Genome wide discovery of long intergenic non-coding RNAs in Diamondback moth (Plutella xylostella) and their expression in insecticide resistant strains

Abstract

Long non-coding RNAs (lncRNAs) play important roles in genomic imprinting, cancer, differentiation and regulation of gene expression. Here, we identified 3844 long intergenic ncRNAs (lincRNA) in Plutella xylostella, which is a notorious pest of cruciferous plants that has developed field resistance to all classes of insecticides, including Bacillus thuringiensis (Bt) endotoxins. Further, we found that some of those lincRNAs may potentially serve as precursors for the production of small ncRNAs. We found 280 and 350 lincRNAs that are differentially expressed in Chlorpyrifos and Fipronil resistant larvae. A survey on P. xylostella midgut transcriptome data from Bt-resistant populations revealed 59 altered lincRNA in two resistant strains compared with the susceptible population. We validated the transcript levels of a number of putative lincRNAs in deltamethrin-resistant larvae that were exposed to deltamethrin, which indicated that this group of lincRNAs might be involved in the response to xenobiotics in this insect. To functionally characterize DBM lincRNAs, gene ontology (GO) enrichment of their associated protein-coding genes was extracted and showed over representation of protein, DNA and RNA binding GO terms. The data presented here will facilitate future studies to unravel the function of lincRNAs in insecticide resistance or the response to xenobiotics of eukaryotic cells.

Long noncoding RNAs: Unexplored players in the drug response of the sea louse Caligus rogercresseyi

“…This wide range of actions means lncRNAs could be involved in regulating multiple biological processes, such as reproduction, development, metabolism, and the immune response, among others (Imamura and Akimitsu, 2014;Taylor et al, 2015;Zhao and Lin, 2015). Recent evidence suggests that lncRNAs are also triggered by different stress factors, including genotoxic agents and insecticides (Mizutani et al, 2012;Etebari et al, 2015). These reports indicate that lncRNAs might fulfill a pivotal role in the response to xenobiotic compounds.…”

“…closely related species has been reported (Pauli et al, 2012;Etebari et al, 2015;Mu et al, 2016;Paneru et al, 2016).…”

“…Furthermore, cumulative evidence suggests little sequence conservation between lncRNAs, even in closely related species (Pauli et al, 2012;Etebari et al, 2015;Paneru et al, 2016). This has hampered the identification of lncRNAs in non-model species, and, hence, the characterization of lncRNAs relies on the removal of transcripts evidencing coding potential.…”

“…The molecular characterization of lncRNAs in different model species has revealed that these transcripts share some common features. As compared to mRNAS, lncRNAs are generally shorter, less enriched in guanine-cytosine (GC), expressed at lower levels, and tend to conform fewer secondary structures (Huang et al, 2012;Pauli et al, 2012;Etebari et al, 2015;Yang and Zhang, 2015;Boltaña et al, 2016;Mu et al, 2016). Despite these common features, few degrees of sequence conservation between…”

Bacillus thuringiensis resistance in Plutella — too many trees?

“…Interestingly of those 3,000 differentially expressed genes only around a third were common to both resistant populations. In order to target a subset of molecules that have recently been implicated in a wide range of cellular processes RNA sequencing was also used to compare the distribution of long non-coding RNAs (lncRNAs) between two resistant and a susceptible population [16]. Between 150-200 differentially expressed lncRNAs were found in the two resistant populations of which 59 were common to both.…”