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Supporting Information Figs S1-S6, Tables S1-S7, Notes S1 Supporting Information Figs S1-S6, Tables S1-S7, Notes S1. Article title: Genomic patterns of species diversity and divergence in Eucalyptus Authors: Corey J Hudson, Jules S Freeman, Alexander A Myburg, Brad M Potts, and René E Vaillancourt Following pages: Supporting Information Fig. S1 Genome-wide patterns of differentiation between six species of Eucalyptus. Marker FST estimates (y-axis) are plotted on the 11 eucalypt chromosomes for each of 15 pair-wise species comparisons. Graphs are grouped by intra- and inter- section comparisons as indicated on the left page margin. Chromosome numbers are given at the top of each page with black vertical lines on individual graphs indicating chromosome boundaries. Species differentiating markers (SDMs) are indicated by asterisk symbols (significant outlier marker) and ‘1’ symbols (markers with fixed differences but not detected as an outlier marker). Section differentiating markers (SEDMs) are highlighted using the same colour coding used to indicate section comparisons. Additionally, SEDMs which differentiated, 1) section Maidenaria species from both Latoangulatae (Lat) and Exsertaria (Ex) species, and 2) section Exsertaria species from both Maidenaria and Latoangulatae species are highlighted in pink and orange, respectively. 1 2 3 4 5 E. grandis v E. globulus * * * * * ** * * 0.7 0.2 E. grandis v E. nitens 0.7 1 11 1 1 1 1 1 11111111 1 0.2 E. grandis v E. dunnii 11 0.7 11 1 11 1 1 1 1 11111 1 11 1 1 1 1 11 1 Latoangulatae 0.2 vs. E. urophylla v E. globulus 0.7 * * * * *** * * 0.2 E. urophylla v E. nitens * 1 Maidenaria 0.7 * ** * * * * ** * * * * * 0.2 E. urophylla v E. dunnii 0.7 1 * * *1 * 1*1* * * 1 * 1 * *1 0.2 E. camaldulensis v E. globulus * * * * * 0.7 * * * * * * *** 0.2 E. camaldulensis v E. nitens Maidenaria * * ** 0.7 *** * * 1 * * * ** * ** *** vs. 0.2 E. camaldulensis v E. dunnii 0.7 * * * * * 1 ***** * * * ** * ** Exsertaria 0.2 E. camaldulensis v E. grandis 0.7 * * *** * *** * * * * * * * . Ex 0.2 vs E. camaldulensis v E. urophylla Lat 0.7 * ** * * * * ** * * 0.2 E. globulus v E. nitens * 0.7 * * * * * * * * * * * * * 0.2 E. globulus v E. dunnii * 0.7 * * * * * * ** * * * * * * * * * * * * * * * * * * * * * * * * 0.2 section - E. nitens v E. dunnii 0.7 * 1*** ** * 1 1 * 1 *** * 1 * ** * *1* * * * Intra 0.2 E. grandis v E. urophylla 0.7 * * ** * * * * * 0.2 0 50 100 150 200 250 300 Cumulative chromosome length (Mbp) 6 7 8 9 10 11 E. grandis v E. globulus 0.7 ** ** * ** * *** * * * * * ****** * ** * 0.2 E. grandis v E. nitens 0.7 111 11 1111 11 1 11 111 1 11 111 111 111 1 1 111 0.2 E. grandis v E. dunnii 0.7 1 11 1 1 11111 11 11 1 11 1111 1 11 1 11 1 11 111111 1111 11 1 111 11 1111111 Latoangulatae 0.2 vs. E. urophylla v E. globulus 0.7 * ** * * * * ** * * * * * * 0.2 E. urophylla v E. nitens Maidenaria 0.7 ** * ** * * ** * * * * ** * 0.2 E. urophylla v E. dunnii 