De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly

Abstract

Background: 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. Results: 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 gapclosing 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.

Separating two tightly linked species-defining phenotypes in Bactrocera with hybrid recombinant analysis

“…Parallel genomic efforts in other tephritid species (e.g. Ceratitis capitata [36], Z. cucurbitae [37], B. oleae [38]) will also provide a useful syntenic comparison between their homologous chromosomal regions amongst these species. Nevertheless, implications of our findings for fundamental questions around species boundaries and for applied issues concerned with SIT are already clear.…”

Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest

“…The olive fruit fly genome is diploid, consisting of six pairs of chromosomes which include a pair of heterochromatic sex chromosomes with the male being the heterogametic sex 15 . We recently submitted to NCBI the B. oleae genome (GenBank accession GCA_001188975.2) which was annotated using the NCBI Eukaryotic Genome Annotation Pipeline yielding the Bactrocera oleae Annotation Release 100 16 . See Supplementary materials for details of the genome and NCBI gene models.…”

The Insect Pest Control Laboratory of the Joint FAO/IAEA Programme: Ten Years (2010–2020) of Research and Development, Achievements and Challenges in Support of the Sterile Insect Technique

“…During the last few years, several initiatives have aimed at characterizing the genome of tephritid species and exploiting this in support of SIT applications. Staff of the IPCL participated in an effort to sequence the genome of C. capitata and B. oleae [ 65 , 66 ]. One of the goals was to characterize the associated microbiome and to detect potential horizontal gene transfer events, that is, bacterial genes which may have been integrated into the insect host genome.…”