International Populus Genome Consortium

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New Phytologist manuscript NPH-MET-2008-07382

Supplemental Figure 1. Distribution of microsatellites encompassed by the SSR primers along each chromosome. Sequences are arranged every 1 Mb from the one end of the chromosome to the other. The physical length is estimated as the mapped sequence scaffold lengths plus the averaged gap length across scaffolds. The A, T, G & C sequences are represented with the black regions of the vertical bar, whereas the gaps are drawn in gray. We used four colors to indicate the different classes of microsatellite repeats. The blue, red, yellow and green horizontal bars in the chart corresponded to penta-, tetra-, tri- and dinucleotide repeats, respectively. The leftmost bar is the size ruler in base pairs. Microsatellite repeat lengths are not drawn to scale.

Supplemental Table 1. Simple sequence repeat primers and parameters database developed from the mapped sequence scaffolds on each chromosome. The primers are in 19 EXCEL spreadsheets that correspond to the 19 chromosomes, respectively.

Supplemental Table 2.Test SSR primer distribution in every 2Mb-window along each chromosome. The valid reading length of each window is the sum of A,T,G,C readings in each window. The distribution of primer density in each window was verified to fit normal distribution by Anderson-Darling test for normality. Confidence interval shows even distribution were calculated by [mean±1.96StDev] and [mean±2.58StDev] respectively, which corresponding P=0.05 and P=0.01 respectively. **+, significantly overabundant at p=0.01; *+, significantly overabundant at p=0.05; **-, significantly sparse at p=0.01; *- significantly sparse at p=0.05.

Supplemental Table 3.PCR amplification results and primer pairs' information used in testing SSR amplification success rate and SSR allelic variability in P. tremuloides. Altogether, 150 SSRs were tested for amplification success rate, out of which, 57 primer pairs generated alleles that can be unambiguously recorded, these primer pairs were subsequently used in testing the SSR allelic variability.