The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology

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Abstract

We report a draft assembly of the genome of Hi5 cells from the lepidopteran insect pest, Trichoplusia ni, assigning 90.6% of bases to one of 28 chromosomes and predicting 14,037 protein-coding genes. Chemoreception and detoxification gene families reveal T. ni-specific gene expansions that may explain its widespread distribution and rapid adaptation to insecticides. Transcriptome and small RNA data from thorax, ovary, testis, and the germline-derived Hi5 cell line show distinct expression profiles for 295 microRNA- and >393 piRNA-producing loci, as well as 39 genes encoding small RNA pathway proteins. Nearly all of the W chromosome is devoted to piRNA production, and T. ni siRNAs are not 2´-O-methylated. To enable use of Hi5 cells as a model system, we have established genome editing and single-cell cloning protocols. The T. ni genome provides insights into pest control and allows Hi5 cells to become a new tool for studying small RNAs ex vivo.

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Yu Fu

Bioinformatics Program, Boston University, Boston, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-1244-9473
Yujing Yang

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States

Competing interests
The authors declare that no competing interests exist.
Han Zhang

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States

Competing interests
The authors declare that no competing interests exist.
Gwen Farley

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States

Competing interests
The authors declare that no competing interests exist.
Junling Wang

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States

Competing interests
The authors declare that no competing interests exist.
Kaycee A Quarles

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States

Competing interests
The authors declare that no competing interests exist.
Zhiping Weng

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States

For correspondence
zhiping.weng@umassmed.edu

Competing interests
The authors declare that no competing interests exist.
Phillip D Zamore

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States

For correspondence
phillip.zamore@umassmed.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-4505-9618

Funding

National Institutes of Health (GM65236)

Phillip D Zamore

Howard Hughes Medical Institute (none)

Phillip D Zamore

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

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This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.