Chromosome-level genome assembly of stem borer Batocera rufomaculata using PacBio HiFi and Hi-C sequencing

Abstract

Batocera rufomaculata (Cerambycidae: Lamiinae), a prominent representative of longhorned beetles, is a globally significant stem-boring pest, infesting over 50 species of deciduous trees. Despite its substantial ecological and economic impact, the genomic basis underlying its host adaptation remain poorly understood. Here, we present a chromosome-level genome assembly of B. rufomaculata, constructed using a combination of Illumina, PacBio HiFi, and Hi-C sequencing data. The genome spans 338.08 Mb, with a scaffold N50 of 37.00 Mb, and is organized into 10 pseudo-chromosomes, including a chromosome X validated by genome collinearity and sequencing depth analyses. Repetitive elements constitute 27.89% of the genome, totaling 94.29 Mb. Out of 17,887 predicted genes, 12,729 were functionally annotated with at least one supporting evidence. The high-quality genome assembly and annotation were confirmed by multiple metrics, including genome size, reads mapping rate (>99.5%), BUSCO completeness (>97.1%), and collinearity analyses. This comprehensive genomic resource provides a foundation for investigating the ecological adaptation of B. rufomaculata and offers valuable insights into the genetic mechanisms that could inform pest management strategies.

Fig. 1

Overview of Batocera rufomaculata (Degeer, 1775). Photos and permission by Yongke Zhang and Tianqi Bai. (a) Frass holes and larval excrement around the infected trunk of Mangifera indica. (b) Emergence holes created by adult on the trunk of Mangifera indica. (c) Longitudinal section of larval galleries within the trunk of Mangifera indica. (d) Egg. (e) Pupa. (f) Adult.

Fig. 2

Assembly of the chromosome-level genome of Batocera rufomaculata. (a) The heatmap displays all interactions among 10 chromosomes. The color of the Hi-C interaction linkages represents the frequency, which ranges from yellow (low) to red (high). (b) Blocks on the outmost circle represent all 10 chromosomes. Peak plots from inner to outer circles represent gene density, repeat density, GC ratio, and the coverage of Hi-C reads, HiFi-reads, and Illumina short-reads of each chromosome, respectively (sliding window size = 50 Kb). (c) Mean sequencing depth of Illumina short-reads and PacBio HiFi-reads for each chromosome of B. rufomaculata genome. (d) Chromosome-level synteny analysis of the B. rufomaculata (Bru) and another two Cerambycidae beetles, Leptura quadrifasciata (Lqu) and Rutpela maculata (Rma).