Quarles, K. A. | Search bioRxiv

bioRxiv2017

Pan-arthropod analysis reveals somatic piRNAs as an ancestral TE defence

In animals, small RNA molecules termed PIWI-interacting RNAs (piRNAs) silence transposable elements (TEs), protecting the germline from genomic instability and mutation. piRNAs have been detected in the soma in a few animals, but these are believed to be specific adaptations of individual species. Here, we report that somatic piRNAs were likely present in the ancestral arthropod more than 500 million years ago. Analysis of 20 species across the arthropod phylum suggests that somatic piRNAs targeting TEs and mRNAs are common among arthropods. The presence of an RNA-dependent RNA polymerase in chelicerates (horseshoe crabs, spiders, scorpions) suggests that arthropods originally used a plant-like RNA interference mechanism to silence TEs. Our results call into question the view that the ancestral role of the piRNA pathway was to protect the germline and demonstrate that small RNA silencing pathways have been repurposed for both somatic and germline functions throughout arthropod evolution.

evolutionary biology↗

bioRxiv2017

The genome of Trichoplusia ni, an agricultural pest and novel model for small RNA biology

The cabbage looper, Trichoplusia ni (Lepidoptera: Noctuidae), is a destructive insect pest that feeds on a wide range of plants. The High Five cell line (Hi5), originally derived from T. ni ovaries, is often used for efficient expression of recombinant proteins. Here, we report a draft assembly of the 368.2 Mb T. ni genome, with 90.6% of all bases assigned to one of its 28 chromosomes and predicted 14,037 predicted protein-coding genes. Manual curation of gene families involved in chemoreception and detoxification reveals T. ni-specific gene expansions that may explain its widespread distribution and rapid adaptation to insecticides. Using male and female genome sequences, we define Z-linked and repeat-rich W-linked sequences. Transcriptome and small RNA data from T. ni thorax, ovary, testis, and Hi5 cells reveal distinct expression profiles for 295 microRNA- and >393 piRNA-producing loci, as well as 39 genes encoding core small RNA pathway proteins. siRNAs target both endogenous transposons and the exogenous TNCL virus. Surprisingly, T. ni siRNAs are not 2{acute}-O-methylated. Five piRNA-producing loci account for 34.9% piRNAs in the ovary, 49.3% piRNAs in the testis, and 44.0% piRNAs in Hi5 cells. Nearly all of the W chromosome is devoted to piRNA production: >76.0% of bases in the assembled W produce piRNAs in ovary. To enable use of the T. ni germline-derived Hi5 cell line as a model system, we have established efficient genome editing and single-cell cloning protocols. Taken together, the T. ni genome provides insights into pest control and allows Hi5 cells to become a new tool for studying small RNAs ex vivo.

genomics↗