title: The draft genome of the pest tephritid fruit fly Bactrocera tryoni: resources for the genomic analysis of hybridising species.
abstract: BACKGROUND
  The tephritid fruit flies include a number of economically important pests of horticulture, with a large accumulated body of research on their biology and control. Amongst the Tephritidae, the genus Bactrocera, containing over 400 species, presents various species groups of potential utility for genetic studies of speciation, behaviour or pest control. In Australia, there exists a triad of closely-related, sympatric Bactrocera species which do not mate in the wild but which, despite distinct morphologies and behaviours, can be force-mated in the laboratory to produce fertile hybrid offspring. To exploit the opportunities offered by genomics, such as the efficient identification of genetic loci central to pest behaviour and to the earliest stages of speciation, investigators require genomic resources for future investigations.
  
  
  RESULTS
  We produced a draft de novo genome assembly of Australia's major tephritid pest species, Bactrocera tryoni. The male genome (650-700 Mbp) includes approximately 150 Mb of interspersed repetitive DNA sequences and 60 Mb of satellite DNA. Assessment using conserved core eukaryotic sequences indicated 98% completeness. Over 16,000 MAKER-derived gene models showed a large degree of overlap with other Dipteran reference genomes. The sequence of the ribosomal RNA transcribed unit was also determined. Unscaffolded assemblies of B. neohumeralis and B. jarvisi were then produced; comparison with B. tryoni showed that the species are more closely related than any Drosophila species pair. The similarity of the genomes was exploited to identify 4924 potentially diagnostic indels between the species, all of which occur in non-coding regions.
  
  
  CONCLUSIONS
  This first draft B. tryoni genome resembles other dipteran genomes in terms of size and putative coding sequences. For all three species included in this study, we have identified a comprehensive set of non-redundant repetitive sequences, including the ribosomal RNA unit, and have quantified the major satellite DNA families. These genetic resources will facilitate the further investigations of genetic mechanisms responsible for the behavioural and morphological differences between these three species and other tephritids. We have also shown how whole genome sequence data can be used to generate simple diagnostic tests between very closely-related species where only one of the species is scaffolded.
authors.affiliation: Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052 Australia. a.gilchrist@unsw.edu.au.
authors.forename: Anthony Stuart
authors.initials: AS
authors.lastname: Gilchrist
authors.forename: Deborah C A
authors.initials: DC
authors.lastname: Shearman
authors.forename: Marianne
authors.initials: M
authors.lastname: Frommer
authors.forename: Kathryn A
authors.initials: KA
authors.lastname: Raphael
authors.forename: Nandan P
authors.initials: NP
authors.lastname: Deshpande
authors.forename: Marc R
authors.initials: MR
authors.lastname: Wilkins
authors.forename: William B
authors.initials: WB
authors.lastname: Sherwin
authors.forename: John A
authors.initials: JA
authors.lastname: Sved
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D005260:Female; D063990:Gene Ontology; D023281:Genomics; D006824:Hybridization, Genetic; D054643:INDEL Mutation / Q000235:genetics; D008297:Male; D058977:Molecular Sequence Annotation; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D017421:Sequence Analysis; D013045:Species Specificity; D033621:Tephritidae / Q000235:genetics*