Variability assessment of 14 SSR loci of <i>Chamelea gallina</i>.

<p>Variability, expressed in terms of number of different alleles, was assessed on 12 individuals collected in Chioggia in 2010 (off Venice lagoon, Italy). The table reports the name of each locus, taken from the contig number, the repeat content, the forward (F) and reverse (R) primer sequences, the fluorescent label, the annealing temperature (Ta) of PCR amplification, the size range of amplified fragments in bp, the allelic range in repeats, the number of alleles (Na) detected and the Hardy-Weinberg probability (pHWE). Significant p-values in bold (α = 0.05). Mean values for allele number, observed and expected heterozygosity are reported in the last row. Standard Deviation is reported in brackets (± SD).</p>*<p>Loci putatively affected by null alleles following MICRO-CHECKER 2.2.3. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044185#pone.0044185-vanOosterhout1" target="_blank">[51]</a>.</p>a<p>p-values were calculated based on a limited number of individuals (n = 12).</p

<i>Chamelea gallina</i> SSR mining results.

<p>The table reports the main results provided by MISA for SSR detection.</p

Set of annotated contigs of <i>Chamelea gallina</i> trascriptome with nucleotide and protein BLAST hits.

<p>The Venn diagram reports the intersection between number of contigs with BLAST hits in nr protein and nt nucleotide databases.</p

Summary of SSR types and frequency in <i>Chamelea gallina</i> transcriptome.

<p>Summary of SSR types and frequency in <i>Chamelea gallina</i> transcriptome.</p

Length and quality of <i>Chamelea gallina</i> transcriptome contigs.

<p>Panel histograms report the contig's length (a) and average quality (b) distribution, while panel c shows the relationship between length and quality.</p

Putative SNPs identified from <i>Chamelea gallina</i> transcriptome database.

<p>More than 20,000 SNPs were identified out of 36,422 contigs and meta-contigs.</p

ChameleaBase.

<p>The screenshots report the <i>Chamelea gallina</i> database online version homepage (on the upper right side), the search facility (bottom right) and an example of the gene-like entry (on the left).</p

Differential expression of 3’-moR-128-2 in PMF (n = 3) vs CTR (3) cells.

<p>A) moR expression in PMF and CTR CD34+ according to RNA-seq data. B) RT-PCR expression (RQ) in CD34+ cells from independent cohort of normal controls (n = 8) and of PMF (20) samples. C) RT-PCR expression (RQ) in granulocytes from independent cohort of normal controls (n = 10) and of PMF (50) samples; ***, ** and * indicate respectively a p-value <0.001, <0.01 or <0.05.</p

Putative targets of 3’-moR-128-2 variants in the “Regulatory RNA” pathway.

<p>Putative targets of 3’-moR-128-2 variants in the “Regulatory RNA” pathway.</p

Origin, sequence variability, and relations beween 3’-moR-128-2 and the adjacent miR-128-3p.

<p>A) 3’-moR-128-2 and miR-128-3p map to the same locus and both shows sequence variability (isomiRs and isomoRs). Both the major and the minor isomoRs are found in normal CD34+ cells and not in PMF samples. Red and blue colors indicate isomiR and isomoR groups that can be produced with an unique sequence cutting sites. The most expressed isomoR is not associated to the corresponding most expressed isomiR. Moreover, expression levels, in CTR and PMF samples, of isomiRs and isomoRs are poorly correlated intragroup. These observations, point against the moRNA being simply a by-product of the miRNA biogenesis. A similar indication is given by the fact that some abundant isomiRs are not associated to detected isomoR sequences. B) 3’-moR-128-2 and miR-128-3p have different, poorly overlapping, sets of predicted targets. C) 3’-moR-128-2 sequence can stably bind a target site in the 3’UTR of the RAN mRNA, causing post transcriptional silencing.</p