAMR1, TMLHE, LCP1, NAGK LI 29 JCHAIN, WWOX, PEG3, RFTN1, DNMT1, TPD52L1, PTER, ARSB, UBR7, OTULINL LI 32 RFTN1, TPD52L1, CYP4F2, MANEA, PTER, SLC38A11, PIGR, JCHAIN, VPS41, HTATSF1 LI 35 RFTN1, TPD52L1, PARP11, TMLHE, MANEA, AVPR1A, CRCP, TBC1D7, C29H11orf86, JCHAIN LN 0 SELE, CCL20, SEL1L3, EFHD1, ATP4B, SPP1, CXCL13, ALB, PLOD2, MME LN 21 FOXO1, SEL1L3, COL16A1, ADAMDEC1, DDT, MOSMO, ATP4B, SELE, EFHD1, LTBP2 LN 35 LTBP2, DNER, IGFBP3, FOXO1, EFEMP1, RARRES2, DNASE1L3, DEFB10, VPS41, TBC1D7 SP 0 CFH, CYP4B1, EFHD1, LTBP2, EXOC7, FAM83D, MCPH1, TM4SF18, DDT, HCLS1 SP 21 CFH, FOXO1, DDT, SCG2, THBS1, BCAT2, PTER, RARRES2, MORN4, C6 SP 35 NELL2, CFH, RARRES2, SCG2, GDPD2, PLAU, SAP18, JSP.1, CD14, FOXO1 39 Supplementary Table B.3. Tissue, days post infection (dpi), and the top 10 most significant genes with increased and decreased expression with valid gene symbols for the N’Dama contrasts. Tissue dpi Genes with increased expression BL 14 SRSF11, HNRNPH1, UPK3B, CEP95, LAP3, NUPR1, PRPF40A, CCAR1, SNORD24, ABCC10 BL 25 NEB, ADORA2B, CMTM3, CPLANE1, CERS4, UPK3B, RHBDF2, ADRA2A, SRSF11, KCNN4 BL 34 NEB, CERS4, ADRA2A, UPK3B, FCRL3, KCNN4, WDR73, CMTM3, RHBDF2, LCAT LI 12 CXCL11, UBD, TMSB10, WARS1, TAP1, PSMB9, BCL2A1, IRF1, BIRC3, PSMB10 LI 15 TMSB10, ADA, CYRIB, CD48, HCK, SPI1, PTPRC, JCHAIN, SLA, TMSB4X LI 18 TMSB10, CYRIB, PTPRC, SPI1, CD48, TMSB4X, ADA, HCK, ARHGDIB, CD53 LI 21 TMSB10, CYRIB, PTPRC, TMSB4X, ARHGDIB, SPI1, CD48, CD53, RAC2, ADA LI 26 TMSB10, TMSB4X, CYRIB, PTPRC, SPI1, CD53, CD48, CCDC191, CD55, SLA LI 29 TMSB10, TMSB4X, PTPRC, CYRIB, SPI1, CD53, CD55, CD48, TMSB4, HTRA4 LI 32 TMSB10, TMSB4X, CYRIB, PTPRC, CD53, SPI1, CD55, CD48, RAP1B, TMSB4 LI 35 TMSB10, TMSB4X, PTPRC, CYRIB, CD53, SPI1, ARHGDIB, SLA, CD48, RAP1B LN 21 ORC1, MZB1, CDC6, SKA3, UBE2S, SPAG5, SLC25A5, SPDL1, NDUFA4, CDC20 LN 35 SPAG5, ORC1, MKI67, TOP2A, TPX2, BUB1, AURKB, CDC6, CENPT, ASPM SP 21 IRF4, CDC6, SPAG5, KIF2C, ESPL1, MKI67, CENPT, H2AC18, H2AC19, KRTCAP2 SP 35 MKI67, ORC1, AURKB, SPAG5, IRF4, ESPL1, BUB1, CDC6, ASPM, UBE2C Tissue dpi Genes with decreased expression BL 14 VAT1L, OLFM4, JAML, PGA5, PMF1, GZMB, ALOX15, FCER1A, PTGDR2, RAVER1, ICAM3 BL 25 JAML, CSF3R, OLFM4, RAVER1, ICAM3, VAT1L, PIP5K1B, GZMB, NFAM1, PTGDR2 BL 34 JAML, PIP5K1B, VAT1L, RAVER1, ICAM3, OLFM4, GZMB, PTGDR2, CSF3R, FCER1A LI 12 MAPK6, SLC25A15, NUDT12, EEF1A1, CRYZ, GLCE, EPB41L5, PHKB, MYO1B, GNA14 LI 15 SIGLEC1, IGFBP6, GSTA2, CDK3, TEN1, ACSM5, GALT, MAPK6, SLC51B, JOSD2 LI 18 SIGLEC1, GCAT, AS3MT, PPOX, SLC51B, PMVK, IGFBP6, EPB41L5, NTN5, RORC LI 21 RORC, GCAT, FAM83H, SIGLEC1, C15H11orf52, DVL1, CARD19, PTPRF, MOSPD1, NAA30 LI 26 SIGLEC1, GCAT, FOXA2, GUCD1, HPN, HOMER2, PTPRF, HSD17B14, THOP1, GPLD1 LI 29 SIGLEC1, GCAT, IYD, SHPK, NMRAL1, GRHPR, PPP2R2B, KHK, ACY1, FARP1 40 Supplementary Table B.3 continued. Tissue dpi Genes with decreased expression LI 32 GCAT, SIGLEC1, ACY1, FOXA2, MGC152281, PDK2, FAAH, GRHPR, GUCD1, SLC27A4 LI 35 SIGLEC1, NIT1, AS3MT, EPB41L5, GCAT, PDZK1, PLPP6, GSR, GRHPR, C15H11orf52 LN 21 CLDN11, ELOVL7, SNTB2, SMCHD1, BRB, SMAD5, CFLAR, NR2F1, ADGRF5, HEPH LN 35 CLDN11, BRB, ELOVL7, SMYD2, HEPH, NR2F1, TJP1, SCARA5, MEIS2, ADGRF5 SP 21 SYT1, GDPD2, NTRK2, NTN4, IGFBP6, DNASE1L3, NDN, FGF2, PENK, F2RL2 SP 35 SYT1, GDPD2, IGFBP6, NTRK2, NTN4, NDN, FBLN5, PGM5, PENK, PYGM 41 Supplementary Table B.4. Tissue, days post infection (dpi), and the top 10 most significant genes with increased and decreased expression with valid gene symbols for the Boran contrasts. Tissue dpi Genes with increased expression BL 14 GZMB, LAP3, SLAMF8, IRF1, FCRL3, NUB1, NLRC5, OASL, WARS1, GBP5 BL 25 CPLANE1, CSTB, NEB, ADORA2B, CMTM3, SRSF11, PIK3C2B, SEC11A, INPP5B, UPK3B BL 34 NEB, ADORA2B, CPLANE1, CMTM3, INPP5B, SLC25A12, CERS4, PIK3C2B, ADRA2A, PYGO1 LI 12 TAP1, UBD, IRF1, PSMB9, TMSB10, CXCL11, B2M, PSMB10, CXCL10, NLRC5 LI 15 TMSB10, CYRIB, ADA, CD48, SPI1, HCK, PTPRC, ARHGDIB, GNG2, CORO1A LI 18 TMSB10, CYRIB, SPI1, PTPRC, CD48, ADA, ARHGDIB, HCK, PLTP, CD53 LI 21 TMSB10, CYRIB, CD53, SPI1, PTPRC, TMSB4X, ARHGDIB, ADA, CD48, ACTR3 LI 26 TMSB10, CYRIB, PTPRC, SPI1, CD53, TMSB4X, PLTP, CDH5, HCK, ARHGDIB LI 29 CYRIB, TMSB10, SPI1, PTPRC, CD53, PLTP, TMSB4X, RAP1B, ARHGDIB, DOCK2 LI 32 TMSB10, CYRIB, PTPRC, SPI1, CD53, TMSB4X, PLTP, CD55, HCK, RAP1B LI 35 TMSB10, CYRIB, CD53, PTPRC, SPI1, TMSB4X, PLTP, RAP1B, CD48, VAV1 LN 21 