Data from: Integrating classical genetics with chromosome-scale genome assembly to characterize a genetic sexing system in Bactrocera cucurbitae (Diptera: Tephritidae)

This data supports the manuscript "Integrating classical genetics with chromosome-scale genome assembly to characterize a genetic sexing system in Bactrocera cucurbitae (Diptera: Tephritidae)". The melon fly, Bactrocera cucurbitae, is a destructive agricultural pest and is the subject of strict quarantines that are enforced to prevent its establishment outside of its current geographic range. In addition to quarantine efforts, additional control measures are necessary for its eradication in the case of invasion to agriculturally rich areas. The sterile insect technique (SIT) has been effective in the control of several invertebrate pest species, and is part of a management strategy that regulatory agencies would like to expand to other important pests such as the melon fly.

To develop an SIT program for new species, a genetic sexing strain (GSS), a strain which enables the automation of sorting males from females so that only sterile males are released, is necessary. There exists a GSS for B. cucurbitae in which pupal color is sexually dimorphic where females have a white pupal case and males have a wild type brown pupal case, but its genetic basis is largely unknown, foundational genomic tools for this species are minimal, and information on gene assembly is sparse.

In this study, the B. cucurbitae genome was sequenced, assembled, and placed into chromosome-scale linkage group using linkage information derived from ddRAD sequences from an F4 mapping population.

Using this chromosome-scale assembly and its annotated gene set, a synteny analysis showed a near-perfect relationship between chromosomes in B. cucurbitae and Muller Elements A-E in Drosophila melanogaster. The assembly and linkage map was also used to identify SNP loci very closely linked to the white pupae gene and lays the foundation for the development of this species for its release in SIT programs. This dataset presents data resources supporting this manuscript, including superscaffolding, gene annotation, orthology and synteny analysis.

• Resource Title: NCBI Genome annotations transferred to super-scaffolded assembly.

  File Name: bcucurbitae_super_scaffold.gff3_.zip

  Resource Description: Lift-over of NCBI Genome annotations onto the superscaffolded assembly. See manuscript associated with this data set for details. File included is a .gff3 (General Feature Format version 3, a file format used for describing genes and other features of DNA, RNA and protein sequences)




• Resource Title: Chain file (UCSC Genome Browser format).

  File Name: bcucurbitae.chain_.zip

  Resource Description: Chain file (UCSC Genome Browser format) for liftover of coordinates from original scaffold assembly to super-scaffold assembly. See manuscript for more details




• Resource Title: Linkage map for B. cucurbitae.

  File Name: bcucurbitae_linkage_map.txt

  Resource Description: Linkage map showing ordering of markers across B. cucurbitae genome scaffolds, placing onto chromosomes. See manuscript associated with dataset for more details.




• Resource Title: rQTL results of scoring of white pupae .

  File Name: bcucurbitae_rQTL.zip

  Resource Description: rQTL formatted results for white pupae trait. See manuscript for details. The file included is a text file with data columns.




• Resource Title: VCF formatted SNP calls .

  File Name: bcucurbitae_SNPS.zip

  Resource Description: VCF formatted SNPs from the ddRAD-seq dataset used to generate the linkage map and perform QTL analysis. See manuscript for more details




• Resource Title: OrthoMCL counts of species included in orthology analysis .

  File Name: bcucurbitae_OrthoMCL_counts.zip

  Resource Description: Counts of number of proteins in each orthogroup across all species used for OrthoMCL analysis. See manuscript for more detail. The file included is a text file with data columns.




• Resource Title: Bactrocera cucurbitae super-scaffolded assembly .

  File Name: bcucurbitae_super_scaffold.fasta_.zip

  Resource Description: Super scaffolded assembly after integration of the initial draft assembly with linkage map. See manuscript supported by this data set for more details on analysis