Collected in the USA on the 27th July 2011. It was found to not be chemical resistant.
Next Generation Sequencing
i) Illumina Hi-C sequencing 150 bp paired end data:
340,568,496 reads and 31x coverage.
ii) Illumina 10X sequencing 150 bp paired end data:
468,733,082 reads and 43x coverage.
ii) Illumina RNA-seq sequencing 150 bp paired end data:
iii) PacBio CLR data, of mean read length 18,295, total reads 5,454,563, read length N50 32,151, and total bases 99,791,115,120. DNA was extracted from a 12x multi-individual sample using MagAttract (6000ng gDNA).
iiii) PacBio isoseq data, x2 smrt cells using Sequel II.
Non-sexed multi-individual DNA used for PacBio CLR (University of Leiden, Netherlands) and multi-individual for Hi-C Illumina sequencing (Arima Genomics USA). 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 10X library data using freebayes.
PGI ISO-seq (BUSCO: C:91.7%[S:34.5%,D:57.2%],F:0.9%,M:7.4%) data was 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. 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, ABC and IRAC gene models were found and curated using mapped RNA-seq and a Maker gene annotation.