Hybrid Genome Assembly and Evidence-Based Annotation of the Egg Parasitoid and Biological Control AgentTrichogramma brassicae

Abstract

Trichogramma brassicae (Bezdenko) are egg parasitoids that are used throughout the world as biological control agents and in laboratories as model species. Despite this ubiquity, few genetic resources exist beyond COI, ITS2, and RAPD markers. Aided by a Wolbachia infection, a wild-caught strain from Germany was reared for low heterozygosity and sequenced in a hybrid de novo strategy, after which several assembling strategies were evaluated. The best assembly, derived from a DBG2OLC-based pipeline, yielded a genome of 235 Mbp made up of 1,572 contigs with an N50 of 556,663 bp. Following a rigorous ab initio-, homology-, and evidence-based annotation, 16,905 genes were annotated and functionally described. As an example of the utility of the genome, a simple ortholog cluster analysis was performed with sister species T. pretiosum, revealing over 6000 shared clusters and under 400 clusters unique to each species. The genome and transcriptome presented here provides an essential resource for comparative genomics of the commercially relevant genus Trichogramma, but also for research into molecular evolution, ecology, and breeding of T. brassicae.

Genome assemblies of three closely related leaf beetle species (Galerucella spp.)

“…Shared clusters between G. calmariensis and G. pusilla (16,594) account for 80.3 and 84.1% of ortholog clusters in G. calmariensis and G. pusilla respectively whereas the shared regions of either G. calmariensis and G. pusilla with G. tenella account for less than 75% of their clusters. Ortholog clusters unique to a single species account for 6.09, 3.87, and 8.11% of the entire cluster set for G. calmariensis , G. pusilla , and G. tenella , which indicates divergent regions between species ( Ferguson et al 2020 ). The inflated numbers of singleton clusters in G. tenella may be due to the high duplication levels in the genome, as BUSCO detected 33.1% complete duplicated BUSCOs in G. tenella .…”

Molecular Characterization of Donacia provosti (Coleoptera: Chrysomelidae) Larval Transcriptome by De Novo Assembly to Discover Genes Associated with Underwater Environmental Adaptations

“…However, we identified 494 clusters that were uniquely present to D. provosti larval transcriptome data compared with other species. The unique clusters could be novel proteins, evidence of unique horizontal gene transfer, or pseudogenes [ 29 ]. The unique genes are often associated with the individual’s unique phenotype, such as adaptability to a specific environment or unique disease resistance.…”

Genome Assembly and Comparative Analysis of the Egg Parasitoid Wasp Trichogramma dendrolimi Shed Light on the Composition and Evolution of Olfactory Receptors and Venoms

“…Since the first three Nasonia species’ genomes initiated a new era of genomic studies of parasitoid wasps [ 18 ], an increasing number of parasitoid wasps have been whole-genome sequenced, due to their unique haplodiploid mating system and development of revolutionary sequencing technologies [ 19 ]. To the best of our knowledge, two draft Trichogramma genomes have been published to date, including T. pretiosum and T. brassicae [ 20 , 21 ]. The genomic study on T. pretiosum showed that its specialized egg parasitoid lifestyle and adaptation to miniaturization may be due to the rapid evolution of its genome [ 20 ].…”