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Identification and characterization of microRNAs in the plant parasitic root-knot nematode Meloidogyne incognita using deep sequencing

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Abstract

The root-knot nematode Meloidogyne incognita is among the most damaging plant-parasitic pests of several crops including cotton (Gossypium hirsutum) and tomato (Lycopersicon escultentum). Recently, a genome has become available for M. incognita, which greatly facilitates investigation of the interactions between M. incognita and its plant hosts at the molecular level and enables formation of hypotheses concerning development at the cellular level. MicroRNAs (miRNAs) are a class of small RNA molecules that serve as endogenous gene regulators. They regulate many biological processes including reproduction, the sequencing of morphological development, and potentially of parasitism as well. Certain miRNAs regulate fundamental metabolism pathways and stress responses in M. incognita. Since a list of miRNAs has not been generated for M. incognita, we employed a bioinformatics tool called mirDeepFinder to identify miRNAs from the small RNA database of M. incognita (GSM611102) that was generated from deep sequencing. A total of 254 conserved miRNAs belonging to 161 miRNA families were identified, as were 35 novel miRNAs belonging to 31 families. The 16 most commonly found miRNAs in order of abundance were min-miR-100a, min-miR-124, min-miR-71a, min-miR-1, min-miR-228, min-miR-92, min-miR-72, min-miR-49b, min-miR-58, min-miR-252, min-miR-lin-4, min-miR-87, min-miR-2a, min-miR-34a, min-miR-50a, and min-miR-279a. The length of the pre-miRNAs varied greatly from 50 to 197 nt, with an average of 88 ± 39 nt. The average minimal folding free energy (MFE) and MFE index (MFEI) of the identified miRNAs were –30.3 Kcal/mol and 0.92, respectively, indicating that these miRNAs can readily fold into a typical hairpin secondary structure.

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Acknowledgments

We would like to thank the Cotton Incorporated for partial support of this research through cooperative research agreement 14-397. We also thank Dr. David Bird lab for generously providing the nematode strain and culture protocols.

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    Authors and Affiliations

    1. Department of Biology, East Carolina University, Greenville, NC, 27858, USA

      Yanqiong Zhang, Fuliang Xie, Chao Li, Baohong Zhang & Xiaoping Pan

    2. College of Plant Protection, Hunan Agricultural University, Hunan, 410128, China

      Yunsheng Wang

    3. Cotton Incorporated, Cary, NC, 27513, USA

      Robert L. Nichols

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    1. Yanqiong Zhang
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    Correspondence to Robert L. Nichols or Xiaoping Pan.

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    This article forms part of a special issue of Functional and Integrative Genomics entitled “miRNA in model and complex organisms” (Issue Editors: Hikmet Budak and Baohong Zhang)

    Yanqiong Zhang, Yunsheng Wang and Fuliang Xie contributed equally to this work.

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    Zhang, Y., Wang, Y., Xie, F. et al. Identification and characterization of microRNAs in the plant parasitic root-knot nematode Meloidogyne incognita using deep sequencing. Funct Integr Genomics 16, 127–142 (2016). https://doi.org/10.1007/s10142-015-0472-x

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