A high‐quality chromosome‐level genome assembly of a generalist herbivore, Trichoplusia ni

Abstract

The cabbage looper, Trichoplusia ni, is a globally distributed highly polyphagous herbivore and an important agricultural pest. T. ni has evolved resistance to various chemical insecticides, and is one of the only two insect species that have evolved resistance to the biopesticide Bacillus thuringiensis (Bt) in agricultural systems and has been selected for resistance to baculovirus infections. We report a 333‐Mb high‐quality T. ni genome assembly, which has N50 lengths of scaffolds and contigs of 4.6 Mb and 140 Kb, respectively, and contains 14,384 protein‐coding genes. High‐density genetic maps were constructed to anchor 305 Mb (91.7%) of the assembly to 31 chromosomes. Comparative genomic analysis of T. ni with Bombyx mori showed enrichment of tandemly duplicated genes in T. ni in families involved in detoxification and digestion, consistent with the broad host range of T. ni. High levels of genome synteny were found between T. ni and other sequenced lepidopterans. However, genome synteny analysis of T. ni and the T. ni derived cell line High Five (Hi5) indicated extensive genome rearrangements in the cell line. These results provided the first genomic evidence revealing the high instability of chromosomes in lepidopteran cell lines known from karyotypic observations. The high‐quality T. ni genome sequence provides a valuable resource for research in a broad range of areas including fundamental insect biology, insect‐plant interactions and co‐evolution, mechanisms and evolution of insect resistance to chemical and biological pesticides, and technology development for insect pest management.

Transcriptional Responses of the Trichoplusia ni Midgut to Oral Infection by the Baculovirus Autographa californica Multiple Nucleopolyhedrovirus

“…), the midguts were excised and pooled (6 larval midguts per replicate, 3 replicates per time point) and used for isolation of poly(A) mRNA and construction of strand-specific RNA sequencing (ssRNA-Seq) libraries for Illumina sequencing. From each replicate sample, we mapped cleaned reads to the T. ni reference genome (14,384 genes) (15). Previously, we also estimated viral reads in each T. ni midgut sample by similarly mapping cleaned reads to the AcMNPV genome (156 genes) (NCBI accession no.…”

“…Graph Level 4 Pie Chart of #Seqs [Biological Process] regulation of macromolecule metabolic process (10) regulation of primary metabolic process (10) regulation of cellular metabolic process (12) organonitrogen compound metabolic process (15) cellular macromolecule metabolic process (15) heterocycle metabolic process (17) nucleobase-containing compound metabolic process (17) cellular nitrogen compound metabolic process (19) cellular aromatic compound metabolic process (19) organic substance biosynthetic process (19) macromolecule metabolic process (41) transport (33) protein metabolic process (21) organic cyclic compound metabolic process (19) oxidation-reduction process (19) cellular biosynthetic process (19)…”

A haplotype-resolved,de novogenome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

“…Quality comparisons were conducted against an assembly of unbinned data from the same F1 offspring (iArcPla.wtdbg2), and against a representative selection of published lepidopteran reference genomes. For this, the latest versions of seven Lepidoptera species were downloaded: Bicyclus anynana version 1.2 [30], Danaus plexippus version 3 [31], Heliconius melpomene version Hmel.2.5 [32], Manduca sexta version Msex_1.0 [33] and Melitaea cinxia version MelCinx1.0 [34] were downloaded from Lepbase version 4.0 [11], whilst Bombyx mori version Bomo_genome_assembly [35] was downloaded from SilkBase version 2.1 [36] and Trichoplusia ni version PPHH01.1 [37] was downloaded from NCBI RefSeq version 94 [38]. Cumulative scaffold plots were visualised in R version 3.5.1 [39] using the ggplot2 package version 3.1.1 [40].…”

Genetic engineering approaches to improve posttranslational modification of biopharmaceuticals in different production platforms

“…For the production of recombinant biopharmaceuticals, insect cells are used in combination with baculovirus infection building the baculovirus-insect cell system (BICS) (Cox, 2012;Maghodia, Geisler, & Jarvis, 2016). Trichoplusia ni from cabbage looper or the "gold genomes (Chen et al, 2019;Nandakumar, Ma, & Khan, 2017). Since BICS is a "plug-and-play" system in which only the baculovirus vector has to be modified for each product prior to transduction of the insect cells, BICS is flexible, fast, and simple to use (Cox, 2012;Maghodia et al, 2016).…”

“…the production of recombinant biopharmaceuticals, insect cells are used in combination with baculovirus infection building the baculovirus-insect cell system (BICS)(Cox, 2012;Maghodia, Geisler, & Jarvis, 2016). Recently, efforts in whole-genome sequencing of insect cells were made resulting in the decoding of the Sf (451 Mb) as well as Trichoplusia ni (333 Mb)genomes(Chen et al, 2019;Nandakumar, Ma, & Khan, 2017). Recently, efforts in whole-genome sequencing of insect cells were made resulting in the decoding of the Sf (451 Mb) as well as Trichoplusia ni (333 Mb)genomes(Chen et al, 2019;Nandakumar, Ma, & Khan, 2017).…”