The next most abundant hits were to members of the order Xanthomonadales (22% for Air-1 and 8% for Air-2), which includes Stenotrophomonas; among the remaining hits, no more than a few percent were to any single genus.
The average coverage, however, is low (∼45%), with the most abundant hits to centromeric sequences of Pinus densiflora and Z. mays (Table S6).
For convenience, hereafter we use TE# to denote abundant hits matching a fixed region within CM# and E TE# to specifically denote the region within CM#.
A surprising finding of our genome search was that some CMs produced abundant hits (e.g., CM7 produced 94335 hits on chromosome 1 in the marmoset genome), strongly suggesting that some ANRIL exons are or contain transposons.
The single most abundant COG hit was to glyceraldehyde-3-phosphate dehydrogenase (GAPDH; COG0057); other common transcripts encoded pyruvate phosphate dikinase (COG0574), phosphoglycerate kinase (COG0126), and glycogen synthase (COG0297) (Table 2).
The next group of abundant BLASTp hits was algal proteins (28 architectures), followed by primitive marine animal proteins (16), metazoan proteins (15), fungal proteins (13) and protozoan (4).
High Z scores indicate that a motif is significantly more abundant within hits than would be expected by chance, taking into account the sequence composition of the transcripts to which the hits map.
In all cases, except the " D. baltica dark" subset, the most abundant top hits corresponded to alveolates, as expected, and the overall distribution is similar between different dinotoms, altogether indicating that the majority of the transcripts probably originates from the host nucleus.
Although there were abundant ChIP-seq hits among these robust candidate genes, the few PPI hits were present only for known clock genes and circadian protein expression was restricted to Por, Gne, Mtss1, Upp2 and Ppp1r3b.
A list of the 20 most abundant InterPro domain hits is reported in the Figure 1B, showing IPR027417 (P-loop containing nucleoside triphosphate hydrolase) to be the most prevalent domain present in 691 transcripts, followed by IPR007087 (Zinc finger, C2H2) and IPR015880 (Zinc finger, C2H2 like).