1 1 1 1 1 1 0.7 ** * * * * * 1* * ** * * * 1** 0.2 E. camaldulensis v E. globulus 0.7 * * ** * * * * * * * ** * * * * * * * * * * ** * * 0.2 E. camaldulensis v E. nitens Maidenaria 0.7 ** * ** ** * * * * * * * * * * * * * * * ** vs. 0.2 E. camaldulensis v E. dunnii 0.7 * ** * * *** * * * *** * ** * * * * *** * ** * * * * * * * * * Exsertaria 0.2 E. camaldulensis v E. grandis 0.7 * * * ** * * * ** * * * * ** * * * * * ** * * * * . Ex vs 0.2 E. camaldulensis v E. urophylla Lat 0.7 * * ** * * ** * ** * * * * * * * 0.2 E. globulus v E. nitens * 0.7 * * * * * * * ** * * * * * * * * 0.2 E. globulus v E. dunnii * 0.7 ** * **** * * * ** * * * * * *** *** *** ** * * * * * ** * * * 0.2 section - E. nitens v E. dunnii 1 ** 0.7 * ** ** * * **** * * * * * ** * * 1 * * * * *** *** ** * ** * ** ** Intra 0.2 E. grandis v E. urophylla 0.7 * * * * * * * * * * * * ** ** 0.2 0 50 100 150 200 250 300 Cumulative chromosome length (Mbp) Following page: Supporting Information Fig. S2 Genome-wide patterns of genetic diversity for six eucalypt species. An 11 marker running average of standardised HHW is plotted for 2408 marker estimates. The x-axis indicates cumulative chromosome positions in million base-pairs, black vertical lines indicate chromosome boundaries. 1 2 3 4 5 6 7 8 9 10 11 E. grandis 0.3 0.2 0.1 0.0 -0.1 -0.2 -0.3 0 50 100 150 200 250 300 350 400 450 500 550 600 E. urophylla 0.3 0.2 0.1 0.0 -0.1 -0.2 -0.3 0 50 100 150 200 250 300 350 400 450 500 550 600 E. camaldulensis 0.3 0.2 0.1 0.0 HW H -0.1 -0.2 -0.3 0 50 100 150 200 250 300 350 400 450 500 550 600 E. globulus Standardised 0.3 0.2 0.1 0.0 -0.1 -0.2 -0.3 0 50 100 150 200 250 300 350 400 450 500 550 600 E. nitens 0.3 0.2 0.1 0.0 -0.1 -0.2 -0.3 0 50 100 150 200 250 300 350 400 450 500 550 600 E. dunnii 0.3 0.2 0.1 0.0 -0.1 -0.2 -0.3 0 50 100 150 200 250 300 350 400 450 500 550 600 Cumulative base-pair position (Mbp) # Gene models x 10 # SDMs # DArT markers 10 20 30 40 50 60 70 10 20 30 40 50 60 70 models across all pair detected SDMs of total number markers; red and line) (2408 study thisof markers annotated DArT to 52.5 (45 plotting for partitioned into 122 bins of (mostly) 5 (mostly) of partitioned bins into 122 the of chromosomes 11 The (SDMs). markers differentiating grandis Eucalyptus Genome S3 Information Fig. Supporting 0 0 0 - 5 0 - 5 5 - 10 5 - 10 ( 10 - 15 10 - 15 × 15 - 20 1 15 - 20 6 10) and annotated markers are indicated by dashed black and blue lines, respectively. lines, respectively. blue annotated and and black indicated are markers dashed 10) by 20 - 25 20 - 25 25 - 30 25 - 30 30 - 35 - 30 - 35 wise comparisons (black bars) were plotted. The average ‘per bin’ number of gene gene of number bin’ ‘per average The plotted. were bars) (black comparisons wise 35 - 40 35 - 41 40 - 45 45 - 50 50 - 55 0 - 5 genome, annotated DArT markers of this study and detected species species detected and study this of markers DArT annotated genome, 5 - 10 0 - 5 10 - 15 Mbp 5 - 10 15 - 20 20 - 25 10 - 15 2 25 - 30 7 15 - 20 ). For each each bin, For ). number the predicted of gene models ( 30 - 35 20 - 25 25 - 30 35 - 40 30 - 35 40 - 45 Chromosome Chromosome 35 - 40 45 - 50 40 - 45 50 - 55 45 - 53 55 - 60 60 - 65 Mbp 0 - 5 - wide relationship between predicted gene models in the the in models gene predicted between relationship wide 5 - 10 0 - 5 10 - 15 5 - 10 , but the last twobinschromosome of 7 were combined 15 - 20 10 - 15 20 - 25 15 - 20 – 25 - 30 20 - 25 genomic genomic (Mbp) interval 30 - 35 8 25 - 30 35 - 40 30 - 35 40 - 45 3 35 - 40 45 - 50 40 - 45 50 - 55 45 - 50 55 - 60 50 - 55 60 - 65 55 - 60 65 - 70 60 - 65 70 - 75 65 - 70 Eucalyptus grandis Eucalyptus 70 - 75 0 - 5 75 - 80 5 - 10 10 - 15 9 15 - 20 0 - 5 20 - 25 5 - 10 25 - 30 10 - 15 30 - 35 4 15 - 20 35 - 40 20 - 25 25 - 30 30 - 35 0 - 5 35 - 42 5 - 10 10 10 - 15 genome were 15 - 20 0 - 5 × 20 - 25 5 - 10 25 - 30 10; gray 10; gray bars), 10 - 15 30 - 35 15 - 20 35 - 40 20 - 25 25 - 30 30 - 35 0 - 5 5 35 - 40 5 - 10 10 - 15 40 - 45 11 15 - 20 45 - 50 20 - 25 50 - 55 25 - 30 55 - 60 30 - 35 60 - 65 35 - 40 65 - 70 40 - 46 70 - 75 Supporting Information Fig. S4 The significant within chromosome relationships of global HHW (six species HHW average; top), global FST (middle) and the proportion of species differentiating markers (SDMs, bottom) with gene density (genes per Mbp). The data represents the variation amongst 5Mbp bins within chromosomes (chromosome differences were removed by standardisation of 5Mbp bin averages to a mean of zero for each chromosome). The 95% confidence intervals for the mean (shaded) and individual (dotted line) predicted values are shown. E. grandis a 0.24 b 0.22 *** 0.2 c 0.18 Hhw 0.16 0.14 0.12 0.1 Genes outside Genes within Within genes Within 5kbp of More than tandem tandemE. urophylla aab gene 5kbpa from a 0.24 clusters ns clusters c gene 0.22 Supporting Information Fig. S5 0.2 0.18 H for (a) DArT markers in genes, Hhw 0.16 HW 0.14 0.12 within 5kb of a gene, and more than 5kb 0.1 Genes outside Genes within Within genes Within 5kbp of More than from a gene (black bars) and (b) DArT tandem tandemE. camaldulensisE. urophylla a gene 5kbpa from a 0.24 clusters *** clusters b gene markers in genes which were outside and 0.22 b 0.2 within clusters of tandemly duplicated 0.18 Hhw 0.16 genes (grey bars). Means with common 0.14 0.12 letters (above black bars) are not 0.1 Genes outside Genes within Within genes Within 5kbp of More than 0.24 tandem tandem E. dunnii a gene 5kbpa from a significantly (P<0.05 ) different based on 0.22 clusters clusters gene *** b pair-wise Kruskal-Wallis tests. The 0.2 c 0.18 significance of the Kruskal-Wallis tests for Hhw 0.16 0.14 the difference between DArT markers 0.12 0.1 Genes outside Genes within Within genes Within 5kbp of More than within genes which were outside and 0.24 tandem tandem a gene 5kbp froma a clusters *** clusters E.
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