Insecticide susceptible. Originally collected in France 2008 or earlier.
Next Generation Sequencing
i) Illumina 10X genomics 150 bp paired end data:
317,918,028 reads, 47,687,704,200 bp.
ii) PacBio CLR data, of mean read length 6,645, total reads 64,063,006, read length N50 7,580, and total bases 424,109,366,461. DNA was extracted at Rothamsted Research using a MagAttract kit (4500ng gDNA).
Single individual DNA used for PacBio CLR (University of Georgia) and 10X genomics sequencing (Georgia genomics). Falcon was used to assemble the PacBio CLR, with Juicer then 3d-dna using Hi-C data for chromosome level assembly. Haplotigs were removed (purge_haplotigs). Manual curation was done to bring the genome together and check for miss-assemblies. Unmapped reads were mapped back to the original assembly to check for missing sequence and incorporated into the final assembly. Error correction was done with Illumina Hi-C data using freebayes.
Public RNA-seq transcriptome assembly BUSCO: C:97.7%[S:70.6%,D:27.1%],F:0.9%,M:1.4% using PRJNA472074 (adult), PRJNA494427 (abdominal sternites of adult male), PRJNA512480 (a dult antennae and mouthparts), PRJNA533834 (salivary glands), PRJNA557118 (4 midgut compartments and carcass) and used in the Maker2 annotation pipeline with trained Augustus and Genemark gene predictors. PASA was used to update the gene models to add UTR, correct existing models and add isoforms. PASA was used to update the gene models to add UTR, correct existing models and add isoforms. Non-coding RNA was annotated using Infernal v1.1.4.
A Pfam genomic track was created by converting to six reading frames and utilizing hmmer to identify loci of interest i.e. P450 pfam domains on the genome. Using this information, loci of interest including UDP, P450, and ABC gene models were found and curated using mapped RNA-seq.
Two endosymbionts were assembled and submitted, a Pantoea sp. 1,386,240bp, and Yokenella regensburgei as three contigs 4,360,201bp.