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Int. J. Mol. Sci. 2016, 17(10), 1758; doi:10.3390/ijms17101758

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

1
Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea
2
Division of Science Education and Institute of Fusion Science, Chonbuk National University, Jeonju 761-756, Korea
3
TheragenEtex Bio Institute, Gwanggyo-ro, Suwon 16229, Korea
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Academic Editor: Kun Yan Zhu
Received: 31 August 2016 / Revised: 10 October 2016 / Accepted: 13 October 2016 / Published: 21 October 2016
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
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Abstract

In this study, we investigated global changes in miRNAs of Meloidogyne incognita throughout its life cycle. Small RNA sequencing resulted in approximately 62, 38, 38, 35, and 39 Mb reads in the egg, J2, J3, J4, and female stages, respectively. Overall, we identified 2724 known and 383 novel miRNAs (read count > 10) from all stages, of which 169 known and 13 novel miRNA were common to all the five stages. Among the stage-specific miRNAs, miR-286 was highly expressed in eggs, miR-2401 in J2, miR-8 and miR-187 in J3, miR-6736 in J4, and miR-17 in the female stages. These miRNAs are reported to be involved in embryo and neural development, muscular function, and control of apoptosis. Cluster analysis indicated the presence of 91 miRNA clusters, of which 36 clusters were novel and identified in this study. Comparison of miRNA families with other nematodes showed 17 families to be commonly absent in animal parasitic nematodes and M. incognita. Validation of 43 predicted common and stage-specific miRNA by quantitative PCR (qPCR) indicated their expression in the nematode. Stage-wise exploration of M. incognita miRNAs has not been carried out before and this work presents information on common and stage-specific miRNAs of the root-knot nematode. View Full-Text
Keywords: Meloidogyne incognita; stage-specific; microRNA expression; quantitative polymerase chain reaction Meloidogyne incognita; stage-specific; microRNA expression; quantitative polymerase chain reaction
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Subramanian, P.; Choi, I.-C.; Mani, V.; Park, J.; Subramaniyam, S.; Choi, K.-H.; Sim, J.-S.; Lee, C.-M.; Koo, J.C.; Hahn, B.-S. Stage-Wise Identification and Analysis of miRNA from Root-Knot Nematode Meloidogyne incognita. Int. J. Mol. Sci. 2016, 17, 1758.

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