Originally sourced from Spain, Almeria. Obtained by Syngenta from Rothamsted Research in 2007.
Next Generation Sequencing
i) Illumina Hi-C sequencing 150 bp paired end data:
120,548,746 reads and 30x coverage.
ii) PacBio CLR data, of mean read length 9,693, total reads 6,484,563, read length N50 13,887, and total bases 62,856,441,162. DNA was extracted in two preparations using Zymo Insect kit and Zymo HMW kit and combined (1539ng gDNA) at the University of Georgia.
Multi-individual used for PacBio CLR (University of Georgia, USA) 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 Hi-C data using freebayes.
Public RNA-seq data was assembled into a transcriptome (BUSCO: C:98.6%[S:96.7%,D:1.9%],F:0.1%,M:1.3%) 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. 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.
Endosymbionts previously reported in NCBI (CP007563.1) Candidatus Portiera aleyrodidarum MED (357,461 bp) and (CP007563.1) Candidatus Hamiltonella defensa (Bemisia tabaci) strain MEAM1 (1,739,504 bp) were assembled with identical identity so were not submitted again.