MicroRNA evolution provides new evidence for a close relationship of Diplura to Insecta

Abstract

The phylogenetic interrelationships among four hexapod lineages (Protura, Collembola, Diplura and Insecta) are pivotal to understanding the origin of insects and the early diversification of Hexapoda, but they have been difficult to clarify based on the available data. In this study, we identified 91 conserved microRNA (miRNA) families from 36 panarthropod taxa, including seven newly sequenced non‐insect hexapods. We found major clade differentiation accompanied by the origin of novel miRNA families, and most miRNA clusters are conserved with a high degree of microsynteny. Importantly, we were able to identify two miRNA families unique to Hexapoda, and four miRNA families and a miRNA cluster that exist exclusively in Diplura and Insecta, suggesting a close relationship between Diplura and Insecta as well as the monophyly of Hexapoda. Combined with a phylogenetic analysis based on the presence/absence matrix of miRNA families, our study demonstrates the effectiveness of miRNA in resolving deep phylogenetic problems.

High‐quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (collembola)

“…The evolutionary divergence of miRNAs may contribute to the diversification of species (Plasterk, 2006 ). Liu et al ( 2020 ) analysed the miRNA data of FCDK based on genome data reported in this study and small RNA (sRNA) data from mixed embryos, juveniles and adults (GenBank accession no. SRP132383).…”

“…SRP308782). Based on the sRNA data and chromosomal‐level genome assemblies of FCDK and FCSH, known miRNAs with homologous genes in the miRBase 21 database (Kozomara & Griffiths‐Jones, 2014 ) were identified, and novel miRNAs were predicted according to the procedure described in Liu et al ( 2020 ). By mapping miRNA precursors to the corresponding genome using mapchart (Voorrips, 2002 ), the locations of miRNAs were recorded and compared between FCDK and FCSH.…”

“…By mapping miRNA precursors to the corresponding genome using mapchart (Voorrips, 2002 ), the locations of miRNAs were recorded and compared between FCDK and FCSH. The miRNA nomenclature followed previous studies (Fromm et al, 2015 ; Liu et al, 2020 ). The prefix MIR‐ indicates family names, and Mir‐ indicates gene names.…”

“…The evolutionary divergence of miRNAs may contribute to the diversification of species (Plasterk, 2006). Liu et al (2020) et al (2020). By mapping miRNA precursors to the corresponding genome using mapchart (Voorrips, 2002), the locations of miRNAs were recorded and compared between FCDK and FCSH.…”

Transposable element expansion and low-level piRNA silencing in grasshoppers may cause genome gigantism

“…The processed reads were compared to the Rfam [119] database using bowtie (v1.3.0) [120] to remove rRNA, tRNA, and snRNA (bowtie -f -a --best --strata -p --al --un). Bowtie was then used to identify miRNAs, with the reference sequence as the miRNA hairpin sequence of L. migratoria [121][122][123]. The remaining small RNAs were mapped to TEs and TE transcripts, of which 23-31nt aligned reads were considered TE-derived piRNAs [97,124] ( bowtie -v 3 -a reads.fa -S --al --un -f).…”