MEA1, ATP5ME, MRPL52, POLR2L, RNASEH2C, SLC25A5, MZB1, COX6B1, TXNDC5, FAM32A LN 35 MEA1, NDUFA4, COX6B1, KIFC1, SPAG5, ATP5ME, AQP3, MKI67, TXNDC5, TOP2A SP 21 CDC6, IRF4, KRTCAP2, RNASEH2C, CSTB, MYDGF, BUB1, TUBG1, CENPT, ESPL1 SP 35 CSTB, LAP, IRF4, CD14, CTLA4, CDC6, MYDGF, TUBG1, ACSL5, NOLC1 Tissue dpi Genes with decreased expression BL 14 PIP5K1B, ADAMDEC1, IFT27, CA5B, S100A7, FCER1A, RGCC, JAML, FOSB, NR4A2 BL 25 JAML, PIP5K1B, CXCR1, CXCR2, IFT27, GZMB, ALOX15, CSF3R, VAT1L, PTGDR2 BL 34 JAML, IFT27, PIP5K1B, CA5B, S100A7, PARP8, CSF3R, CXCL8, NFAM1, PTGDR2 LI 12 RPS2, SNORA64, CA5A, TRIM6, PAF1, FGA, HSD17B14, 7SK, SLC7A9, HEXIM2 LI 15 COLEC11, TCEA3, EPB41L5, SIGLEC1, IMMP2L, PYURF, AS3MT, AUH, APOM, AGMAT LI 18 SIGLEC1, PTPRF, PMVK, TEAD2, APLNR, TCEA3, DHRS11, EPB41L5, ANKS4B, CBS LI 21 PHACTR4, APLNR, TCEA3, RORC, GCGR, GCAT, SIGLEC1, FAM149A, ST7L, CRYBG2 LI 26 PMVK, SIGLEC1, GCAT, CBS, HSD17B14, PTPRF, ACY1, HAGH, CIDEA, PAFAH2 LI 29 GCAT, GRHPR, FAAH, EPB41L5, DPYS, PMVK, CBS, NIPSNAP1, TCEA3, ACY1 42 Supplementary Table B.4 continued. Tissue dpi Genes with decreased expression LI 32 GCAT, PMVK, CES1, SIGLEC1, KCTD21, ACY1, FAAH, EBP, FOXA2, MMAB LI 35 GCAT, GCGR, EBP, PMVK, ACY1, GRHPR, PTPRF, FAH, NTN5, HPN LN 21 MSANTD2, MFSD4A, SMCHD1, NPNT, SHISA3, ZNF318, MDFIC, BPTF, KMT2C, TSC1 LN 35 MSANTD2, LUM, CLDN11, SMCHD1, MFSD4A, KMT2C, MINDY2, COL6A3, NR2F1, AGO3 SP 21 SYT1, NTN4, DNASE1L3, GDPD2, IGFBP6, NTRK2, PGM5, NXPH1, FBLN5, GPR34 SP 35 NTRK2, IGFBP6, GDPD2, SYT1, NTN4, FBLN5, PGM5, PYGM, DNASE1L3, TPM2 43 Supplementary Figure B.1. Boxplots showing the log2 expression intensity of the probe sets for each sample of the A. raw and B. normalised data after quality control filtering separated into NDAM and BORA populations and coloured according to tissue. The position along the horizontal axis indicates the days post infection. Outlier probe sets are shown as grey dots. 44 Supplementary Figure B.2. A. Principal component analysis (PCA) of the microarray data set with samples coloured according to days post infection (dpi) with the outer colour representing the tissue and shape indicating the population showing the first and third principal components (PC1 and PC3), and B. bar chart of proportion of variance of the top ten PCs. 51 Supplementary Figure B.9. UpSet plot showing the top 20 intersections among all 64 contrasts. The horizontal bars indicate the total number of significant differentially expressed genes (DEGs) for each contrast while the vertical bars indicate the number of significant DEGs in common between the contrasts annotated with black dots connected by lines in the intersection matrix. The background colour of the stripes in the intersection matrix and horizontal bars represents the tissue. The colour of the bars represents the contrast type with black bars indicating an overlap between different contrast types. The outline colour of the bars also represents the tissue with no outline representing an overlap between different tissues. 52 Supplementary Figure B.10. UpSet plot showing the top 20 intersections among the RESP contrasts. The horizontal bars indicate the total number of significant differentially expressed genes (DEGs) for each contrast while the vertical bars indicate the number of significant DEGs in common between the contrasts annotated with black dots connected by lines in the intersection matrix. The background colour of the stripes in the intersection matrix and horizontal bars represents the tissue. The colour of the bars represents the days post infection (dpi) with black bars indicating an overlap between different timepoints. The outline colour of the bars also represents the tissue with no outline representing an overlap between different tissues. 53 Supplementary Figure B.11. UpSet plot showing the top 20 intersections among the DIRE contrasts. The horizontal bars indicate the total number of significant differentially expressed genes (DEGs) for each contrast while the vertical bars indicate the number of significant DEGs in common between the contrasts annotated with black dots connected by lines in the intersection matrix. The background colour of the stripes in the intersection matrix and horizontal bars represents the tissue. The colour of the bars represents the days post infection (dpi) with black bars indicating an overlap between different timepoints. The outline colour of the bars also represents the tissue with no outline representing an overlap between different tissues. 