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

Keyur Talsania; Monika Mehta; Castle Raley; Yuliya Kriga; Sujatha Gowda; Carissa Grose; Matthew Drew; Veronica Roberts; Kwong Tai Cheng; Sandra Burkett; Steffen Oeser; Robert Stephens; Daniel Soppet; Xiongfeng Chen; Parimal Kumar; Oksana German; Tatyana Smirnova; Christopher Hautman; Jyoti Shetty; Bao Tran; Yongmei Zhao; Dominic Esposito

doi:10.3390/genes10020079

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

Genes (Basel). 2019 Jan 23;10(2):79. doi: 10.3390/genes10020079.

Authors

Keyur Talsania¹, Monika Mehta², Castle Raley³, Yuliya Kriga⁴, Sujatha Gowda⁵, Carissa Grose⁶, Matthew Drew⁷, Veronica Roberts⁸, Kwong Tai Cheng⁹, Sandra Burkett¹⁰, Steffen Oeser¹¹, Robert Stephens¹², Daniel Soppet¹³, Xiongfeng Chen¹⁴, Parimal Kumar¹⁵, Oksana German¹⁶, Tatyana Smirnova¹⁷, Christopher Hautman¹⁸, Jyoti Shetty¹⁹, Bao Tran²⁰, Yongmei Zhao²¹, Dominic Esposito²²

Affiliations

¹ Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
² Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
³ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
⁴ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
⁵ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
⁶ NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
⁷ NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
⁸ NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
⁹ NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
¹⁰ Comparative Molecular Cytogenetics Core Facility, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
¹¹ Bionano Genomics, San Diego, CA 92121, USA. [email protected].
¹² NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
¹³ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
¹⁴ Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
¹⁵ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
¹⁶ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
¹⁷ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
¹⁸ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
¹⁹ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
²⁰ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
²¹ Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].
²² NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. [email protected].

Abstract

Background: Trichoplusiani 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 Trichoplusiani-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.

Keywords: PacBio single molecule real-time sequencing; Tricoplusia ni; de novo assembly; insect genome; next generation sequencing; optical mapping.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Animals
Cell Line
Contig Mapping
Genome, Insect*
High-Throughput Nucleotide Sequencing
Insect Proteins / chemistry
Insect Proteins / genetics
Lepidoptera / cytology
Lepidoptera / genetics*
Molecular Sequence Annotation*
Protein Domains
Sequence Analysis, DNA

Substances

Insect Proteins

Grants and funding

HHSN261200800001E/CA/NCI NIH HHS/United States