Figure 1.
Figure 1.

Relationship between length of each contig (bp) and depth of coverage of each contig (number of reads).

 


Figure 2.
Figure 2.

Arbitrary enumeration of the 15 aggregates of the biological process gene ontology functional classification of PCG contigs.

 


Figure 3.
Figure 3.

Overlap of the alignment of PCG contigs to the three grass libraries and gene ontology classification. The total number of contigs are indicated for each species or classification and their respective intersection.

 


Figure 4.
Figure 4.

PCG contigs and ESTs mapped to the sorghum genome. The 10 individual sorghum chromosomes (multicolored) are shown in association with the respective PCG sequence. An additional 17 clusters that did not assemble with the sorghum genome are represented as mint green. The positive strand is represented by the outward clusters of contig frequency (red) and EST frequency (blue).The negative strand is represented by the inward clusters of contig frequency (yellow) and EST frequency (green).

 


Figure 5.
Figure 5.

Example of the observed polymorphism of PCG EST–SSRs in eight different genotypes of PCG collected from South Dakota, North Dakota, Iowa, and Nebraska. PCR products were visualized on an 8% (w/v) nondenaturing PAGE. Contigs from which primers were developed were as follows: a. contig17168, b. contig16969, c. contig16767, d. contig16063, e. contig15096. The figure contains a 100-bp ladder for reference (far right).

 


Figure 6.
Figure 6.

Neighbor joining unrooted tree constructed from the pairwise distance between the protein sequences of 82 phenylpropanoid biosynthetic pathway enzymes. Clustering occurred in relation to the three contigs annotated as the enzyme COMT and five contigs annotated as CCoAOMT and their respective NCBI accessions identified by BLASTx (clades are designated by number). Clades 1, 2, and 3 represent the sequences associated with the enzyme COMT. Clades 4, 5, 6, and 7 represent the sequences associated with the enzyme CCoAOMT. Accession names are detailed in Table 7.