Chromosome-Scale Genome Assembly of the Solitary Parasitoid Wasp Microplitis manilae Ashmead, 1904 (Braconidae: Microgastrinae)

Abstract

Parasitoid wasps are invaluable natural enemies extensively used to control coleopteran, dipteran, and lepidopteran pests in agriculture and forestry owing to their killing and reproductive actions on hosts. The important larval endoparasitoid wasp Microplitis manilae, which belongs to the Microgastrinae subfamily, parasitizes the larval stages of Spodoptera spp., such as Spodoptera litura and Spodoptera frugiperda. The absence of a genomic resource for M. manilae has impeded studies on chemosensory- and detoxification-related genes. This study presents a chromosome-level genome assembly of M. manilae with a genome size of 293.18 Mb, which includes 222 contigs (N50 size, 7.58 Mb) and 134 scaffolds (N50 size, 27.33 Mb). A major proportion of the genome (284.76 Mb; 97.13%) was anchored to 11 pseudochromosomes with a single-copy BUSCO score of 98.4%. Furthermore, 14,316 protein-coding genes, 165.14 Mb (57.99%) repetitive elements, and 871 noncoding RNAs were annotated and identified. Additionally, a manual annotation of 399 genes associated with chemosensation and 168 genes involved in detoxification was conducted. This study provides a valuable and high-quality genomic resource to facilitate further functional genomics research on parasitoid wasps.

Keywords: bitter receptors; chemosensory- and detoxification-related genes; comparative genomics; gene annotation; gene family evolution; hymenoptera.

Fig. 1.

The genomic characteristics of Microplitis manilae. (a) Hi-C contact map showing the interactions among 11 pseudochromosomes. (b) Circos graph of the genome characteristics of M. manilae. Element distribution in 100 kb sliding windows, from outer to inner circles: length of 11 chromosomes, GC content, density of protein-coding genes, DNA transposons, SINE/LINE/LTR retrotransposons, and simple repeats. (c) Chromosomal synteny blocks between M. manilae and Cotesia glomerata/Aphidius gifuensis. The Mman8 and Mman11 had better syntenic relationships with Cglo8 and Cglo9, respectively. The abbreviations “Mman,” “Cglo,” and “Agif” indicate chromosomes of M. manilae, C. glomerata, and Aph. gifuensis.