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

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0568-4) contains supplementary material, which is available to authorized users.

Genetic analysis of salicylic acid-mediated defenses responses and histopathology in the huanglongbing pathosystem

“…Both the SA dependent and SA-independent functions of EDS1 and PAD4 contribute to plant basal immunity and effector-triggered immunity (ETI) (Rietz et al, 2011;Cui et al, 2017). These genes were also significantly induced in other recent transcriptional studies on HLB pathosystem (Fan et al, 2011;Mafra et al, 2013;Rawat et al, 2015).…”

Gene coexpression network analysis of fruit transcriptomes uncovers a possible mechanistically distinct class of sugar/acid ratio-associated genes in sweet orange

“…Towards this, we have identified a total of 72 genes strongly correlated with the sugar/acid ratios, and yet most of them do not correlate with either sugar or acid contents alone. Furthermore, since our first report of using systems biology approach in unraveling the citrus host response to the attack by one of the most constructive disease Huanglongbing [ 22 ], the gene coexpression-based approach has been increasingly used by us and other groups to further understand the gene networks involved in Huanglongbing pathogenesis and fruit development or predict gene annotations [ 14 , 23 – 25 ]. Therefore, in this study we also use the network approach to analyze the fruit transcriptome data, leading us to conclude that these 72 sugar/acid ratio-related genes belong to four modules of the fruit development gene coexpression network, two of which have no overlap with the sugar- and acid-related network modules.…”

Identification and Profiling of microRNAs and Their Target Genes in Tibetan Hulless Barley in Response to Barley Leaf Stripe (BLS) Infection

“…MicroRNA (miRNA) is a type of non-coding small RNA consisting of 21-24 nt that plays various critical roles in the growth and development of plants, including how plants respond to abiotic and biotic stressors, such as pests and diseases [18,19,20]. High-throughput sequencing of microRNA has become a fast, e cient, informative, and cost-effective strategy for gene discovery [21,22,23].…”