The pathways with most representation by the unique sequences were "metabolic pathways", "Ribosome", and "Biosynthesis of secondary metabolites".
The pathways with most representation by the unique sequences were starch and sucrose metabolism (553 members); purine metabolism (458 members) and galactose metabolism (183 members).
The pathways with the most representation by the unique sequences were ribosome (769 members); carbon metabolism (659) and Oxidative phosphorylation (417).
The pathways most represented by the unique sequences were metabolic pathways (3,381 members), biosynthesis of secondary metabolites (1,935 members), spliceosome (847 members), phenylpropanoid biosynthesis (513 members), starch and sucrose metabolism (423 members) and flavonoid biosynthesis (316 members).
The most represented pathways by the unique sequences were metabolic pathways (5,488 members), biosynthesis of secondary metabolites (2,904 members), plant-pathogen interaction (2,389 members), and spliceosome (1,121 members).
The pathways with the most representation by the unique sequences were starch and sucrose metabolism (2801 members, 11.62%), pathways in cancer (1126 members, 4.67%), and regulation of actin cytoskeleton (1029 members, 4.27%).
By clustering the unique sequences differing by 3 or less nucleotides, we further reduced the number of sequences to 8,309 OTUs.
Although the repetitive sequences themselves are not tiled, the enrichment of unmethylated genome can assess methylation status of the repetitive sequences by probing the unique sequences flanking the repeats (gaps in the tiling microarrays) (Supplementary Material, Fig. S1B).
Using bioinformatics methods, we annotated approximately 65.51% of the unique sequences by conducting a similarity search with known genes in the National Center for Biotechnology Information's non-redundant database.
Blast2GO software was used to obtain the gene ontology (GO) terms for the unique sequences by comparing them through the Gene Ontology Consortium [ 47].
Additional file 1: Length distribution of the coding sequence (CDS) and predicted proteins by BLASTX and ESTScan software from the unique sequences.
