A chromosome-level assembly of the harlequin ladybird Harmonia axyridis as a genomic resource to study beetle and invasion biology.

Abstract

The harlequin ladybird, Harmonia axyridis (Pallas), is a well-known model organism for genetic studies and is also a well-studied natural enemy used for pest control. It became an invasive species after being introduced to North America and Europe as a pest control agent. Though two genome assemblies for this insect have been previously reported, a high-quality genome assembly at the chromosome level is still not available. Here, we obtained a new chromosome-level genome assembly of H.axyridis by combining various sequencing technologies, namely Illumina short reads, PacBio long reads, 10X Genomics and Hi-C. The chromosome-level genome assembly is 423Mb with a scaffold N50 of 45.92Mb. Using Hi-C data 1,897 scaffolds were anchored to eight chromosomes. A total of 730,068 repeat sequences were identified, making up 51.2% of the assembled genome. After masking these repeat sequences, we annotated 22,810 protein-encoding genes. The X chromosome and Y-linked scaffolds were also identified by resequencing male and female genomes and calculating the male to female coverage ratios. Two gene families associated with environmental adaptation, odorant receptor and cytochrome P450, were analysed and showed no obvious expansion in H.axyridis. We successfully constructed a putative biosynthesis pathway of harmonine, a defence compound in the haemolymph of H.axyridis, which is a key factor for H.axyridis strong immunity. The chromosome-level genome assembly of H.axyridis is a helpful resource for studies of beetle biology and invasive biology.