54 Supplementary Figure B.12. UpSet plot showing the top 20 intersections among the NDAM contrasts. The horizontal bars indicate the total number of significant differentially expressed genes (DEGs) for each contrast while the vertical bars indicate the number of significant DEGs in common between the contrasts annotated with black dots connected by lines in the intersection matrix. The background colour of the stripes in the intersection matrix and horizontal bars represents the tissue. The colour of the bars represents the days post infection (dpi) with black bars indicating an overlap between different timepoints. The outline colour of the bars also represents the tissue with no outline representing an overlap between different tissues. 55 Supplementary Figure B.13. UpSet plot showing the top 20 intersections among the BORA contrasts. The horizontal bars indicate the total number of significant differentially expressed genes (DEGs) for each contrast while the vertical bars indicate the number of significant DEGs in common between the contrasts annotated with black dots connected by lines in the intersection matrix. The background colour of the stripes in the intersection matrix and horizontal bars represents the tissue. The colour of the bars represents the days post infection (dpi) with black bars indicating an overlap between different timepoints. The outline colour of the bars also represents the tissue with no outline representing an overlap between different tissues. 56 Supplementary Figure B.14. Volcano plot showing the results of the RESP contrast for the peripheral blood mononuclear cell (PBMC) samples at 14 days post infection (dpi). Each data point represents a gene with the position on the xand y-axes indicating the log2 fold change and -log10Padj., respectively. Genes above the horizontal dashed line are significantly differentially expressed with the colours representing the change in expression. The top 10 most significant genes for increased and decreased expression with gene symbols are labelled. 57 Supplementary Figure B.15. Volcano plot showing the results of the RESP contrast for the peripheral blood mononuclear cell (PBMC) samples at 25 days post infection (dpi). Each data point represents a gene with the position on the xand y-axes indicating the log2 fold change and -log10Padj., respectively. Genes above the horizontal dashed line are significantly differentially expressed with the colours representing the change in expression. The top 10 most significant genes for increased and decreased expression with gene symbols are labelled. 58 Supplementary Figure B.16. Volcano plot showing the results of the RESP contrast for the liver samples at 12 days post infection (dpi). Each data point represents a gene with the position on the xand y-axes indicating the log2 fold change and -log10Padj., respectively. Genes above the horizontal dashed line are significantly differentially expressed with the colours representing the change in expression. The top 10 most significant genes for increased and decreased expression with gene symbols are labelled. 59 Supplementary Figure B.17. Volcano plot showing the results of the RESP contrast for the liver samples at 15 days post infection (dpi). Each data point represents a gene with the position on the xand y-axes indicating the log2 fold change and -log10Padj., respectively. Genes above the horizontal dashed line are significantly differentially expressed with the colours representing the change in expression. The top 10 most significant genes for increased and decreased expression with gene symbols are labelled. 60 Supplementary Figure B.18. Volcano plot showing the results of the RESP contrast for the liver samples at 18 days post infection (dpi). Each data point represents a gene with the position on the xand y-axes indicating the log2 fold change and -log10Padj., respectively. Genes above the horizontal dashed line are significantly differentially expressed with the colours representing the change in expression. The top 10 most significant genes for increased and decreased expression with gene symbols are labelled. 