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Genome Assembly and Annotation of the Trichoplusia ni Tni-FNL Insect Cell Line Enabled by Long-Read Technologies

  1. Author:
    Talsania,Keyur
    Mehta,Monika
    Raley, Castle
    Kriga,Yuliya
    Gowda,Sujatha
    Grose,Carissa
    Drew,Matt
    Roberts,Veronica
    Cheng,Oscar
    Burkett,Sandra
    Oeser, Steffen
    Stephens,Bob
    Soppet,Daniel
    Chen, Xiongfeng
    Kumar,Parimal
    German,Oksana
    Smirnova,Tatyana
    Hautman, Christopher
    Shetty,Jyoti
    Tran,Bao
    Zhao,Yongmei
    Esposito,Dom

  2. Author Address

    NCI, Adv Biomed Computat Sci, Frederick Natl Lab Canc Res, Frederick, MD 21701 USA.NCI, Canc Res Technol Program, Frederick Natl Lab Canc Res, Frederick, MD 21701 USA.NCI, NCI RAS Initiat, Frederick Natl Lab Canc Res, Frederick, MD 21701 USA.NCI, Comparat Mol Cytogenet Core Facil, Frederick Natl Lab Canc Res, Frederick, MD 21701 USA.Bionano Genom, San Diego, CA 92121 USA.
    1. Year: 2019
    2. Date: Feb
    3. Epub Date: 2019 01 23
  2. Journal: Genes
  3. MDPI,
    1. 10
    2. 2
  5. Type of Article: Article
  6. Article Number: 79
  7. ISSN: 2073-4425
  1. Abstract:

    Background: Trichoplusia ni derived cell lines are commonly used to enable recombinant protein expression via baculovirus infection to generate materials approved for clinical use and in clinical trials. In order to develop systems biology and genome engineering tools to improve protein expression in this host, we performed de novo genome assembly of the Trichoplusia ni-derived cell line Tni-FNL. Methods: By integration of PacBio single-molecule sequencing, Bionano optical mapping, and 10X Genomics linked-reads data, we have produced a draft genome assembly of Tni-FNL. Results: Our assembly contains 280 scaffolds, with a N50 scaffold size of 2.3 Mb and a total length of 359 Mb. Annotation of the Tni-FNL genome resulted in 14,101 predicted genes and 93.2% of the predicted proteome contained recognizable protein domains. Ortholog searches within the superorder Holometabola provided further evidence of high accuracy and completeness of the Tni-FNL genome assembly. Conclusions: This first draft Tni-FNL genome assembly was enabled by complementary long-read technologies and represents a high-quality, well-annotated genome that provides novel insight into the complexity of this insect cell line and can serve as a reference for future large-scale genome engineering work in this and other similar recombinant protein production hosts.

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External Sources

  1. View Full Text
  2. DOI: 10.3390/genes10020079
  3. PMID: 30678108
  4. PMCID: PMC6409714
  5. View record in Web of Science®
  6. WOS: 000460742800008

Library Notes

  1. Fiscal Year: FY2018-2019
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