Genome assembly and annotation of the parasitoid jewel wasp Nasonia oneida

Abstract

The jewel wasp, Nasonia (Hymenoptera: Pteromalidae), is a well-established model system for evolutionary genetics and host-microbial interactions. Here, we present the genome of N. oneida, a species lacking prior genomic characterization, using 10× Genomics linked-read (400× coverage), Illumina short-read (120× coverage), and transcriptome data (30× coverage). The assembled genome size is 267 Mb, comprising 4,675 scaffolds, with a scaffold N50 of 1 Mb and 98.40% Benchmarking Universal Single-Copy Orthologues (BUSCOs) completeness score. Annotation revealed 32.29% (86.46 Mb) of repetitive sequences and 14,221 protein-coding genes. Comparative genomics of N. oneida with 15 other hymenopteran species validated the presence of 5,939 gene families shared among them, including 3643 single-copy and 2296 multicopy gene families. This study provides the first de novo assembly of N. oneida, providing a significant addition to the growing repertoire of molecular tools for comparative genomics and functional studies to understand the evolution of closely related species as well as the evolution of parasitic wasps.

Fig. 1

A representative figure of the four Nasonia species (only males shown here). From left to right: N. vitripennis, N. longicornis, N. giraulti and N. oneida. The phylogeny is modified from Werren et al. (2010).

Fig. 2

GenomeScope profile of 21-mer analysis. K-mer visualization of Illumina short-reads to estimate the genome size, heterozygosity, and repetitive content.

Fig. 3

Synteny analysis: N. oneida synteny compared with N. vitripennis (top) and N. giraulti (bottom).

Fig. 4

The distribution of shared and lineage-specific genes from different Hymenoptera species: “1:1:1” represents shared single-copy genes; “N:N:N” represents multicopy genes; “species-specific” represents unique genes from different species and “unassigned” represents genes which cannot be assigned into any gene families.

Fig. 5

Phylogenomic analysis of hymenopterans: A phylogenomic tree of N. oneida and 15 other Hymenoptera species was constructed using the maximum likelihood method with concatenated protein sequences of 3,643 single-copy orthologs with 1,000 bootstrap replicates (please see Methods for details). Numbers over the branches indicate the number of gene families showing expansion (in green) and contraction (in red).