. 2019 Jan 23;10(2):79.

doi: 10.3390/genes10020079.

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

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. keyur.talsania@nih.gov.
² Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. monika.mehta@nih.gov.
³ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. castleraley@gwu.edu.
⁴ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. krigay@mail.nih.gov.
⁵ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. sujatha.gowda2@nih.gov.
⁶ NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. carissa.grose@nih.gov.
⁷ NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. matt.drew@nih.gov.
⁸ NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. veronica.roberts@nih.gov.
⁹ NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. xiongfong.chen2@nih.gov.
¹⁰ Comparative Molecular Cytogenetics Core Facility, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21701, USA. sandra.burkett@nih.gov.
¹¹ Bionano Genomics, San Diego, CA 92121, USA. soeser@bionanogenomics.com.
¹² NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. stephensr@mail.nih.gov.
¹³ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. soppetdr@mail.nih.gov.
¹⁴ Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21701, USA. xiongfong.chen2@nih.gov.
¹⁵ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. parimal.kumar@nih.gov.
¹⁶ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. oksana.german@nih.gov.
¹⁷ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. tatyana.smirnova@nih.gov.
¹⁸ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. christopher.hautman@nih.gov.
¹⁹ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. jyoti.shetty@nih.gov.
²⁰ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. bao.tran@nih.gov.
²¹ Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21701, USA. yongmei.zhao@nih.gov.
²² NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. dominic.esposito@nih.gov.

PMID: 30678108
PMCID: PMC6409714
DOI: 10.3390/genes10020079

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

Keyur Talsania et al. Genes (Basel). 2019.

. 2019 Jan 23;10(2):79.

doi: 10.3390/genes10020079.

Authors

Affiliations

¹ Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21701, USA. keyur.talsania@nih.gov.
² Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. monika.mehta@nih.gov.
³ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. castleraley@gwu.edu.
⁴ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. krigay@mail.nih.gov.
⁵ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. sujatha.gowda2@nih.gov.
⁶ NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. carissa.grose@nih.gov.
⁷ NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. matt.drew@nih.gov.
⁸ NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. veronica.roberts@nih.gov.
⁹ NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. xiongfong.chen2@nih.gov.
¹⁰ Comparative Molecular Cytogenetics Core Facility, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21701, USA. sandra.burkett@nih.gov.
¹¹ Bionano Genomics, San Diego, CA 92121, USA. soeser@bionanogenomics.com.
¹² NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. stephensr@mail.nih.gov.
¹³ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. soppetdr@mail.nih.gov.
¹⁴ Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21701, USA. xiongfong.chen2@nih.gov.
¹⁵ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. parimal.kumar@nih.gov.
¹⁶ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. oksana.german@nih.gov.
¹⁷ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. tatyana.smirnova@nih.gov.
¹⁸ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. christopher.hautman@nih.gov.
¹⁹ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. jyoti.shetty@nih.gov.
²⁰ Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. bao.tran@nih.gov.
²¹ Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21701, USA. yongmei.zhao@nih.gov.
²² NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA. dominic.esposito@nih.gov.

PMID: 30678108
PMCID: PMC6409714
DOI: 10.3390/genes10020079

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.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

**Figure 1**
Genome assembly and optical maps hybrid scaffold workflow. The workflow steps for de novo assembly, hybrid scaffold, genome assembly error correction and polishing.

**Figure 2**
Gene ontology classification of the genes predicted. Gene Ontology (GO) classification of the predicted genes. Only the most abundance ones are displayed. (a) biological processes, (b) cellular components, (c) molecule functions.

**Figure 3**
Functional annotation of the Tni-FNL (*Trichoplusia ni*), *B. mori* and *D. melanogaster* results comparison. The circos plot describes the shared cellular components, molecular functions and biological processes among the three species.

**Figure 4**
BUSCO assessment results of orthologs among 10 species. Colors refer to the percentage of the complete single-copy orthologs (blue), complete duplicated orthologs (green), fragmented or incomplete orthologs (orange), and missing orthologs (red).

**Figure 5**
Phylogenetic analysis of *Trichoplusia ni* and closely related insect genomes. Phylogenetic analyses from 10 species including 6 lepidopterans. It depicts the relationship of *Trichoplusia ni* with the other nine insects. Maximum Likelihood tree based on a genome-wide one-to-one orthologs from 10 species. The scale bar denotes substitutions per site.

See this image and copyright information in PMC

References

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

Affiliations

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

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Substances

Grants and funding

LinkOut - more resources

Full Text Sources

Miscellaneous