High quality, chromosome-scale genome assemblies: Comparisons of three Diaphorina citri (Asian Citrus Psyllid) geographic populations

The Asian citrus psyllid, Diaphorina citri, is the insect vector of the causal agent of huanglongbing (HLB), a devastating bacterial disease of commercial citrus. Few genomic resources exist for D. citri. In this study, we utilized PacBio HiFi and chromatin confirmation contact (Hi-C) sequencing to sequence, assemble, and compare three high quality, chromosome-scale genome assemblies of D. citri collected from California, Taiwan, and Uruguay. Our assemblies had final sizes of 282.67 Mb (California), 282.89 Mb (Taiwan), and 266.67 Mb (Uruguay) assembled into 13 pseudomolecules – a reduction in assembly size of 41% to 45% compared to previous assemblies which we validated using flow cytometry. We identified the X chromosome in D. citri and found it to use an XX/X0 sex-determination system. Annotation of repetitive elements revealed differing repeat class content between assemblies and showed that the bulk of repeat DNA is found on chromosomes 8 through 13. We annotated between 19,083 and 20,357 protein-coding genes and orthologous clustering of these suggested Taiwan and Uruguay D. citri are more closely related. Structural variant analyses identified chromosome 1 as having the largest variation in size between assemblies. We provide new python scripts to predict and filter endogenous viral elements (EVEs), finding 30 EVEs in California, 40 EVEs in Taiwan, and 32 EVEs in Uruguay, including a large, conserved integration with a closest BLASTx hit to Diaphorina citri flavi-like virus (DcFLV). We predicted differing numbers and sizes of piwi-interacting RNA (piRNA) clusters in each assembly, identifying 29 clusters in California, 41 in Taiwan, and 11 in Uruguay. Mitochondrial haplotype networks indicate that Taiwan and Uruguay D. citri are closely related, while California is related to Florida D. citri. These high quality, chromosome-scale assemblies provide new genomic resources to researchers to further D. citri and HLB research.Funding provided by: National Institute of Food and AgricultureCrossref Funder Registry ID: http://dx.doi.org/10.13039/100005825Award Number: 2020-70029-33200Funding provided by: HLB Multi-Agency Coordination*Crossref Funder Registry ID: Award Number: AP19PPQS&T00C23