Dual RNA‐seq reveals Meloidogyne graminicola transcriptome and candidate effectors during the interaction with rice plants

Abstract

Root-knot nematodes secrete proteinaceous effectors into plant tissues to facilitate infection by suppressing host defences and reprogramming the host metabolism to their benefit. Meloidogyne graminicola is a major pest of rice (Oryza sativa) in Asia and Latin America, causing important crop losses. The goal of this study was to identify M. graminicola pathogenicity genes expressed during the plant-nematode interaction. Using the dual RNA-sequencing (RNA-seq) strategy, we generated transcriptomic data of M. graminicola samples covering the pre-parasitic J2 stage and five parasitic stages in rice plants, from the parasitic J2 to the adult female. In the absence of a reference genome, a de novo M. graminicola transcriptome of 66 396 contigs was obtained from those reads that were not mapped on the rice genome. Gene expression profiling across the M. graminicola life cycle revealed key genes involved in nematode development and provided insights into the genes putatively associated with parasitism. The development of a 'secreted protein prediction' pipeline revealed a typical set of proteins secreted by nematodes, as well as a large number of cysteine-rich proteins and putative nuclear proteins. Combined with expression data, this pipeline enabled the identification of 15 putative effector genes, including two homologues of well-characterized effectors from cyst nematodes (CLE-like and VAP1) and a metallothionein. The localization of gene expression was assessed by in situ hybridization for a subset of candidates. All of these data represent important molecular resources for the elucidation of M. graminicola biology and for the selection of potential targets for the development of novel control strategies for this nematode species.

A Meloidogyne graminicola C‐type lectin, Mg01965, is secreted into the host apoplast to suppress plant defence and promote parasitism

“…It is known that J2s of RKNs penetrate into host roots and migrate intercellularly before the establishment of permanent feeding sites (Wyss et al ., ). Combined with the previous findings that the highest expression of Mg01965 was in J2s, including pre‐J2s and parasitic J2s of 2 dpi (Petitot et al ., ), the lower infection rate suggests that Mg01965 is an effector contributing to the early parasite–host interaction, which affects the initial infection of M. graminicola , but not development.…”

“…For instance, the effectors MgGPP and MgMO237 have been shown to suppress plant defences by inhibiting cell death and manipulating rice basal immunity, respectively, thereby promoting M. graminicola parasitism (Chen et al ., ). Although research on M. graminicola effectors is limited, transcriptomic data from different life cycle stages have been reported (Chen et al ., ; Haegeman et al ., ; Petitot et al ., ), offering a starting point to functionally characterize effectors from rice RKNs.…”

Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant‐parasitic nematode Meloidogyne incognita

“…Gene Ontology analysis of genes affected by CNVs identified several overrepresented functions playing a putative role in RKN parasitism. These functions include cell redox homeostasis (involved in detoxification of the environment), signal transduction, binding, peptidase activity (involved in the degradation of host tissues) and transport activity (Gahoi & Gautam, ; Petitot et al., ; Shukla et al., ). The overabundance of these functional categories may suggest a direct role of many of the identified CNVs in the ability of M. incognita to infect resistant plants.…”

The Meloidogyne graminicola effector Mg16820 is secreted in the apoplast and cytoplasm to suppress plant host defense responses

“…Possibly, Mg16820 works on the receptors or enzymes embedded in the plasma membrane to reduce the ROS response (Jwa and Hwang, ). For example, respiratory burst oxidase homologues (RBOHs) are an important group of enzymes in plants, responsible for electron transfer from cytosolic NADPH or FAD to oxygen present in the apoplast to form O 2 – , which is subsequently converted to H 2 O 2 (Qi et al, ). Recently, the M. graminicola effector MgM0237, targeting the cytoplasm, has been shown to be able to suppress the PTI response in N. benthamiana (Chen et al, ).…”