Genomes of the willow-galling sawflies Euura lappo and Eupontania aestiva (Hymenoptera: Tenthredinidae): a resource for research on ecological speciation, adaptation, and gall induction.

Craig Michell,Saskia Wutke,Manuel Aranda,Tommi Nyman

doi:10.1093/g3journal/jkab094

Abstract

Hymenoptera is a hyperdiverse insect order represented by over 153,000 different species. As many hymenopteran species perform various crucial roles for our environments, such as pollination, herbivory, and parasitism, they are of high economic and ecological importance. There are 99 hymenopteran genomes in the NCBI database, yet only five are representative of the paraphyletic suborder Symphyta (sawflies, woodwasps, and horntails), while the rest represent the suborder Apocrita (bees, wasps, and ants). Here, using a combination of 10X Genomics linked-read sequencing, Oxford Nanopore long-read technology, and Illumina short-read data, we assembled the genomes of two willow-galling sawflies (Hymenoptera: Tenthredinidae: Nematinae: Euurina): the bud-galling species Euura lappo and the leaf-galling species Eupontania aestiva. The final assembly for E. lappo is 259.85 Mbp in size, with a contig N50 of 209.0 kbp and a BUSCO score of 93.5%. The E. aestiva genome is 222.23 Mbp in size, with a contig N50 of 49.7 kbp and a 90.2% complete BUSCO score. De novo annotation of repetitive elements showed that 27.45% of the genome was composed of repetitive elements in E. lappo and 16.89% in E. aestiva, which is a marked increase compared to previously published hymenopteran genomes. The genomes presented here provide a resource for inferring phylogenetic relationships among basal hymenopterans, comparative studies on host-related genomic adaptation in plant-feeding insects, and research on the mechanisms of plant manipulation by gall-inducing insects.

Highlights

The hyperdiverse insect order Hymenoptera includes over 153,000 described species (Aguiar et al 2013), but the true number may be ten times higher (Forbes et al 2018)
To determine how our two focal genomes fit phylogenetically with other published hymenopteran genomes, we identified benchmarking universal single copy orthologs (BUSCO) for 13 other hymenopteran species (Athalia rosae (GCF_000344095), Neodiprion lecontei (GCA_001263575), Neodiprion pinetum (GCA_004916985), Cephus cinctus (GCF_000341935), Orussus abietinus (GCF_000612105), Ormyrus nitidulus (GCA_900474335), Nasonia vitripennis (GCF_000002325), Cecidostiba fungosa (GCA_900474305), Ceciostiba semifascia (GCA_900474235), Polistes dominula (GCF_001465965), Apis mellifera (GCF_003254395), Atta cephalotes (GCF_000143395), and Solenopsis invicta (GCF_000188075)) and one outgroup (Tribolium castaneum (GCA_000002335))
The genomes of Euura lappo and Eupontania aestiva presented in this work are of good draft quality, with a contiguity and coverage comparable to previously-published hymenopteran genome assemblies

Summary

Introduction

The hyperdiverse insect order Hymenoptera includes over 153,000 described species (Aguiar et al 2013), but the true number may be ten times higher (Forbes et al 2018). A further methodological benefit follows from their haplodiploid sex determination system, which leads to the presence of haploid males, for which genome assembly is technically easier than for diploid individuals with intragenomic sequence variation. Coupling these favourable genomic features with new sequencing technologies such as 10X Genomics linked-read sequencing and MinION ONT long-read sequencing, it is becoming easier to sequence and assemble high-quality genomes of these important insects

Methods

Results

Conclusion