Figure 1.
Framework DArT/microsatellite linkage map for Eucalyptus.
The map includes 1,029 markers positioned with high confidence for locus order, involving 861 DArT (in black) and 168 microsatellites (in red) with a centiMorgan scale on the left.
Table 1.
Mapping statistics of the DArT/microsatellite consensus maps of Eucalyptus grandis x E. urophylla.
Figure 2.
Alignment of the Framework map to the Eucalyptus grandis reference genome.
Correspondence of the DArT and microsatellite marker positions on the Framework linkage map (green bars) with their location on the 11 Eucalyptus grandis pseudochromosome scaffolds (white bars). The scale on the left corresponds simultaneously to centiMorgan distances for the linkage map and to Mbp of sequence for the pseudochromosome scaffolds.
Figure 3.
Genome-wide correspondence of DArT markers and predicted gene models in the Eucalyptus grandis genome.
The 11 pseudochromosomes of the Eucalyptus grandis genome (Version 1.0 in Phytozome 6.0), were partitioned into 122 bins of 5 Mbp. For each bin the numbers of DArT marker probe positions (blue bars), the number of genetically mapped DArT markers (red bars) and the number of predicted gene models (green bars) were plotted.
Figure 4.
Correlations between DArT markers probes, mapped DArT markers and gene models.
Spearman Rank correlations were estimated between: (A) the number of DArT marker probes and the number of gene models; and (B) the number of mapped DArT markers and the number of gene models, for every 5 Mbp genome bin.
Figure 5.
Distribution of the physical distance between DArT markers and gene models in the Eucalyptus genome.
Distribution of the proportions of the 6,571 DArT marker probe positions according to distance classes in kbp from the closest predicted gene model in the Eucalyptus grandis genome (version 1.0).
Table 2.
Results of redundancy analysis of the 6,918 DArT marker probe sequences under four different sets of assembly parameters from the most stringent (A1) to the most relaxed (A4) (see Material and Methods for details).