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Background  Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of  Timema cristinae  has been published to date.  Clitarchus hookeri  is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo genome assembly of a female  C. hookeri  and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large genome size in stick insects.    Results  The  C. hookeri  genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest insect genome sequenced and assembled to date. Like the large genome of  Locusta migratoria , the genome of  C. hookeri  is also highly repetitive and the predicted gene models are much longer than those from most other sequenced insect genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller  T. cristinae  genome, is the most abundant repeat type in the  C. hookeri  genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified.    Conclusions  The evolution of large insect genomes such as  L. migratoria  and  C. hookeri  genomes is most likely due to the accumulation of repetitive regions and intron elongation. MITEs contributed significantly to the growth of  C. hookeri  genome size yet are surprisingly absent from the  T. cristinae  genome. Sex-biased genes identified from gonadal tissues, including genes involved in juvenile hormone synthesis, provide interesting candidates for the further study of flexible reproduction in stick insects.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4245-x) contains supplementary material, which is available to authorized users.

bmc genomics

Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction