Fig. 3

Phylogeny of (a) pSc200 and (b) pSc250 monomers present on each of the seven rye chromosomes. The chromosome-specific 454 libraries obtained by Martis et al. (2013) were used to reconstruct phylogenetic networks and assign pSc200 and pSc250 monomers to each of the seven rye chromosomes (1R and 1RS chromosomes, red color: ERX140512 ERX140519 libraries; 2R chromosome, orange: ERX140513 library; 3R and 3RS chromosomes, yellow: ERX140514 and ERX140520 libraries; 4R chromosome, green: ERX140515 library; 5R chromosome, cyan: ERX140516 library; 6R chromosome, blue: ERX140517 library; 7R and 7RS chromosomes, violet: ERX140518 and ERX140521 libraries). The phylogenetic trees shown represent galled phylogenetic networks generated by Dendroscope v3.2.8 software based on the trees obtained by maximum likelihood method. Black circles at branch ends refer to sequenced pSc200 monomers present in the ВАС clone 119С15 (see Table 1). The scale bar corresponds to the weighted evolutionary distance (GTR nucleotide substitution model) and indicates the weighted number of substitutions per alignment site. The two histograms depicting the distribution of pairwise distances are shown: the x-axis plots the sequence pairwise distance (=100 - % of sequence identity) while the y-axis plots the occurrence frequency