Comparative analysis of lincRNA in insect species

Abstract

BackgroundThe ever increasing availability of genomes makes it possible to investigate and compare not only the genomic complements of genes and proteins, but also of RNAs. One class of RNAs, the long noncoding RNAs (lncRNAs) and, in particular, their subclass of long intergenic noncoding RNAs (lincRNAs) have recently gained much attention because of their roles in regulation of important biological processes such as immune response or cell differentiation and as possible evolutionary precursors for protein coding genes. lincRNAs seem to be poorly conserved at the sequence level but at least some lincRNAs have conserved structural elements and syntenic genomic positions. Previous studies showed that transposable elements are a main contribution to the evolution of lincRNAs in mammals. In contrast, plant lincRNA emergence and evolution has been linked with local duplication events. However, little is known about their evolutionary dynamics in general and in insect genomes in particular.ResultsHere we compared lincRNAs between seven insect genomes and investigated possible evolutionary changes and functional roles. We find very low sequence conservation between different species and that similarities within a species are mostly due to their association with transposable elements (TE) and simple repeats. Furthermore, we find that TEs are less frequent in lincRNA exons than in their introns, indicating that TEs may have been removed by selection. When we analysed the predicted thermodynamic stabilities of lincRNAs we found that they are more stable than their randomized controls which might indicate some selection pressure to maintain certain structural elements. We list several of the most stable lincRNAs which could serve as prime candidates for future functional studies. We also discuss the possibility of de novo protein coding genes emerging from lincRNAs. This is because lincRNAs with high GC content and potentially with longer open reading frames (ORF) are candidate loci where de novo gene emergence might occur.ConclusionThe processes responsible for the emergence and diversification of lincRNAs in insects remain unclear. Both duplication and transposable elements may be important for the creation of new lincRNAs in insects.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0985-0) contains supplementary material, which is available to authorized users.

Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis

“…Overall, protein-coding genes are longer, have a larger number of exons, have higher GC content and are expressed at higher levels than lncRNAs and, in all cases, differences are significant (p-value<2.2e-16 for all comparisons, Figure 2). Thus, our results are in agreement with previous findings in other species [8,41] and suggest that, despite the radically different sexual behaviours in the studied species, the major differences are protein-coding-lncRNA instead of species driven.…”

“…However, our knowledge of lncRNAs in non vertebrate species is very limited, with insects being the only exception. Indeed, several recent studies have annotated lncRNAs in several insect genera, including Drosophila [4,5], Anopheles [6], Aedes [7], Apis [8], Polistes [9], Plutella [10], Tribolium [8], Nasonia [8]. and Bombyx [11].…”

Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis

“…1). Thus, our results are in agreement with previous findings in other species 8,49 and suggest that, despite the radically different sexual behaviours in the studied species, the major differences are protein-coding-lncRNA instead of species driven.…”

“…However, our knowledge of lncRNAs in non vertebrate species is very limited, with insects being the only exception. Indeed, several recent studies have annotated lncRNAs in several insect genera, including Drosophila 4,5 , Anopheles 6 , Aedes 7 , Apis 8 , Polistes 9 , Plutella 10 , Tribolium 8 , Nasonia 8 . and Bombyx 11 .…”

Identification of LincRNA from Dermatophagoides farinae (Acari: Pyroglyphidae) for Potential Allergen-Related Targets

“…Finally, comparison of cura, showed low sequence conservation among different species. Further, similarities within a species are due to lncRNA association with transposable elements (TEs) and simple repeats, and TEs are less frequent in lincRNA exons than in introns, indicating that TEs may have been removed by selection (Lopez-Ezquerra et al, 2017).…”