67 Supplementary Figure B.25. Volcano plot showing the results of the RESP contrast for the lymph node samples at 35 days post infection (dpi). Each data point represents a gene with the position on the xand y-axes indicating the log2 fold change and -log10Padj., respectively. Genes above the horizontal dashed line are significantly differentially expressed with the colours representing the change in expression. The top 10 most significant genes for increased and decreased expression with gene symbols are labelled. 68 Supplementary Figure B.26. Volcano plot showing the results of the RESP contrast for the spleen samples at 21 days post infection (dpi). Each data point represents a gene with the position on the xand y-axes indicating the log2 fold change and -log10Padj., respectively. Genes above the horizontal dashed line are significantly differentially expressed with the colours representing the change in expression. The top 10 most significant genes for increased and decreased expression with gene symbols are labelled. 69 Supplementary Figure B.27. Volcano plot showing the results of the RESP contrast for the spleen samples at 35 days post infection (dpi). Each data point represents a gene with the position on the xand y-axes indicating the log2 fold change and -log10Padj., respectively. Genes above the horizontal dashed line are significantly differentially expressed with the colours representing the change in expression. The top 10 most significant genes for increased and decreased expression with gene symbols are labelled. 70 Supplementary Figure B.28. g:Profiler functional enrichment of significantly differentially expressed genes (DEGs) in the peripheral blood mononuclear cell (PBMC) sample RESP contrasts. Each circle represents a significantly enriched GO term with the size indicating the ratio of the intersection between the term and the DEGs. The vertical axis shows the -log10Padj. value and the vertical panels and colours indicate the direction of change in expression. The horizontal panels indicate the source of the term and the position within the panels groups terms from the same GO subtree. The top driver GO terms (up to a maximum of 10) are indicated with a black outline and label. 71 Supplementary Figure B.29. g:Profiler functional enrichment of significantly differentially expressed genes (DEGs) in the liver sample RESP contrasts. Each circle represents a significantly enriched GO term with the size indicating the ratio of the intersection between the term and the DEGs. The vertical axis shows the -log10Padj. value and the vertical panels and colours indicate the direction of change in expression. The horizontal panels indicate the source of the term and the position within the panels groups terms from the same GO subtree. The top driver GO terms (up to a maximum of 10) are indicated with a black outline and label. 72 Supplementary Figure B.30. g:Profiler functional enrichment of significantly differentially expressed genes (DEGs) in the lymph node sample RESP contrasts. Each circle represents a significantly enriched GO term with the size indicating the ratio of the intersection between the term and the DEGs. The vertical axis shows the -log10Padj. value and the vertical panels and colours indicate the direction of change in expression. The horizontal panels indicate the source of the term and the position within the panels groups terms from the same GO subtree. The top driver GO terms (up to a maximum of 10) are indicated with a black outline and label. 73 Supplementary Figure B.31. g:Profiler functional enrichment of significantly differentially expressed genes (DEGs) in the spleen sample RESP contrasts. Each circle represents a significantly enriched GO term with the size indicating the ratio of the intersection between the term and the DEGs. The vertical axis shows the -log10Padj. value and the vertical panels and colours indicate the direction of change in expression. The horizontal panels indicate the source of the term and the position within the panels groups terms from the same GO subtree. The top driver GO terms (up to a maximum of 10) are indicated with a black outline and label. 74 Supplementary Figure B.32. EnrichmentMap network of significantly enriched GO terms identified from g:Profiler functional enrichment of significant differentially expressed genes (DEGs) for the DIRE contrasts. Each node represents a GO term with the colour of the node representing the tissue and the size representing the number of genes in the GO term. The edges indicate overlap between the GO terms with the width of the edges representing the similarity coefficient for the connected GO terms. The GO terms are clustered by AutoAnotate with the background colour of the clusters representing the direction of expression. The clusters are labelled with the size of the label scaling with the number of GO terms in the cluster. 