The 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. Genomic 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. 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. 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.

中文翻译：

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橄榄果蝇（Bactrocera oleae）基因组的从头组装，采用链读和长读技术，可将缺口最小化并提供出色的Y染色体组装

橄榄果蝇Bactrocera oleae是橄榄果农业综合企业中最重要的害虫。这是因为雌蝇将卵产在未成熟的果实上，孵化后幼虫以果实为食，从而将其破坏。缺乏高质量的基因组以及其他基因组和转录组学数据，阻碍了人们对果蝇生物学的理解以及对农药使用的替代控制方法的提出。从雄性和雌性Demokritos菌株蝇中提取基因组DNA，并在实验室中保存了45年以上。我们使用了短，伴侣对和长读测序技术来生成组合的男女基因组装配体（GenBank登录号为GCA_001188975.2）。使用10x Genomics连锁阅读技术对雄性昆虫进行基因组DNA测序，然后进行配对和长读支架和空位关闭，生成了高度连续的489 Mb基因组，其N50为4.69 Mb支架，L50为30个支架（GenBank登录号GCA_001188975 .4）。从12个组织和/或发育阶段产生的RNA-seq数据可用于基因组注释。从男性和女性的短读和染色体商方法使得能够鉴定Y-染色体支架，所述支架被PCR广泛验证。产生的高质量基因组代表了橄榄果蝇研究的关键工具。我们提供了广泛的RNA-seq数据集和基因组注释，对于深入了解橄榄果蝇的生物学至关重要。此外，