PT - JOURNAL ARTICLE AU - Haig Djambazian AU - Anthony Bayega AU - Konstantina T. Tsoumani AU - Efthimia Sagri AU - Maria-Eleni Gregoriou AU - Kristina Giorda AU - George Tsiamis AU - Kostas Bourtzis AU - Spyridon Oikonomopoulos AU - Ken Dewar AU - Deanna Church AU - Kostas D. Mathiopoulos AU - Jiannis Ragoussis TI - <em>De novo</em> genome assembly of the olive fruit fly (<em>Bactrocera oleae</em>) developed through a combination of linked-reads and long-read technologies AID - 10.1101/505040 DP - 2018 Jan 01 TA - bioRxiv PG - 505040 4099 - http://biorxiv.org/content/early/2018/12/26/505040.short 4100 - http://biorxiv.org/content/early/2018/12/26/505040.full AB - Long-read sequencing has greatly contributed to the generation of high quality assemblies, albeit at a high cost. It is also not always clear how to combine sequencing platforms. We sequenced the genome of the olive fruit fly (Bactrocera oleae), the most important pest in the olive fruits agribusiness industry, using Illumina short-reads, mate-pairs, 10x Genomics linked-reads, Pacific Biosciences (PacBio), and Oxford Nanopore Technologies (ONT). The 10x linked-reads assembly gave the most contiguous assembly with an N50 of 2.16 Mb. Scaffolding the linked-reads assembly using long-reads from ONT gave a more contiguous assembly with scaffold N50 of 4.59 Mb. We also present the most extensive transcriptome datasets of the olive fly derived from different tissues and stages of development. Finally, we used the Chromosome Quotient method to identify Y-chromosome scaffolds and show that the long-reads based assembly generates very highly contiguous Y-chromosome assembly.JR is a member of the MinION Access Program (MAP) and has received free-of-charge flow cells and sequencing kits from Oxford Nanopore Technologies for other projects. JR has had no other financial support from ONT.AB has received re-imbursement for travel costs associated with attending Nanopore Community meeting 2018, a meeting organized my Oxford Nanopore Technologies.