De novo chromosome-level genome assemblies and comparative genomics of tamarisk biocontrol agents: Diorhabda carinulata, D. carinata, D. elongata, and D. sublineata

Cryptic species of classical biological control agents (BCA), natural enemies from the native range of a target pest introduced for control in the invaded range, offer unique opportunities to examine the outcomes of anthropogenic translocations and secondary contact among closely related species. We generated high-quality de novo reference genomes from PacBio HiFi and Illumina Hi-C data of a single male of tamarisk beetles Diorhabda carinata, D. carinulata, D. elongata, and D. sublineata, BCA of invasive Tamarix, generated basic annotations including repeat content and conserved single-copy orthologs, and compared chromosomal synteny. Relevant gene evidence was based on RNAseq data from D. carinulata, and existing population genomic data was incorporated to identify sex chromosomes. Each of the Diorhabda assemblies were highly contiguous, including 12-14 chromosome-level scaffolds, and total assembly lengths were in agreement with flow-cytometry estimated sizes between 417-481 MB. All four Diorhabda assemblies were annotated with about 50% repeat content, which could indicate a role for transposable elements in modulating rapid evolution. Putative telomeres, centromeres, and male sex chromosomes were annotated including high repeat content. By examining synteny among conserved single-copy orthologs, we found evidence of chromosomal homology among D. carinata, D. elongata, and D. sublineata, contrasted by likely chromosomal rearrangements between D. carinulata and the other species, reflecting the current frequencies of hybridization in the introduced range. Together these assemblies and basic annotations provide insight to the outcomes of secondary contact among cryptic species and possible mechanisms of rapid evolution.