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

Abstract

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.