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

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.

Structural Insights into the SPRED1-Neurofibromin-KRAS Complex and Disruption of SPRED1-Neurofibromin Interaction by Oncogenic EGFR

“…Bacteria were cultured in Dynamite medium for protein expression ( Taylor et al, 2017 ). SPRED1 was expressed in the baculovirus expression vector system using Tni-FNL cells ( Talsania et al, 2019 ).…”

De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly

“…Pooling and Illumina sequencing of all barcoded oligos and computationally linking all oligos taken from the same DNA molecule using the bespoke Supernova assembly tool [20] provides a new powerful approach for using short-read technologies in de novo genome assembly. This method has previously been applied to insect genomes with varying levels of success [21,22]. This is probably partly because this entire methodology is optimized around human genomes and genomes of similar size, while for genomes of significantly smaller sizes, optimization of assembly parameters is needed [20].…”

Monitoring Insect Transposable Elements in Large Double-Stranded DNA Viruses Reveals Host-to-Virus and Virus-to-Virus Transposition

“…Though our earlier study identified Tni_contig_27 and Tni_contig_21 into AcMNPV genomes purified from T. ni larvae, we were unable to trace the origin of these TEs because no WGS was available for T. ni at the time ( Gilbert et al 2016 ). A BlastN similarity search for these TEs against the two now available T. ni genomes ( Chen et al 2019 ; Talsania et al 2019 ) revealed no hit. This result suggested the presence of Tni_contig_27 and Tni_contig_21 in the G0 AcMNPV population purified from T. ni larvae did not result from transposition of TEs located in the T. ni genome.…”