Multi-individual clonal population. In culture at Bayer since 2001, originally collected from greenhouse cucumber (Hohenheim, Germany).
Next Generation Sequencing
i) Illumina Hi-C sequencing 150 bp paired end data:
475,901,602 reads and 219x coverage.
ii) Illumina 10X sequencing 150 bp paired end data:
519,690,998 reads and 239x coverage.
iii) PacBio CLR data using low input protocol after sample bead clean-up (~50% contaminated with myzus persicae), of mean read length 9,349, total reads 2,606,695, read length N50 17,236, and total bases 24,371,365,388. DNA was extracted using DNAzol at Rothamsted Research (1250ng gDNA).
Non-sexed multi-individual DNA (mixed species sample with Myzus persicae) used for low input 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). Aphis contigs were selected using uncontaminated Illumina reads mapped to the assembly. Manual curation was done to bring the genome together and check for miss-assemblies. Error correction was done with Illumina 10X library data using pilon.
PGI RNA-seq data was assembled into a transcriptome (BUSCO: C:96.0%[S:75.6%,D:20.4%],F:0.7%,M:3.3%) 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.
An endosymbiont previously reported in NCBI (CP056771.1) Buchnera aphidicola (628,098 bp) was assembled with identical identity so was not submitted again.