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.
Highlights
Cell lines derived from Trichoplusia ni, the cabbage looper moth, have been used for many years to produce recombinant proteins by means of the baculovirus expression vector system (BEVS).While cell lines from other lepidopteran hosts such as Spodoptera frugiperda have commonly been used for production of baculoviruses, Trichoplusia cell lines have been shown in several cases to out-perform these cell lines for production yield and protein quality, with regard to secreted proteins [1]
All sizing and quantitation measurements were performed using the genomic kit for the TapeStation 2200 (Agilent Technologies, Santa Clara, CA, USA)
We used a combination of three technologies, including PacBio singlemolecule long-read sequencing, Bionano optical genome mapping, and 10X Genomics long linked-reads
Summary
Cell lines derived from Trichoplusia ni, the cabbage looper moth, have been used for many years to produce recombinant proteins by means of the baculovirus expression vector system (BEVS).While cell lines from other lepidopteran hosts such as Spodoptera frugiperda have commonly been used for production of baculoviruses, Trichoplusia cell lines have been shown in several cases to out-perform these cell lines for production yield and protein quality, with regard to secreted proteins [1]. Cell lines derived from Trichoplusia ni, the cabbage looper moth, have been used for many years to produce recombinant proteins by means of the baculovirus expression vector system (BEVS). One of them is the silkworm Bombyx mori, that has been published [4], while an incomplete draft genome of Spodoptera frugiperda (the host from which Sf9 and Sf21 lines were derived) is the only sequence available for the more commonly used protein production hosts [5]. 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. Ortholog searches within the superorder Holometabola provided further evidence of high accuracy and completeness of the
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