A Chromosome-scale assemby of the Bactrocera cucurbitae genome provides insight to the genetic basis of white pupae

Authors: SIM, SHEINA - University Of Hawaii; Geib, Scott

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/17/2017
Publication Date: 6/1/2017
Citation: Sim, S., Geib, S.M. 2017. A Chromosome-scale assemby of the Bactrocera cucurbitae genome provides insight to the genetic basis of white pupae. G3, Genes/Genomes/Genetics. doi:10.1534/g3.117.040170.

Interpretive Summary: Though the genetic basis of some traits are simple, they are often largely unknown. In the case of a novel pupal color polymorphism in a genetic sexing strain of the melon fly, a major agricultural pest, it is known to be a single locus recessive trait, but the gene governing the trait and the mutation causing the polymorphism has not been characterized. In the process of characterizing this mutation, we sequenced and assembled the melon fly genome, generated a linkage map using an F4 back-cross, and further assembled the genome into chromosome-scale linkage groups. This gave us the genomic tools necessary to identify SNP loci that are tightly linked to our gene of interest and determine that gene organization is largely conserved between melon fly and the model system Drosophila melanogaster. The results of this study will be used to identify novel gene targets in this species that can be used to improve eradication efforts such as the Sterile Insect Technique.

Technical Abstract: 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.