Adult stage: Collected June 2021 Syngenta research campus in Stein (collected in Switzerland/Aargau)
larval stage: Collected May 2021 i2L Research Ltd (collected in the UK).
Next Generation Sequencing
Adult stage sample used in PacBio HiFi sequencing.
i) Illumina Omni-C (Dovetail) sequencing 150 bp paired end data:
438,460,378 reads and ~20x coverage.
ii) Illumina RNA-seq stranded sequencing 150 bp paired end data, totalling 52,326,278 reads.
iii) PacBio HiFi data, of mean read length 12,963, total reads 4,549,23, read length N50 12,679, and total bases 58,971,308,893. DNA was extracted using the Qiagen Kit.
Dovetail pipeline - HiFiasm, purging and Omni-C. No Mt or bacteria assembled.
Rothamsted Pipeline - HiFiasm, purging. Mitochondria, Acinetobacter and Entomomonas assembled. Due to duplication present I had issues to get Hi-C step to work but using Juicer and 3d-dna should work well and if can scaffold and then remove duplication then should end up better than dovetail assembly, as the BUSCO is better.