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 2 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 T. kaykai isofemale colony KSX58. Using Oxford Nanopore sequencing, we produced a final genome assembly of 205 Mbp with 34× coverage, consisting of 154 contigs with an N50 of 2.2 Mbp. The assembly is quite complete, with 92.67% complete Hymenoptera 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. Finally, we identified copies of the parthenogenesis-inducing (PI) genes pifA and pifB in a remnant prophage region of the wTkk genome and compared their evolution to pifs from a suite of other PI Wolbachia. The T. kaykai assembly is one of the highest quality genome assemblies for the genus to date and will serve as a great resource for understanding the evolution of sex and selfish genetic elements.

Keywords: Wolbachia; B-chromosome; genome assembly; parthenogenesis; selfish genetic element; sex ratio; symbiosis.

Fig. 1.

Trichogramma kaykai biology. a) Three T. kaykai females ovipositing into host moth eggs (E. 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) Range map of T. kaykai. The predicted geographic range is shaded. The sample collection site for KSX58 is represented by a diamond, and other known collection locations of T. kaykai are circles. Basemap data sources: Esri, Maxar, Earthstar Geographics, and the GIS User Community, Mono County, TomTom, Garmin, FAO, NOAA, USGS, EPA, USFWS.

Fig. 2.

Comparative genomics of Trichogramma. a) Whole genome phylogeny of 5 Trichogramma species and outgroup P. 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.

Fig. 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.

Fig. 4.

Mitochondrial genome of T. 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 are denoted by IPUC-IUB amino acid codes.

Fig. 5.

PI 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, in wTkk and wTpre. c–f) Wolbachia protein divergence. Percent identity of c) FitsZ, d) Wsp, e) PifA, and f) PifB. Parthenogenesis inducing (PI) factor (pif), coding sequence (CDS).