Workflow of the contig-based strategy with current mainstream method for miRNA identification.

<p>Acquiring candidate miRNA precursors for hairpin structures is the first step in miRNA identification. This strategy is based on contigs from genomic DNA sequencing, replacing available dataset-based methods (represented by EST+GSS). <b>Blue-flow</b>. Pipeline of DNA sequencing <b>[It is the innovation of this strategy]</b>; <b>Red-flow</b>. Pipeline of small RNA sequencing.</p

The binding pattern between HBII-52 and 5-HT_2CR mRNA in mammals.

<p>(A) Left panels indicate the length distribution of perfect base-pairing between HBII-52 and 5-HT_2CR mRNA. Right panels indicate the distance of base-pairing from the D box motif. Analyses of primates, rodents and other mammals are indicated with different colors. In primates and rodents, the length of the base-pairing was centered approximately 18 nt and started just upstream of the D box. In other species, the length of the base-pairing ranged from 9–14 nt and started several nucleotides away from the D box. (B) The best base complementarity between the antisense element of the human, elephant or horse HBII-52 snoRNA and the corresponding 5-HT_2CR receptor. Nucleotides in red indicate the A to I editing sites (A to E); nucleotides in orange indicate proximal splice site. Box, D box. Red crosses indicate mismatch within the RNA duplex.</p

Ka/Ks tests of protein-coding genes in the PWS locus.

<p><i>P</i> values<0.05 for purifying selection are in bold.</p

Genetic divergence of snoRNA genes and their flanking sequences in primates for both imprinted and non-imprinted snoRNAs.

<p>Species abbreviation: HS, humans; PT, chimpanzees; RM, rhesus. Standard deviations are shown in parentheses.</p

Evolutionary divergence rates for each part of the imprinted snoRNA genes between the human and other mammals.

<p>A diagram of box C/D snoRNA structure with different partitions was illustrated in the left [modified from 25]. <i>K</i> denotes the number of substitutions per site. Each color represents a comparison between human and another species.</p

The length distribution of miRNA precursors in the miRBase Release 19.

<p>Most miRNA precursors were smaller than 200 nt (95.9%), with only a few over 500 nt (0.1%, most of which are plant miRNAs).</p

Evolutionary divergence of PWS-related imprinted vs. non-imprinted snoRNA gene families between the human and other mammals.

<p>(A) The evolutionary divergence of HBII-52, HBII-85, non-imprinted guide and orphan snoRNA genes between human and other species. <i>K</i> denotes the number of substitutions per site. (B) Relative sequence substitution rate between imprinted and non-imprinted snoRNA genes of eutherian mammals.</p

Statistics of imprinted snoRNA genes in the PWS locus of mammalians.

<p>Statistics of imprinted snoRNA genes in the PWS locus of mammalians.</p

Tajima’s <i>D</i> test of Euarchontoglires imprinted snoRNA gene family.

<p>Species abbreviation: HS, humans; PT, chimpanzees; RM, rhesus; MM, mice; RN, rats. The significant (<i>P</i><0.05) test results were labeled bold.</p

Birth rates of new genes among PWS-related imprinted and non-imprinted snoRNAs.

<p>Ratios of gene birth rate between imprinted and non-imprinted snoRNAs: human: 80.37; mouse: 127.91.</p