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

DOI10.5524/102195

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.

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 IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
ACP Adult Bacteriome Clas121845 Asian citrus psyllidDiaphorina citri Description:RNA extracted from the bacteriome of a...
Alternative accession-BioSample:SAMN22082298
Alternative accession-BioProject:PRJNA385527
...
+
ACP Adult Bacteriome Healthy121845 Asian citrus psyllidDiaphorina citri Description:RNA extracted from the bacteriome of a...
Alternative accession-BioSample:SAMN22082297
Alternative accession-BioProject:PRJNA385527
...
+
ACP Adult Heads Clas121845 Asian citrus psyllidDiaphorina citri Description:RNA extracted from the heads of a pool...
Alternative accession-BioSample:SAMN22082296
Alternative accession-BioProject:PRJNA385527
...
+
ACP Adult Heads Healthy121845 Asian citrus psyllidDiaphorina citri Description:RNA extracted from the heads of a pool...
Alternative accession-BioSample:SAMN22082295
Alternative accession-BioProject:PRJNA385527
...
+
ACP-Gut-Clas121845 Asian citrus psyllidDiaphorina citri Description:RNA extracted from the midgut of a poo...
Alternative accession-BioSample:SAMN06892344
Alternative accession-BioProject:PRJNA385527
...
+
ACP-Gut-Healthy121845 Asian citrus psyllidDiaphorina citri Description:RNA extracted from the midgut of a poo...
Alternative accession-BioSample:SAMN06892345
Alternative accession-BioProject:PRJNA385527
...
+
ACP Salivary Glands CLas121845 Asian citrus psyllidDiaphorina citri Description:RNA extracted from the salivary glands...
Alternative accession-BioSample:SAMN22082294
Alternative accession-BioProject:PRJNA385527
...
+
ACP Salivary Glands Healthy121845 Asian citrus psyllidDiaphorina citri Description:RNA extracted from the salivary glands...
Alternative accession-BioSample:SAMN22082293
Alternative accession-BioProject:PRJNA385527
...
+
Displaying 1-8 of 8 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Tabular dataCSV3.44 KB2022-02-10
Tabular dataCSV17.97 KB2022-02-10
Tabular dataCSV4.21 MB2022-02-10
Mixed archiveGZIP119.84 GB2022-02-10
ScriptUNKNOWN2.86 KB2022-02-10
Tabular dataCSV2.02 MB2022-02-10
Tabular dataCSV3.41 KB2022-02-10
Tabular dataCSV3.1 MB2022-02-10
Tabular dataCSV3.61 MB2022-02-10
ReadmeTEXT5.12 KB2022-02-22
Displaying 1-10 of 15 File(s).
Funding body Awardee Award ID Comments
USDA-NIFA M Mann 2021-67011-35143 Pre-doctoral Fellowship
USDA-NIFA M Heck 2015-70016-23028
USDA-NIFA L Mueller 2015-70016-23028
USDA-NIFA L Mueller 2020-70029-33199
USDA ARS M Heck 8062-22410-007-00-D
Date Action
February 22, 2022 Dataset publish
March 24, 2022 Manuscript Link added : 10.1093/gigascience/giac035
October 7, 2022 Manuscript Link updated : 10.1093/gigascience/giac035
November 15, 2022 Title updated from : 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."
November 15, 2022 Title updated from : 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."