Quantification of new and archived Diaphorina citri transcriptome data using a chromosomal length D. citri genome assembly reveals the vector’s tissue-specific transcriptional response to citrus greening disease

Background: Huanglongbing (HLB) is the most serious disease of citrus. HLB is caused by the obligate, intracellular bacterium “ Candidatus Liberibacter asiaticus” ( C Las). C Las is transmitted by Diaphorina citri , the Asian citrus psyllid. Development of transmission blocking strategies to manage HLB relies on knowledge of C Las- D. citri interactions at the molecular level. Prior transcriptome analyses of C Las-infected and un-infected D. citri point to changes in psyllid biology due to C Las-infection. These studies relied on incomplete versions of the D. citri genome, lacked proper host plant controls, and/or were analyzed using different statistical approaches. Therefore, we used standardized experimental and computational approaches to identify differentially expressed genes in both CLas (+) and CLas (-) D. citri. The comparative analysis utilized the newest chromosomal length D. citri genome assembly Diaci_v3. In this work, we present a quantitative transcriptome analysis of excised heads, salivary glands, midguts and bacteriomes from C Las (+) and C Las (-) insects. Results: Each organ had unique transcriptome profiles and responses to C Las infection. Though most psyllids were infected with C Las, C Las-derived transcripts were not detected in all organs. By analyzing the midgut dataset using both the Diaci_v1.1 and v3.0 D. citri genomes, we showed that improved genome assembly led to significant and quantifiable differences in RNAseq data interpretation. Conclusions: Our results support the hypothesis that future transcriptome studies on circulative, vector-borne pathogens should be conducted at the tissue specific level using complete, chromosomal-length genome assemblies for the most accurate understanding of pathogen-induced changes in vector gene expression.