Abstract
BackgroundThe olive fruit fly, Bactrocera oleae, is the most important pest in the olive fruit agribusiness industry. This is because female flies lay their eggs in the unripe fruits and upon hatching the larvae feed on the fruits thus destroying them. The lack of a high-quality genome and other genomic and transcriptomic data has hindered progress in understanding the fly’s biology and proposing alternative control methods to pesticide use.ResultsGenomic DNA was sequenced from male and female Demokritos strain flies, maintained in the laboratory for over 45 years. We used short-, mate-pair-, and long-read sequencing technologies to generate a combined male-female genome assembly (GenBank accession GCA_001188975.2). Genomic DNA sequencing from male insects using 10x Genomics linked-reads technology followed by mate-pair and long-read scaffolding and gap-closing generated a highly contiguous 489 Mb genome with a scaffold N50 of 4.69 Mb and L50 of 30 scaffolds (GenBank accession GCA_001188975.4). RNA-seq data generated from 12 tissues and/or developmental stages allowed for genome annotation. Short reads from both males and females and the chromosome quotient method enabled identification of Y-chromosome scaffolds which were extensively validated by PCR.ConclusionsThe high-quality genome generated represents a critical tool in olive fruit fly research. We provide an extensive RNA-seq data set, and genome annotation, critical towards gaining an insight into the biology of the olive fruit fly. In addition, elucidation of Y-chromosome sequences will advance our understanding of the Y-chromosome’s organization, function and evolution and is poised to provide avenues for sterile insect technique approaches.
Highlights
The olive fruit fly, Bactrocera oleae, is the most important pest in the olive fruit agribusiness industry
The high-quality genome generated represents a critical tool in olive fruit fly research
We provide an extensive RNA-seq data set, and genome annotation, critical towards gaining an insight into the biology of the olive fruit fly
Summary
The olive fruit fly, Bactrocera oleae, is the most important pest in the olive fruit agribusiness industry. Non-model insects or insects with less important public health or global agricultural impact had a much harder time having their whole genomes sequenced. This held back several advances that would be based on understanding their genomes, including tools for developing alternative pest control methods. In 2011, the “i5k” initiative was launched to provide the genomic sequences of 5000 insect or related arthropod species [3]. In this project, the onus was placed on individual labs with a specific interest in these genomes to organize the sequencing, analysis, and curation of their genomes [4]. As of March 2019, only 1219 insect genomes had been registered in the National Center for Biotechnology Information (NCBI) and only 401 of them have had at least a draft genome assembly [5]
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