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

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.