75 Supplementary Figure B.33. EnrichmentMap network of significantly enriched GO terms identified from g:Profiler functional enrichment of significant differentially expressed genes (DEGs) for the NDAM contrasts. Each node represents a GO term with the colour of the node representing the tissue and the size representing the number of genes in the GO term. The edges indicate overlap between the GO terms with the width of the edges representing the similarity coefficient for the connected GO terms. The GO terms are clustered by AutoAnotate with the background colour of the clusters representing the direction of expression. The clusters are labelled with the size of the label scaling with the number of GO terms in the cluster. 76 Supplementary Figure B.34. EnrichmentMap network of significantly enriched GO terms identified from g:Profiler functional enrichment of significant differentially expressed genes (DEGs) for the BORA contrasts. Each node represents a GO term with the colour of the node representing the tissue and the size representing the number of genes in the GO term. The edges indicate overlap between the GO terms with the width of the edges representing the similarity coefficient for the connected GO terms. The GO terms are clustered by AutoAnotate with the background colour of the clusters representing the direction of expression. The clusters are labelled with the size of the label scaling with the number of GO terms in the cluster. 83 Supplementary Table C.4 continued. Symbol Modules ATF3 MICRO BL 34, MICRO LI 35, MICRO SP 35, RNA NDAM 40 ATP5J MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 ATR MICRO LN 35, MICRO SP 35, RNA LAGU 40, RNA NDAM 40 BCAR3 MICRO LN 35, MICRO SP 35, RNA LAGU 40, RNA NDAM 40 BCR MICRO BL 34, MICRO LN 35, MICRO SP 35, RNA LAGU 40 BDNF MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 BECN1 MICRO LI 35, MICRO LN 35, MICRO SP 35, RNA LAGU 40 BIRC3 MICRO LN 35, MICRO SP 35, RNA BAOU 40, RNA NDAM 40 C20ORF18 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 C2ORF29 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 C3H1orf52 MICRO BL 34, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 CCR5 MICRO BL 34, MICRO LN 35, MICRO SP 35, RNA LAGU 40 CCRL1 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 CD28 MICRO BL 34, MICRO LN 35, MICRO SP 35, RNA LAGU 40 CDC25C MICRO BL 34, MICRO SP 35, RNA LAGU 40, RNA NDAM 40 CDC73 MICRO BL 34, MICRO LI 35, RNA LAGU 40, RNA BAOU 40 CDK1 MICRO LN 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 CLU MICRO BL 34, MICRO SP 35, RNA LAGU 40, RNA NDAM 40 CMYA5 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 CNOT6 MICRO LN 35, MICRO SP 35, RNA LAGU 40, RNA BAOU 40 CNOT7 MICRO BL 34, MICRO LI 35, MICRO SP 35, RNA BORG 40 CNTF MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 CRYAB MICRO LI 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 CSF2 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 CSNK1G1 MICRO SP 35, RNA LAGU 40, RNA BAOU 40, RNA NDAM 40 CSNK2A2 MICRO BL 34, MICRO SP 35, RNA LAGU 40, RNA NDAM 40 CTPS MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 CXCR7 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 DDIT4 MICRO LI 35, RNA LAGU 40, RNA NDAM 40, RNA BORG 40 DHFR MICRO BL 34, MICRO LI 35, MICRO LN 35, MICRO SP 35 DPF1 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 DVL2 MICRO BL 34, MICRO LI 35, MICRO SP 35, RNA NDAM 40 EIF2AK2 MICRO LI 35, MICRO SP 35, RNA LAGU 40, RNA NDAM 40 ELA2 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 EP300 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 FBXO32 MICRO LN 35, RNA LAGU 40, RNA BAOU 40, RNA BORG 40 FBXO5 MICRO LN 35, MICRO SP 35, RNA BAOU 40, RNA BORG 40 FKBP5 MICRO SP 35, RNA LAGU 40, RNA NDAM 40, RNA BORG 40 FLJ20565 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 FN1 MICRO LN 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 GEMIN2 MICRO BL 34, MICRO LI 35, MICRO LN 35, MICRO SP 35 GNB2L1 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 GR-A MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 