1. Chromosomes and Gene Expression
  2. Genetics and Genomics
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The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology

  1. Yu Fu
  2. Yujing Yang
  3. Han Zhang
  4. Gwen Farley
  5. Junling Wang
  6. Kaycee A Quarles
  7. Zhiping Weng  Is a corresponding author
  8. Phillip D Zamore  Is a corresponding author
  1. Boston University, United States
  2. University of Massachusetts Medical School, United States
Research Article
  • Cited 22
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Cite this article as: eLife 2018;7:e31628 doi: 10.7554/eLife.31628

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.

Article and author information

Author details

  1. Yu Fu

    Bioinformatics Program, Boston University, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1244-9473
  2. Yujing Yang

    RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Han Zhang

    RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Gwen Farley

    RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Junling Wang

    RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Kaycee A Quarles

    RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. 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.
  8. 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.
    ORCID icon "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.

Reviewing Editor

  1. David Baulcombe, University of Cambridge, United Kingdom

Publication history

  1. Received: September 1, 2017
  2. Accepted: January 26, 2018
  3. Accepted Manuscript published: January 29, 2018 (version 1)
  4. Version of Record published: March 9, 2018 (version 2)

Copyright

© 2018, Fu et al.

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.

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