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The microRNA toolkit of insects

View Article: PubMed Central - PubMed

ABSTRACT

Is there a correlation between miRNA diversity and levels of organismic complexity? Exhibiting extraordinary levels of morphological and developmental complexity, insects are the most diverse animal class on earth. Their evolutionary success was in particular shaped by the innovation of holometabolan metamorphosis in endopterygotes. Previously, miRNA evolution had been linked to morphological complexity, but astonishing variation in the currently available miRNA complements of insects made this link unclear. To address this issue, we sequenced the miRNA complement of the hemimetabolan Blattella germanica and reannotated that of two other hemimetabolan species, Locusta migratoria and Acyrthosiphon pisum, and of four holometabolan species, Apis mellifera, Tribolium castaneum, Bombyx mori and Drosophila melanogaster. Our analyses show that the variation of insect miRNAs is an artefact mainly resulting from poor sampling and inaccurate miRNA annotation, and that insects share a conserved microRNA toolkit of 65 families exhibiting very low variation. For example, the evolutionary shift toward a complete metamorphosis was accompanied only by the acquisition of three and the loss of one miRNA families.

No MeSH data available.


Expression changes due to Dicer-1 depletion in Blattella germanica expressed as ranges of fold change in log2 scale.(A) For conserved miRNAs. (B) For non-coding RNAs from regions of B. germanica genome that not contain miRNAs, used as negative control. The expression was computed as the number of reads per million reads of each feature in each library. The red line indicates the log2 fold change = 0.
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f1: Expression changes due to Dicer-1 depletion in Blattella germanica expressed as ranges of fold change in log2 scale.(A) For conserved miRNAs. (B) For non-coding RNAs from regions of B. germanica genome that not contain miRNAs, used as negative control. The expression was computed as the number of reads per million reads of each feature in each library. The red line indicates the log2 fold change = 0.

Mentions: In addition, our predictions gave 2,675 miRNA candidates with no significant similarity with any previously known miRNA. To discard false positives, we depleted Dicer-1 by RNAi, which resulted in significant reduction of miRNA levels, in general, as previously reported19. Subsequently, we prepared and sequenced two libraries from B. germanica treated with a dsRNA targeting Dicer-1, and two libraries from control specimens (treated with an unspecific dsRNA). The reads obtained from sequencing them are shown in Table 1. Then, the read counts for each arm of each miRNA candidate were recorded (Supplementary Table S2). To set the limits for discarding false positives, we considered the effects of Dicer-1 depletion on conserved miRNAs. Thus, we recorded the read counts for conserved miRNAs (Supplementary Table S3). The expression of 90% of the conserved miRNAs was reduced in some degree, whereas that of 81% of them was reduced with a log2(FC) lower than −0.5 (Fig. 1A). As a negative control, we selected 558 non-coding RNA regions and we compared the expression change of them in Dicer-1 libraries and in control libraries, which resulted in a median fold change of −0.18 (Fig. 1B). These results suggest that miRNA expression differences between control and dsDicer-1libraries are due to Dicer-1 processing of miRNA precursors and not to unspecific effects.


The microRNA toolkit of insects
Expression changes due to Dicer-1 depletion in Blattella germanica expressed as ranges of fold change in log2 scale.(A) For conserved miRNAs. (B) For non-coding RNAs from regions of B. germanica genome that not contain miRNAs, used as negative control. The expression was computed as the number of reads per million reads of each feature in each library. The red line indicates the log2 fold change = 0.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5121899&req=5

f1: Expression changes due to Dicer-1 depletion in Blattella germanica expressed as ranges of fold change in log2 scale.(A) For conserved miRNAs. (B) For non-coding RNAs from regions of B. germanica genome that not contain miRNAs, used as negative control. The expression was computed as the number of reads per million reads of each feature in each library. The red line indicates the log2 fold change = 0.
Mentions: In addition, our predictions gave 2,675 miRNA candidates with no significant similarity with any previously known miRNA. To discard false positives, we depleted Dicer-1 by RNAi, which resulted in significant reduction of miRNA levels, in general, as previously reported19. Subsequently, we prepared and sequenced two libraries from B. germanica treated with a dsRNA targeting Dicer-1, and two libraries from control specimens (treated with an unspecific dsRNA). The reads obtained from sequencing them are shown in Table 1. Then, the read counts for each arm of each miRNA candidate were recorded (Supplementary Table S2). To set the limits for discarding false positives, we considered the effects of Dicer-1 depletion on conserved miRNAs. Thus, we recorded the read counts for conserved miRNAs (Supplementary Table S3). The expression of 90% of the conserved miRNAs was reduced in some degree, whereas that of 81% of them was reduced with a log2(FC) lower than −0.5 (Fig. 1A). As a negative control, we selected 558 non-coding RNA regions and we compared the expression change of them in Dicer-1 libraries and in control libraries, which resulted in a median fold change of −0.18 (Fig. 1B). These results suggest that miRNA expression differences between control and dsDicer-1libraries are due to Dicer-1 processing of miRNA precursors and not to unspecific effects.

View Article: PubMed Central - PubMed

ABSTRACT

Is there a correlation between miRNA diversity and levels of organismic complexity? Exhibiting extraordinary levels of morphological and developmental complexity, insects are the most diverse animal class on earth. Their evolutionary success was in particular shaped by the innovation of holometabolan metamorphosis in endopterygotes. Previously, miRNA evolution had been linked to morphological complexity, but astonishing variation in the currently available miRNA complements of insects made this link unclear. To address this issue, we sequenced the miRNA complement of the hemimetabolan Blattella germanica and reannotated that of two other hemimetabolan species, Locusta migratoria and Acyrthosiphon pisum, and of four holometabolan species, Apis mellifera, Tribolium castaneum, Bombyx mori and Drosophila melanogaster. Our analyses show that the variation of insect miRNAs is an artefact mainly resulting from poor sampling and inaccurate miRNA annotation, and that insects share a conserved microRNA toolkit of 65 families exhibiting very low variation. For example, the evolutionary shift toward a complete metamorphosis was accompanied only by the acquisition of three and the loss of one miRNA families.

No MeSH data available.