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Genome-wide identification and characterization of miRNAome from tomato roots (Solanum lycopersicum) and root-knot nematode (Meloidogyne incognita) during susceptible and resistant interactions.

ABSTRACT: RKNs are economically most damaging, obligate sedentary endoparasites that form giant cells within host roots to obtain nutrition and complete their life cycle. We report genome-wide identification of miRNAs from both host and RKN using RKN-infected susceptible tomato roots through high-throughput sequencing. Eleven small RNA libraries were made from five disease development stages, their five corresponding uninfected development stages and uninfected development stage 0. A total of 52 conserved miRNAs, 4 variants of conserved miRNAs and 281 novel miRNAs of host were identified. A significantly upregulated expression of majority of the miRNAs was observed during susceptible response and downregulated expression during resistance response through qRT-PCR. The miRNA targets were predicted and validated through 5’RLM-RACE. Furthermore, correlation between the expression profile of selected conserved miRNAs viz., miR164, miR156, miR396, miR159, and novel Sly_miRNA996 with their target transcription factors viz., NAC, SBP, GRF1, GAMYB-like, and MYB-like, respectively was also determined. This study suggests a potential role of host miRNAs in regulating transcription factor genes involved in plant developmental processes and defense responses during RKN infection. Additionally, 328 RKN miRNAs including 38 conserved miRNAs, 106 novel miRNAs, and 184 candidate novel miRNAs were identified from same dataset. The differential expression of conserved and RKN-specific miRNAs at different development stages of nematode in tomato roots suggests their probable role during nematode development and adaptation to parasitic behavior. This is the most comprehensive study reporting the identification and characterization of miRNAs from both tomato and RKN in five different disease development stages under soil grown conditions and their potential roles during RKN infection in tomato roots.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE87651 | GEO | 2017/06/12

SECONDARY ACCESSION(S): PRJNA345485

REPOSITORIES: GEO

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Project description:Biotrophic plant pathogens have evolved sophisticated strategies to manipulate their host. They derive all of their nutrients from living plant tissues, by making intimate contact with their host while avoiding a resistance response. Rice is one of the most important crop plants worldwide and an excellent model system for studying monocotyledonous plants. Estimates of annual yield losses due to plant-parasitic nematodes on this crop range from 10 to 25% worldwide. One of the agronomically most important nematodes attacking rice is the rice root knot nematode Meloidogyne graminicola. Attack of plant roots by sedentary plant parasitic nematodes, like the root knot nematodes (RKN; Meloidogyne spp.) involves the development of specialized feeding cells in the vascular tissue. The second stage juvenile of the RKN punctures selected vascular cells with its stylet, injects pharyngeal secretions, and this ultimately leads to the reorganisation of these cells into typical feeding structures called giant cells (GCs), from which the nematode feeds for the remainder of its sedentary life cycle (Gheysen & Mitchum, 2011). Morphological and physiological reprogramming of the initial feeding cell leads to nucleus enlargement, proliferation of mitochondria and plastids, metabolic activation, cell cycle alterations and cell wall changes (Gheysen and Mitchum, 2011). The hyperplasia and hypertrophy of the surrounding cells leads to the formation of a root gall, which is typically formed at the root tips in the case of the rice RKN M. graminicola. In comparison with other RKN, M. graminicola has a very fast life cycle, with swelling of the root tips observed as early as 1 day after infection (dai). At 3 dai, terminal hook-like galls are clearly visible (Bridge et al., 2005). After 3 moults the nematodes are mature, around 10 dai. The M. graminicola females lay their eggs inside the galls, while most other RKN deposit egg masses at the gall surface, and hatched juveniles can reinfect the same or adjacent roots. In well-drained soil at 22-29 degrees C the life cycle of M. graminicola is completed in 19 days. 2 biological replicates of nematode infected giant cells and control vascular cells were sampled at two time points: 7 and 14 dai

Project description:Biotrophic plant pathogens have evolved sophisticated strategies to manipulate their host. They derive all of their nutrients from living plant tissues, by making intimate contact with their host while avoiding a resistance response. Rice is one of the most important crop plants worldwide and an excellent model system for studying monocotyledonous plants. Estimates of annual yield losses due to plant-parasitic nematodes on this crop range from 10 to 25% worldwide. One of the agronomically most important nematodes attacking rice is the rice root knot nematode Meloidogyne graminicola. Attack of plant roots by sedentary plant parasitic nematodes, like the root knot nematodes (RKN; Meloidogyne spp.) involves the development of specialized feeding cells in the vascular tissue. The second stage juvenile of the RKN punctures selected vascular cells with its stylet, injects pharyngeal secretions, and this ultimately leads to the reorganisation of these cells into typical feeding structures called giant cells (GCs), from which the nematode feeds for the remainder of its sedentary life cycle (Gheysen & Mitchum, 2011). Morphological and physiological reprogramming of the initial feeding cell leads to nucleus enlargement, proliferation of mitochondria and plastids, metabolic activation, cell cycle alterations and cell wall changes (Gheysen and Mitchum, 2011). The hyperplasia and hypertrophy of the surrounding cells leads to the formation of a root gall, which is typically formed at the root tips in the case of the rice RKN M. graminicola. In comparison with other RKN, M. graminicola has a very fast life cycle, with swelling of the root tips observed as early as 1 day after infection (dai). At 3 dai, terminal hook-like galls are clearly visible (Bridge et al., 2005). After 3 moults the nematodes are mature, around 10 dai. The M. graminicola females lay their eggs inside the galls, while most other RKN deposit egg masses at the gall surface, and hatched juveniles can reinfect the same or adjacent roots. In well-drained soil at 22-29ºC the life cycle of M. graminicola is completed in 19 days.

Dataset Information

Genome-wide identification and characterization of miRNAome from tomato roots (Solanum lycopersicum) and root-knot nematode (Meloidogyne incognita) during susceptible and resistant interactions.

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