July 7, 2019  |  

De novo genome assembly of the olive fruit fly (Bactrocera oleae) developed through a combination of linked-reads and long-read technologies

Authors: Djambazian, Haig and Bayega, Anthony and Tsoumani, Konstantina T and Sagri, Efthimia and Gregoriou, Maria-Eleni and Giorda, Kristina and Tsiamis, George and Bourtzis, Kostas and Oikonomopoulos, Spyridon and Dewar, Ken and Church, Deanna and Mathiopoulos, Kostas D and Ragoussis, Jiannis

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.

Journal: BioRxiv
DOI: 10.1101/505040
Year: 2018

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