Chromosome-level genome assembly of the mirid predator Cyrtorhinus lividipennis Reuter (Hemiptera: Miridae), an important natural enemy in the rice ecosystem.

Abstract

Though the genomes of many rice herbivorous pests have recently been well characterized, little is known about the genome of their natural enemies. Here, by using the Illumina and PacBio platforms, we sequenced and assembled the whole genome of the mirid species Cyrtorhinus lividipennis Reuter (Hemiptera: Miridae), which is an economically and ecologically important natural enemy in the rice ecosystem acting as a dominant predator for planthoppers and leafhoppers in the field. Through Hi-C scaffolding, 1615scaffolds with a total size of 338.08Mb were successfully anchored onto 13 chromosomes. The assembled genome size was 345.75Mb with a final scaffold N50 of 27.58Mb. Approximately 107.51Mb of sequences accounting for 31.10% of the genome were identified as repeat elements, and 14,644 protein-coding genes were annotated. Phylogenetic analysis showed that C.lividipennis clustered with other Hemipteran species and diverged from Apolygus lucorum about 66.7million years ago. Gene families related to detoxification, environmental adaptation and digestion were analysed comparatively with other Hemipteran species, but no significant expansion or contraction was found in C.lividipennis. We also observed male meiosis in C.lividipennis, which showed a typical post-reduction of sex chromosomes and a karyotype of 2n=22+XY. As the first natural-enemy genome in the rice ecosystem, the genomic resource of C.lividipennis not only expands our understanding of the multitrophic interactions (host plant-prey-predator), but also provides a genomic basis for better understanding this dominant predator and therefore promotes sustainable rice pest management and food grain production.