Comprehensive meta-analysis, co-expression, and miRNA nested network analysis identifies gene candidates in citrus against Huanglongbing disease

BMC Plant Biology

Research Article

Sandhya P. Kiran¹  Dongliang Du²  Fred G. Gmitter²  Zhanao Deng³  Nidhi Rawat³ 

[1] Ocimum BioSolutions, Banjara Hills Road No. 1, VI Floor Reliance Classic, 500039, Hyderabad, India;University of Florida, Institute of Food and Agricultural Sciences, Citrus Research and Education Center, 33850, Lake Alfred, FL, USA;University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, 33598, Wimauma, FL, USA;

关键词: Citrus;    Gene co-expression analysis;    Gene ontology;    Huanglongbing;    HLB resistance;    Meta-analysis;    miRNA network analysis;    Common and R-specific probe sets;   

DOI  :  10.1186/s12870-015-0568-4

 received in 2015-04-09, accepted in 2015-07-07,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundHuanglongbing (HLB), the most devastating disease of citrus, is associated with infection by Candidatus Liberibacter asiaticus (CaLas) and is vectored by the Asian citrus psyllid (ACP). Recently, the molecular basis of citrus–HLB interactions has been examined using transcriptome analyses, and these analyses have identified many probe sets and pathways modulated by CaLas infection among different citrus cultivars. However, lack of consistency among reported findings indicates that an integrative approach is needed. This study was designed to identify the candidate probe sets in citrus–HLB interactions using meta-analysis and gene co-expression network modelling.ResultsTwenty-two publically available transcriptome studies on citrus–HLB interactions, comprising 18 susceptible (S) datasets and four resistant (R) datasets, were investigated using Limma and RankProd methods of meta-analysis. A combined list of 7,412 differentially expressed probe sets was generated using a Teradata in-house Structured Query Language (SQL) script. We identified the 65 most common probe sets modulated in HLB disease among different tissues from the S and R datasets. Gene ontology analysis of these probe sets suggested that carbohydrate metabolism, nutrient transport, and biotic stress were the core pathways that were modulated in citrus by CaLas infection and HLB development. We also identified R-specific probe sets, which encoded leucine-rich repeat proteins, chitinase, constitutive disease resistance (CDR), miraculins, and lectins. Weighted gene co-expression network analysis (WGCNA) was conducted on 3,499 probe sets, and 21 modules with major hub probe sets were identified. Further, a miRNA nested network was created to examine gene regulation of the 3,499 target probe sets. Results suggest that csi-miR167 and csi-miR396 could affect ion transporters and defence response pathways, respectively.ConclusionMost of the potential candidate hub probe sets were co-expressed with gibberellin pathway (GA)-related probe sets, implying the role of GA signalling in HLB resistance. Our findings contribute to the integration of existing citrus–HLB transcriptome data that will help to elucidate the holistic picture of the citrus–HLB interaction. The citrus probe sets identified in this analysis signify a robust set of HLB-responsive candidates that are useful for further validation.

【 授权许可】

Unknown   
© Rawat et al. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.