Characterization of the Asian citrus psyllid transcriptome

Authors: REESE, JUSTIN - Reese Consulting, Ltd; CHRISTENSON, MATTHEW - Valmont Industries, Inc; LENG, NAN - Illumina, Inc; SAHA, SURYA - Cornell University; CANTAREL, BRANDI - Reese Consulting, Ltd; LINDEBERG, MAGDALEN - Cornell University; TAMBORINDEGUY, CECILIA - Texas A&M University; MACCARTHY, JUSTIN - Reese Consulting, Ltd; WEAVER, DANIEL - Reese Consulting, Ltd; TREASE, ANDREW - University Of Nebraska; READY, STEVEN - University Of Nebraska; DAVIS, VINCENT - Heteroskedastic, Llc; MCCORMICK, COURTNEY - Illumina, Inc; HAUDENSCHILD, CHRISTIAN - Illumina, Inc; HAN, SHUNSHENG - Los Alamos National Research Laboratory; JOHNSON, SHANNON - Los Alamos National Research Laboratory; Shelby, Kent; HUANG, HONG - University Of South Florida; BEXTINE, BLAKE - University Of Texas; Shatters, Robert - Bob; Hall, David; DAVIS, PAUL - University Of Nebraska; Hunter, Wayne

Submitted to: Journal of Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/2/2013
Publication Date: 10/11/2013
Citation: Reese, J., Christenson, M.K., Leng, N., Saha, S., Cantarel, B., Lindeberg, M., Tamborindeguy, C., MacCarthy, J., Weaver, D., Trease, A.J., Ready, S.V., Davis, V.M., Mccormick, C., Haudenschild, C., Han, S., Johnson, S.L., Shelby, K., Huang, H., Bextine, B.R., Shatters, R.G., Hall, D.G., Davis, P.H., Hunter, W.B. 2013. Characterization of the Asian citrus psyllid transcriptome. Journal of Genomics. 2:54-58.
DOI: https://doi.org/10.7150/jgen.7692

Interpretive Summary: The first transcriptome of a psyllid species was completed. The transcriptome identifies the sequences of the active genes being expressed inside the insect. The Asian citrus psyllid (Diaphorina citri Kuwayama) threatens the citrus industry sustainability due to extensive economic damage as a vector of plant pathogens, specifically citrus greening disease, known as Huanglongbing. Being the first psyllid to have such extensive examination of its genome provides new information on the developmental aspects of gene regulation during development. To support basic research on psyllids, the transcriptome of the Asian citrus psyllid was characterized. Approximately 137 million Illumina paired-end reads were generated from Ribonucleic acid (RNA) isolated from the psyllid tissues from eggs, nymphs and adults. Transcriptomes were constructed from all Riboonucleic acid (RNA) sequence data, which identified developmental stage-specific transcripts for eggs, nymphs and adult tissues. These data were used to expand phylogenetic comparisons within the Psyllidae family and related Insecta taxa, plus to characterize genetic homologs, co-activators and chromatin remodeling complexes. Our sequencing strategy provided a microbiota sequence data, allowing comparison of the classes of microbes inside these psyllids. Gene functions were predicted using Gene Ontology, Eukaryotic Orthologous Group and Kyoto Encyclopedia of Genes and Genomes software tools. The data presented here provide support for ongoing research examining psyllid biology and pathogen transmission, and permits the development of innovative pest and disease management strategies, such as RNA interference, and paratransgenesis of the microbes that live inside of psyllids. These results will aid the current efforts to reduce the economic damage caused by D. citri, setting the foundation for future work on other Psyllidae species.

Technical Abstract: The Asian citrus psyllid (Diaphorina citri Kuwayama) and other psyllids are important agricultural pests that cause extensive economic damage by feeding and as vectors of plant pathogens. No psyllid genomes have been characterized, and little is known about the composition of psyllid genomes or the developmental aspects of gene regulation during development. To support basic research on psyllids, the transcriptome of the Asian citrus psyllid was characterized. Approximately 137 million Illumina paired-end reads were generated from RNA isolated from the psyllid tissues from eggs, nymphs and a mixed collection of adults. A de novo transcriptome was constructed from all RNA sequence data, as well as developmental stage-specific de novo transcriptome assemblies for whole egg, nymph and adult tissues. These data were used to provide phylogenetic context of the Psyllidae within related Insecta taxa, and to characterize homologs, stage specific transcripts, simple repeat sequences, transcription factors, co-activators and chromatin remodeling complexes. Our sequencing strategy provided a plethora of D. citri microbiota sequence data, allowing a metagenomic comparison of abundance of general classes of microbes in the organism throughout development. The functions of thousands of D. citri genes were predicted using Gene Ontology, Eukaryotic Orthologous Group and Kyoto Encyclopedia of Genes and Genomes tools. Finally, insecticide-related genes were identified, including insecticide targets and genes involved in detoxification and resistance and xenobiotic metabolism genes. The data presented here provide support for ongoing research examining psyllid biology and pathogen transmission, and permit the development of innovative pest and disease management strategies, such as RNA interference, and paratransgenesis of the microbes that live inside of psyllids. These results will aid the current efforts to ameliorate the economic damage caused by D. citri, setting the foundation for future work on other Psyllidae species.