GRB2 MICRO SP 35, RNA LAGU 40, RNA BAOU 40, RNA NDAM 40 HGS MICRO LI 35, MICRO SP 35, RNA LAGU 40, RNA NDAM 40 84 Supplementary Table C.4 continued. Symbol Modules HMGA2 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 HMGB1 MICRO BL 34, MICRO LI 35, MICRO LN 35, MICRO SP 35 HTT MICRO BL 34, MICRO LN 35, MICRO SP 35, RNA BORG 40 ICT1 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 IL10 MICRO LN 35, MICRO SP 35, RNA LAGU 40, RNA NDAM 40 IL11 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 IL12A MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 ILF3 MICRO BL 34, MICRO LN 35, MICRO SP 35, RNA NDAM 40 IRF2 MICRO BL 34, MICRO LI 35, MICRO LN 35, MICRO SP 35 ISG15 MICRO BL 34, MICRO LN 35, MICRO SP 35, RNA LAGU 40 ITGB2 MICRO LN 35, MICRO SP 35, RNA LAGU 40, RNA NDAM 40 JAKMIP1 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 KAT5 MICRO BL 34, MICRO LN 35, RNA LAGU 40, RNA BORG 40 KSR1 MICRO LN 35, MICRO SP 35, RNA LAGU 40, RNA NDAM 40 LARS MICRO LI 35, MICRO LN 35, MICRO SP 35, RNA NDAM 40 LCK MICRO LN 35, MICRO SP 35, RNA BAOU 40, RNA NDAM 40 LEO1 MICRO SP 35, RNA LAGU 40, RNA BAOU 40, RNA NDAM 40 LIFR MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 MAFG MICRO BL 34, MICRO LI 35, MICRO LN 35, MICRO SP 35 MAP3K7IP1 MICRO BL 34, MICRO SP 35, RNA BAOU 40, RNA NDAM 40 MAPK6 MICRO SP 35, RNA LAGU 40, RNA BAOU 40, RNA NDAM 40 MDH2 MICRO LI 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 MIB1 MICRO SP 35, RNA LAGU 40, RNA BAOU 40, RNA NDAM 40 NANOG MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 NANOS2 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 NFAT5 MICRO SP 35, RNA LAGU 40, RNA BAOU 40, RNA BORG 40 NFATC2 MICRO BL 34, MICRO LI 35, MICRO LN 35, MICRO SP 35 NFKBIE MICRO BL 34, MICRO SP 35, RNA LAGU 40, RNA BAOU 40 NFKBIL1 MICRO BL 34, MICRO LI 35, MICRO LN 35, MICRO SP 35 NPM1 MICRO LI 35, MICRO LN 35, MICRO SP 35, RNA BAOU 40 NR4A1 MICRO BL 34, MICRO LI 35, MICRO SP 35, RNA NDAM 40 PCAF MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 PGD MICRO BL 34, MICRO LI 35, RNA LAGU 40, RNA NDAM 40 PGHS-2 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 PGR MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 PIK3R2 MICRO BL 34, MICRO SP 35, RNA LAGU 40, RNA NDAM 40 POU2F1 MICRO BL 34, MICRO LI 35, MICRO LN 35, RNA LAGU 40 PPP2R1B MICRO LI 35, MICRO LN 35, RNA LAGU 40, RNA NDAM 40 PRDX5 MICRO BL 34, MICRO LI 35, MICRO LN 35, RNA LAGU 40 PRKCI MICRO BL 34, MICRO LN 35, MICRO SP 35, RNA LAGU 40 PROS1 MICRO LN 35, MICRO SP 35, RNA BAOU 40, RNA NDAM 40 PTPN1 MICRO LN 35, MICRO SP 35, RNA LAGU 40, RNA NDAM 40 PTPN6 MICRO BL 34, MICRO SP 35, RNA BAOU 40, RNA BORG 40 RAG1 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 RAG2 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 85 Supplementary Table C.4 continued. Symbol Modules RGS7 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 RQCD1 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 RRM2B MICRO BL 34, MICRO LN 35, MICRO SP 35, RNA LAGU 40 SELL MICRO BL 34, MICRO LI 35, MICRO SP 35, RNA LAGU 40 SNCA MICRO BL 34, MICRO SP 35, RNA NDAM 40, RNA BORG 40 SRRM2 MICRO BL 34, MICRO LI 35, RNA BAOU 40, RNA BORG 40 STAT5B MICRO BL 34, MICRO LI 35, RNA BAOU 40, RNA BORG 40 TBPL1 MICRO LI 35, MICRO LN 35, MICRO SP 35, RNA NDAM 40 TGFB1 MICRO BL 34, MICRO SP 35, RNA LAGU 40, RNA NDAM 40 TLR4 MICRO BL 34, MICRO LI 35, MICRO SP 35, RNA LAGU 40 TMEM66 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 TNF MICRO LI 35, MICRO SP 35, RNA LAGU 40, RNA BAOU 40 TNIP3 MICRO SP 35, RNA LAGU 40, RNA BAOU 40, RNA NDAM 40 TOMM70A MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 TRAIP MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 UBA1 MICRO BL 34, MICRO LI 35, MICRO LN 35, MICRO SP 35 UBE2D1 MICRO BL 34, MICRO LI 35, MICRO SP 35, RNA LAGU 40 UBE2N MICRO LI 35, MICRO LN 35, MICRO SP 35, RNA BORG 40 UNC5CL MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 VDR MICRO BL 34, MICRO LN 35, MICRO SP 35, RNA LAGU 40 VIM MICRO BL 34, RNA LAGU 40, RNA BAOU 40, RNA NDAM 40 VPS4A MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 WDR96 MICRO SP 35, RNA BAOU 40, RNA NDAM 40, RNA BORG 40 YY1 MICRO BL 34, MICRO LI 35, MICRO SP 35, RNA BAOU 40 86 Supplementary Table C.5. Numbers of intervals within 1 Mb upand downstream of SNPs with z-score ≥ 2.0 for mean European B. taurus, African B. taurus and B. indicus ancestry