MicroRNA Discovery and Analysis of Pinewood Nematode Bursaphelenchus xylophilus by Deep Sequencing

Abstract

BackgroundMicroRNAs (miRNAs) are considered to be very important in regulating the growth, development, behavior and stress response in animals and plants in post-transcriptional gene regulation. Pinewood nematode, Bursaphelenchus xylophilus, is an important invasive plant parasitic nematode in Asia. To have a comprehensive knowledge about miRNAs of the nematode is necessary for further in-depth study on roles of miRNAs in the ecological adaptation of the invasive species.Methods and FindingsFive small RNA libraries were constructed and sequenced by Illumina/Solexa deep-sequencing technology. A total of 810 miRNA candidates (49 conserved and 761 novel) were predicted by a computational pipeline, of which 57 miRNAs (20 conserved and 37 novel) encoded by 53 miRNA precursors were identified by experimental methods. Ten novel miRNAs were considered to be species-specific miRNAs of B. xylophilus. Comparison of expression profiles of miRNAs in the five small RNA libraries showed that many miRNAs exhibited obviously different expression levels in the third-stage dispersal juvenile and at a cold-stressed status. Most of the miRNAs exhibited obviously down-regulated expression in the dispersal stage. But differences among the three geographic libraries were not prominent. A total of 979 genes were predicted to be targets of these authentic miRNAs. Among them, seven heat shock protein genes were targeted by 14 miRNAs, and six FMRFamide-like neuropeptides genes were targeted by 17 miRNAs. A real-time quantitative polymerase chain reaction was used to quantify the mRNA expression levels of target genes.ConclusionsBasing on the fact that a negative correlation existed between the expression profiles of miRNAs and the mRNA expression profiles of their target genes (hsp, flp) by comparing those of the nematodes at a cold stressed status and a normal status, we suggested that miRNAs might participate in ecological adaptation and behavior regulation of the nematode. This is the first description of miRNAs in plant parasitic nematodes. The results provide a useful resource for further in-depth study on molecular regulation and evolution of miRNAs in plant parasitic nematodes.

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

“…The first nucleotide position of the known and novel mature miRNAs in the present study was found to be dominated by A and U. This is a ubiquitous phenomenon observed in miRNA studies [15,18,31,32]. This can also be taken as a putative marker for confirmation of sRNA sequences as miRNAs, and our results are also in accordance with previous reports.…”

Toll-like receptor-associated sequence variants and prostate cancer risk among men of African descent

“…In particular, it is estimated that approximately 20% of all human cancers, including prostate cancer (PCA), are associated with chronic inflammation [28, 50]. TLR activation, a key initiator of inflammation and dysregulation of TLR-responsive pathways, has been associated with cancer susceptibility.…”

Neurobiology of plant parasitic nematodes

“…Six flp genes were identified as targets of the miRNAs viz, fl-2, flp-3, flp-6, flp-12, flp-14 and flp-16. Huang et al (2010) further propose that flp genes are involved in chemically mediated interactions between B. xylophilus and its beetle vector. The expression of flp genes varied depending on the life cycle stage, for example, flp-3 is more highly expressed in the dispersal stage than in the propagative stage (Kang et al 2009).…”

“…This comes from a study on miRNAs from the pinewood nematode, Bursaphelenchus xylophilus. The miRNAs were found to be involved in the regulation of flp genes (Huang et al 2010). Six flp genes were identified as targets of the miRNAs viz, fl-2, flp-3, flp-6, flp-12, flp-14 and flp-16.…”