Lessons learned about the biology and genomics of Diaphorina citri infection with “Candidatus Liberibacter asiaticus” by integrating new and archived organ-specific transcriptome data

Authors: MANN, MARINA - Cornell University; SAHA, SURYA - Boyce Thompson Institute; PITINO, MARCO - Agrosource, Inc; Moulton, Kathryn; CANO, LILIANNA - University Of Florida; Hunter, Wayne; MUELLER, LUKAS - Boyce Thompson Institute; Heck, Michelle

Submitted to: Gigascience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/16/2022
Publication Date: 4/28/2022
Citation: Mann, M., Saha, S., Pitino, M., Moulton, K.M., Cano, L., Hunter, W.B., Mueller, L.A., Heck, M.L. 2022. Lessons learned about the biology and genomics of Diaphorina citri infection with “Candidatus Liberibacter asiaticus” by integrating new and archived organ-specific transcriptome data. Gigascience. 11:1-16. https://doi.org/10.1093/gigascience/giac035.
DOI: https://doi.org/10.1093/gigascience/giac035

Interpretive Summary: Citrus greening disease is the most serious disease of citrus worldwide. The disease is caused by a bacteria that is spread from tree to tree by a tiny insect called the Asian citrus psyllid. Half of decade of research on interactions between the Asian citrus psyllid and the citrus greening pathogen relied on an incomplete version of the psyllid genome. In the past 5 years, ARS researchers have cooperated with University colleagues to generate a high quality genome sequence of this tiny and economically important insect pest which is a vast improvement over the initial genome sequencing effort. In this work, we used transcriptomics, the study of all the mRNAs produced by a cell, tissue, or organism, to probe the biology of psyllid organs involved in transmission of the citrus greening bacteria. This research allowed us to understand how the bacteria impacts the psyllid's biology and the molecular pathways involved in transmission, research that will lead to new strategies to control citrus greening disease. This research showed that improved genome assemblies influences interpretation of transcriptomic data and that investigators have reason to re-analyze their previous transcriptomic data with the new genome release. The more accurate quantification provided by the new genome may reduce the need to validate transcriptomic measurements using other methods. The study underscores the importance of arthropod genome communities and funding bodies to continue to invest funds on arthropod genome improvement projects such as i5k and Ag100Pest.

Technical Abstract: Background Huanglongbing (HLB) is the most serious disease of citrus. HLB is caused by the obligate, intracellular bacterium “Candidatus Liberibacter asiaticus” (CLas). CLas is transmitted by Diaphorina citri, the Asian citrus psyllid. Development of transmission blocking strategies to manage HLB relies on knowledge of CLas-D. citri interactions at the molecular level. Prior transcriptome analyses of CLas-infected and un-infected D. citri point to changes in psyllid biology due to CLas-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 CLas (+) and CLas (-) insects. Results Each organ had unique transcriptome profiles and responses to CLas infection. Though most psyllids were infected with CLas, CLas-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.