Stage-Wise Identification and Analysis of miRNA from Root-Knot Nematode Meloidogyne incognita

Subramanian, Parthiban; Choi, Inchan; Mani, Vimalraj; Park, Jun Hyung; Subramaniyam, Sathiyamoorthy; Choi, Kang-Hyun; Sim, Ji Hyun; Lee, Chang-Muk; Koo, Jun Mo; Hahn, Bum-Soo

doi:10.3390/ijms17101758

Cited by 12 publications

(12 citation statements)

References 51 publications

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“…The digital expression profile of these miRNAs showed differential expression across five disease development stages suggesting their probable role during nematode parasitism. For example, conserved miRNAs including miR-100_3, miR-58_1 and lin-4 showed a notable differential expression at different stages in concordance to the previous studies [ 25 – 27 ]. The target prediction of RKN miRNAs provided limited data due to the lack of 3’UTRs annotation of some RKN genes.…”

Section: Discussionsupporting

confidence: 90%

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

et al. 2017

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Root-knot nematodes (RKNs, Meloidogyne spp.) are the most damaging plant parasites causing severe losses to crop production. The present study reports genome-wide identification and characterization of both tomato and RKN miRNAs simultaneously from RKN-infected susceptible tomato roots using high-throughput sequencing technique. RNAseq data from 11 small RNA libraries derived from 5 disease development stages identified 281 novel miRNAs of tomato in addition to 52 conserved and 4 variants of conserved miRNAs. Additionally, the same set of RNAseq data identified 38 conserved and 290 novel RKN miRNAs. Both tomato and RKN miRNAs showed differential expression at 5 stages of disease development based on digital expression profiles. In tomato, further validation through qRT-PCR confirmed that majority of miRNAs were significantly upregulated during susceptible response whereas downregulated during resistance response. The predicted targets of 8 conserved and 1 novel miRNAs were validated through 5’RLM-RACE. A negative correlation between expression profiles of a few conserved miRNAs (miR156, miR159, miR164 and miR396) and their targets (SBP, GAMYB-like, NAC and GRF1 transcription factor) was confirmed. A novel Sly_miRNA996 also showed a negative correlation with its target MYB-like transcription factor. These results indicate that the conserved and novel tomato miRNAs are involved in regulating developmental changes in host root during RKN infection. In RKN, the targets of conserved miRNAs were also predicted and a few of their predicted target genes are known to be involved in nematode parasitism. Further, the potential roles of both tomato and RKN miRNAs have been discussed.

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Section: Discussionsupporting

confidence: 90%

“…Recently, cancer associated gender specific miRNAs were identified among human males and females [ 24 ]. Additionally, recent studies on identification and characterization of RKN miRNAs suggested their role in nematode development and parasitism [ 25 – 27 ].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2017

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“…A putative mechanism to establish massive gene repression is the activation of small RNA (sRNA) pathways that repress gene expression at the transcriptional or translational level (Ruiz-Ferrer and Voinnet, 2009). In line with this, the roles of different microRNAs (miRNAs) on the plant-RKN interaction have been addressed recently Díaz-Manzano et al, 2016a, 2018Kaur et al, 2017;Medina et al, 2017;Subramanian et al, 2016;Zhang et al, 2016;Zhao et al, 2015). However, little is known about the regulatory role of other types of siRNA in this interaction.…”

Section: Introductionmentioning

confidence: 99%

Silenced retrotransposons are major rasiRNAs targets in Arabidopsis galls induced by Meloidogyne javanica

Ruiz‐Ferrer

Cabrera

Martínez‐Argudo

et al. 2018

Molecular Plant Pathology

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Root-knot nematodes (RKNs, Meloidogyne spp.) are sedentary biotrophic pathogens that establish within the vascular cylinder of plant roots, forming a gall and inducing several feeding cells, giant cells (GCs), essential for completion of their life cycle. GCs suffer gene expression changes, repeated mitosis and endoreduplication events. Transcriptomics has revealed that an extensive down-regulation of transcripts, a molecular signature of early-developing galls and GCs that is conserved in tomato and Arabidopsis, may be achieved through small RNA (sRNA) gene silencing pathways. The role of some microRNAs (miRNAs) in plant-RKN interactions has recently been addressed, but little is known about the regulatory roles of other sRNA types. Here, we perform a differential accumulation analysis to show which repeat-associated small interfering RNAs (rasiRNAs) are distinctive or enriched in early Arabidopsis galls vs. uninfected roots. Those distinctive from galls are preferentially located in pericentromeric regions with predominant sizes of 24 and 22 nucleotides. Gall-distinctive rasiRNAs target primarily GYPSY and COPIA retrotransposons, which show a marked repression in galls vs. uninfected roots. Infection tests and phenotypic studies of galls from Meloidogyne javanica in Arabidopsis mutants impaired in post-transcriptional gene silencing and/or canonical RNA-directed DNA methylation (RdDM) pathways, as well as quantitative polymerase chain reaction analysis, suggest the implication of canonical and non-canonical RdDM pathways during gall formation, possibly through the regulation of retrotransposons. This process may be crucial for the maintenance of genome integrity during the reprogramming process of galls/GCs from their vascular precursor cells, and/or to ensure a faithful DNA replication during the repeated mitosis/endoreduplication that concurs with feeding site formation.

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“…After the report on the whole genome sequence of M. incognita in the year 2008, research has focused on a search for stage-specific genomic or molecular markers which can be developed into potential targets to control this plant-parasitic nematode [ 1 , 7 ]. Currently, there is no available resource on general and/or stage-specific metabolites from M. incognita .…”

Section: Introductionmentioning

confidence: 99%

Differential Metabolic Profiles during the Developmental Stages of Plant-Parasitic Nematode Meloidogyne incognita

Subramanian

Mani

et al. 2017

IJMS

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Meloidogyne incognita is a common root-knot nematode with a wide range of plant hosts. We aimed to study the metabolites produced at each stage of the nematode life cycle to understand its development. Metabolites of Meloidogyne incognita were extracted at egg, J2, J3, J4, and female stages and 110 metabolites with available standards were quantified using CE-TOF/MS. Analyses indicated abundance of stage-specific metabolites with the exception of J3 and J4 stages which shared similar metabolic profiles. The egg stage showed increased abundance in glycolysis and energy metabolism related metabolites while the J2 metabolites are associated with tissue formation, motility, and neurotransmission. The J3 and J4 stages indicated amino acid metabolism and urea cycle- related metabolites. The female stage was characterized with polyamine synthesis, antioxidant activity, and synthesis of reproduction related metabolites. Such metabolic profiling helps us understand the dynamic physiological changes related to each developmental stage of the root-knot nematode life cycle.

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Stage-Wise Identification and Analysis of miRNA from Root-Knot Nematode Meloidogyne incognita

Cited by 12 publications

References 51 publications

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

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

Silenced retrotransposons are major rasiRNAs targets in Arabidopsis galls induced by Meloidogyne javanica

Differential Metabolic Profiles during the Developmental Stages of Plant-Parasitic Nematode Meloidogyne incognita

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