A reference genome for Trichogramma kaykai: A tiny desert-dwelling parasitoid wasp with competing sex-ratio distorters

Abstract

The tiny parasitoid wasp Trichogramma kaykai inhabits the Mojave Desert of the southwest United States. Populations of this tiny insect variably host up to two different sex-distorting genetic elements: (1) the endosymbiotic bacterium Wolbachia which induces the parthenogenetic reproduction of females, and (2) a B-chromosome, "Paternal Sex Ratio" (PSR), which converts would-be female offspring to PSR-transmitting males. We report here the genome of a Wolbachia-infected Trichogramma kaykai isofemale colony KSX58. Using Oxford Nanopore sequencing we produced a final genome assembly of 203 Mbp with 45x coverage, consisting of 213 contigs with an N50 of 1.9 Mbp. The assembly is quite complete, with 91.41% complete BUSCOs recovered: a very high score for Trichogrammatids that have been previously characterized for having high levels of core gene losses. We also report a complete mitochondrial genome for T. kaykai, and an assembly of the associated Wolbachia, strain wTkk. We identified copies of the parthenogenesis-inducing genes pifA and pifB in a remnant prophage region of the wTkk genome. The Trichogramma kaykai assembly is the highest quality genome assembly for the genus to-date and will serve as a great resource for understanding the evolution of sex and selfish genetic elements.

Keywords: B chromosome; Trichogramma kaykai; Wolbachia; selfish genetic element; sex ratio; symbiosis.

Figure 1.. Trichogramma kaykai biology.

(A) Three Trichogramma kaykai females ovipositing into host moth eggs (Ephestia kuehniella). (B) An exemplary specimen of T. kaykai (female). (C) Sex in T. kaykai is determined based on haplodiploidy, mediated by the presence or absence of Wolbachia (maternally transmitted) and the PSR chromosome (paternally transmitted). (D) The sample collection site for KSX58 and predicted geographic range of Trichogramma kaykai.

Figure 2.. Comparative genomics of Trichogramma.

(A) Whole genome phylogeny of five Trichogramma species and outgroup Phymastichus coffea (Hymenoptera: Eulophidae). Double slashes indicate branches that were shortened to half their length for ease of visualization. (B) Repetitive content of each genome, corresponding to the taxa in (A). “Other” includes rolling circles, simple repeats, and low complexity repeats.

Figure 3.. Synteny is highly conserved between T. kaykai and T. pretiosum.

Dot plot indicating syntenic regions between Trichogramma genomes. Dots are colored according to percent identity.

Figure 4.. Mitochondrial genome of Trichogramma kaykai.

Genes were annotated with MITOS2 (Bernt et al. 2013). Putative regions of rRNAs that were not correctly annotated by MITOS2 are indicated with stripes. The control region and the putative full length rRNAs were identified based on homology and gene order of other Trichogramma mitochondria (Chen et al. 2018). Transfer RNAs (tRNAs) are denoted by IPUC-IUB amino acid codes.

Figure 5.. Parthenogenesis-inducing Wolbachia strain wTkk.

(A) Maximum likelihood-based phylogeny of Wolbachia strains and Rickettsiales outgroups based on 78 core, single-copy, protein coding genes (a total of 30,477 aligned amino acid sites). (B) Gene models for a predicted remnant prophage region that contains the parthenogenesis factors pifA and pifB. Three tandem CDS were annotated as mutL, which is likely a pseudogenization of mutL due to nonsense mutations and fragmentation of the coding region into multiple open reading frames. Abbreviations: insertion element (IS), parthenogenesis inducing factor (pif), coding sequence (CDS).