components for the six populations with gene expression data available across all autosomes and groups of populations from the original local ancestry analysis. Analysis Software Data Group/Population European Bos taurus intervals African Bos taurus intervals Bos indicus intervals Updated ELAI LD LAGU 1,237 0 1,169 Updated ELAI LD BAOU 1,262 0 1,111 Updated ELAI LD NDAM 1,302 102 1,049 Updated ELAI LD BORG 1,084 426 864 Updated ELAI LD FULA 1,150 711 580 Updated ELAI LD BORA 1,203 1,053 260 Original ELAI HD Selected European hybrids 0 9,296 12,898 Original ELAI HD Selected trypanotolerant African hybrids 10,748 3,408 6,966 Original ELAI HD Trypanosusceptible African hybrids 10,273 8,930 2,871 Original ELAI LD Selected European hybrids 132 1,220 1,306 Original ELAI LD Selected trypanotolerant African hybrids 1,153 582 738 Original ELAI LD Trypanosusceptible African hybrids 1,091 1,013 398 Original MOSAIC HD Selected European hybrids 0 6,737 12,802 Original MOSAIC HD Selected trypanotolerant African hybrids 9,924 3,457 6,774 Original MOSAIC HD Trypanosusceptible African hybrids 10,634 7,352 3,415 87 Supplementary Figure C.1. Heatmap of mean identity by state values for SNP data in European, African, and Asian cattle populations. 88 Supplementary Figure C.2. Tukey box plots showing the distribution of inbreeding values (F) for SNP data for each population of European, African, and Asian cattle. Outliers are indicated with a black outline. 89 Supplementary Figure C.3. A. Principal component analysis (PCA) of SNP data for cattle coloured according to population showing the first two principal components and B. bar chart of proportion of variance of the top ten principal components. 90 Supplementary Figure C.4. A. Principal component analysis (PCA) of the high-density SNP data for the cattle samples from Chapter 2 coloured according to population showing the first two principal components and B. bar chart of proportion of variance of the top ten principal components. The transparency indicates the availability of microarray gene expression data for the sample. 91 Supplementary Figure C.5. A. Principal component analysis (PCA) of the low-density SNP data for the cattle samples from Chapter 2 coloured according to population showing the first two principal components and B. bar chart of proportion of variance of the top ten principal components. The transparency indicates the availability of microarray gene expression data for the sample. 92 Supplementary Figure C.6. Hierarchical clustering of the SNP data for European, African, and Asian cattle populations. Results are shown for an assumed value of the number of ancestral populations K = 3. The transparency indicates the availability of gene expression data for the sample. 99 Supplementary Figure C.13. Bar chart showing the numbers of significantly differentially expressed genes for the response contrasts of the RNA-seq data. The extent of the bar above and below 0 on the y-axis indicates the numbers of significantly differentially expressed genes with increased and decreased expression respectively. The position on the x-axis indicates the number of days post infection and the colour and shapes within the bars represent the population. 100 Supplementary Figure C.14. Volcano plot showing the results of the response contrast for the RNA-seq data from the LAGU population at 40 days post infection. Each dot represents a gene with the position on the xand y-axes indicating the log2 fold change and -log10Padj., respectively. Genes above the horizontal dashed line are significantly differentially expressed with the colours representing the change in expression. The top 10 most significant genes for increased and decreased expression with gene symbols are labelled. 101 Supplementary Figure C.15. Volcano plot showing the results of the response contrast for the RNA-seq data from the BAOU population at 40 days post infection. Each dot represents a gene with the position on the xand y-axes indicating the log2 fold change and -log10Padj., respectively. Genes above the horizontal dashed line are significantly differentially expressed with the colours representing the change in expression. The top 10 most significant genes for increased and decreased expression with gene symbols are labelled. 102 Supplementary Figure C.16. Volcano plot showing the results of the response contrast for the RNA-seq data from the NDAM population at 40 days post infection. Each dot represents a gene with the position on the xand y-axes indicating the log2 fold change and -log10Padj., respectively. Genes above the horizontal dashed line are significantly differentially expressed with the colours representing the change in expression. The top 10 most significant genes for increased and decreased expression with gene symbols are labelled. 103 Supplementary Figure C.17. Volcano plot showing the results of the response contrast for the RNA-seq data from the BORG population at 40 days post infection. Each dot represents a gene with the position on the xand y-axes indicating the log2 fold change and -log10Padj., respectively. Genes above the horizontal dashed line are significantly differentially expressed with the colours representing the change in expression. The top 10 most significant genes for increased and decreased expression with gene symbols are labelled. 104 Supplementary Figure C.18. Base network generated using InnateDB with the top results of a search of the GeneCards® for genes relating to the term “trypano*”. Each node in the network represents a gene while the edges connecting the nodes represent gene interactions. The nodes are sized according to their degree or number of interactions. 105 Supplementary Figure C.19. Functional module identified using jActiveModules and differential expression results for the MICRO BL 34 contrast. Each node in the network represents a gene coloured according to expression with significant differential expression indicated by the outline. The edges connecting the nodes represent gene interactions and the nodes are sized according to their number of interactions or degree. 106 Supplementary Figure C.20. Functional module identified using jActiveModules and differential expression results for the MICRO LI 35 contrast. Each node in the network represents a gene coloured according to expression with significant differential expression indicated by the outline. The edges connecting the nodes represent gene interactions and the nodes are sized according to their number of interactions or degree. 107 Supplementary Figure C.21. Functional module identified using jActiveModules and differential expression results for the MICRO LN 35 contrast. Each node in the network represents a gene coloured according to expression with significant differential expression indicated by the outline. The edges connecting the nodes represent gene interactions and the nodes are sized according to their number of interactions or degree. 108 Supplementary Figure C.22. Functional module identified using jActiveModules and differential expression results for the MICRO SP 35 contrast. Each node in the network represents a gene coloured according to expression with significant differential expression indicated by the outline. The edges connecting the nodes represent gene interactions and the nodes are sized according to their number of interactions or degree. 115 Supplementary Figure C.29. g:Profiler functional enrichment of the genes in the MICRO LI 35 functional module with no background data set specified. Each dot represents a significantly enriched GO term with the size indicating the ratio of the intersection between the term and the introgressed genes. The y-axis shows the -log10Padj. value up to a maximum of 16 and the panels along the y-axis and colours indicate the module. The panels along the x-axis indicate the source of the term and the position within the panels groups terms from the same GO subtree. The top driver GO terms up to a maximum of ten are indicated with a black outline and label. 116 Supplementary Figure C.30. g:Profiler functional enrichment of the genes in the base network with no background data set specified. Each dot represents a significantly enriched GO term with the size indicating the ratio of the intersection between the term and the introgressed genes. The y-axis shows the -log10Padj. value up to a maximum of 16 and the panels along the y-axis and colours indicate the module. The panels along the x-axis indicate the source of the term and the position within the panels groups terms from the same GO subtree. The top driver GO terms up to a maximum of ten are indicated with a black outline and label. 117 Bibliography Pickrell J.K. & Pritchard J.K. 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