Pea aphid miRNAs and plasticity

Pea aphids encode dozens of miRNAs whose expression tracks phenotypic plasticity.

Source

Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum

Legeai F, Rizk G, Walsh T, et al. · BMC genomics · 2010

Study at a glance

Design: Computational / modelling — Homology, deep sequencing (~3M reads), and RT-PCR validation of pea aphid miRNAs
N: 43 putative miRNAs (33 RT-PCR validated); sequencing resource study without a sample N
Population: Acyrthosiphon pisum (pea aphid) genome and small-RNA libraries
Outcome: Predicted and validated pea aphid microRNA repertoire

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Pea aphid miRNAs and plasticity

These passages occur verbatim in the stored paper text. They support the points listed below; they do not verify every statement in the explanation.

43 putative aphid miRNAs.

In total 43 different putative aphid miRNAs showed both sequence homology and a potential hairpin structure (Additional file ).

33 validated by RT-PCR.

The expression of 33 of them was verified by RT-PCR (data not shown).

What they did

Combined homology, deep sequencing (~3M reads), and genome scans to predict miRNAs, then RT-PCR validated many and compared morphs.

43 putative miRNAs (44 precursors); 33 validated by RT-PCR; size peak at 22 nt.

The limits

Does not fully prove each miRNA’s causal target network in every morph.

Key terms

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Putative miRNAs:

Common questions

Putative miRNAs?

43.

RT-PCR validated?

33.

Deep-seq reads?

~3 million.

Mature length peak?

22 nt.