Identification of Novel and Conserved MicroRNAs of Root-knot Nematode Using a Deep-sequencing Approach

111,556,278 high-quality reads were obtained by a deep-sequencing approach that show an exact match to the genome of Meloidogyne incognita from the library of J2 juveniles of M. incognita (Mi). Based on these Solexa reads, 89 M. incognita microRNA genes were identified, which grouped into 67 non-redundant miRNAs with mature sequences. All of these candidate miRNAs were confirmed by qRT-PCR, and 26 of them could be detected in the library of the galls of cucumber root infected by M. incognita (GC). MiR-100 was found in a cluster with let-7, which is similar with B. malayi, a human parasitic nematode. Based on the results of deep sequencing, the expression of miR-100 was much more abundant than that of let-7, which indicated that they may not be co-expressed. The ortholog of let-7, a key regulator that controls the nematode from L4 to adult in C. elegans, could be frequently sequenced in the GC library, the later stages of development of M. incognita, while it had a relative low expression level in J2, which indicated that let-7 may have a similar role in the development regulation in plant parasitic nematodes. Frequently sequenced microRNAs, including miR-71, miR-100 and miR-124, should play an important role in the growth and proliferation of M. incognita. Overall design: Identifying microRNAs of M. incognita based on deep-sequencing of the small RNAs of an Mi library, the J2 juveniles, and comparing their expression levels with those in a GC library, the gall of cucumber root infected with M. incognita.