Supporting data for "Lessons learned about the biology and genomics of Diaphorina citri infection with “Candidatus Liberibacter asiaticus” by integrating new and archived organ-specific transcriptome data."
Dataset type: Transcriptomic
Data released on February 22, 2022
Mann M; Saha S; Cicero JM; Pitino M; Moulton K; Hunter WB; Cano L; Mueller LA; Heck M (2022): Supporting data for "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 Database. http://dx.doi.org/10.5524/102195
Huanglongbing (HLB), a devastating disease of citrus, 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 D. citri point to changes in psyllid biology due to CLas-infection but have been hampered by incomplete versions of the D. citri genome, proper host plant controls, and/or a lack of a uniform data analysis approach. Therefore, using the scaffold of the newest chromosomal length D. citri genome assembly, Diaci_v3.0, we computationally identified differentially expressed genes in both CLas (+) and CLas (-) D. citri. In this work, we present lessons learned from a quantitative transcriptome analysis of excised heads, salivary glands, midguts and bacteriomes from CLas (+) and CLas (-) insects.
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.
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.
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Additional details
Read the peer-reviewed publication(s):
(PubMed: 35482489)
Additional information:
https://citrusgreening.org/organism/Diaphorina_citri/genome
https://cgen.citrusgreening.org/expression_viewer/input
Accessions (data generated as part of this study):
BioProject:
PRJNA385527
Sample ID | Taxonomic ID | Common Name | Genbank Name | Scientific Name | Sample Attributes |
---|---|---|---|---|---|
ACP Adult Bacteriome Clas | 121845 | Asian citrus psyllid | Diaphorina citri | Description:RNA extracted from the bacteriome of a... Alternative accession-BioSample:SAMN22082298 Alternative accession-BioProject:PRJNA385527 ... + | |
ACP Adult Bacteriome Healthy | 121845 | Asian citrus psyllid | Diaphorina citri | Description:RNA extracted from the bacteriome of a... Alternative accession-BioSample:SAMN22082297 Alternative accession-BioProject:PRJNA385527 ... + | |
ACP Adult Heads Clas | 121845 | Asian citrus psyllid | Diaphorina citri | Description:RNA extracted from the heads of a pool... Alternative accession-BioSample:SAMN22082296 Alternative accession-BioProject:PRJNA385527 ... + | |
ACP Adult Heads Healthy | 121845 | Asian citrus psyllid | Diaphorina citri | Description:RNA extracted from the heads of a pool... Alternative accession-BioSample:SAMN22082295 Alternative accession-BioProject:PRJNA385527 ... + | |
ACP-Gut-Clas | 121845 | Asian citrus psyllid | Diaphorina citri | Description:RNA extracted from the midgut of a poo... Alternative accession-BioSample:SAMN06892344 Alternative accession-BioProject:PRJNA385527 ... + | |
ACP-Gut-Healthy | 121845 | Asian citrus psyllid | Diaphorina citri | Description:RNA extracted from the midgut of a poo... Alternative accession-BioSample:SAMN06892345 Alternative accession-BioProject:PRJNA385527 ... + | |
ACP Salivary Glands CLas | 121845 | Asian citrus psyllid | Diaphorina citri | Description:RNA extracted from the salivary glands... Alternative accession-BioSample:SAMN22082294 Alternative accession-BioProject:PRJNA385527 ... + | |
ACP Salivary Glands Healthy | 121845 | Asian citrus psyllid | Diaphorina citri | Description:RNA extracted from the salivary glands... Alternative accession-BioSample:SAMN22082293 Alternative accession-BioProject:PRJNA385527 ... + |