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

Abstract

Long non-coding RNAs (lncRNAs) are a heterogeneous class of genes that do not code for proteins. Since lncRNAs (or a fraction thereof) are expected to be functional, many efforts have been dedicated to catalog lncRNAs in numerous organisms, but our knowledge of lncRNAs in non vertebrate species remains very limited. Here, we annotated lncRNAs using transcriptomic data from the same larval stage of four Caenorhabditis species. The number of annotated lncRNAs in self-fertile nematodes was lower than in out-crossing species. We used a combination of approaches to identify putatively homologous lncRNAs: synteny, sequence conservation, and structural conservation. We classified a total of 1,532 out of 7,635 genes from the four species into families of lncRNAs with conserved synteny and expression at the larval stage, suggesting that a large fraction of the predicted lncRNAs may be species specific. Despite both sequence and local secondary structure seem to be poorly conserved, sequences within families frequently shared BLASTn hits and short sequence motifs, which were more likely to be unpaired in the predicted structures. We provide the first multi-species catalog of lncRNAs in nematodes and identify groups of lncRNAs with conserved synteny and expression, that share exposed motifs. ARTICLE HISTORY

Dynamic Expression of Long Non-Coding RNAs Throughout Parasite Sexual and Neural Maturation in Schistosoma Japonicum

“…Sequence similarity search and synteny conservation indicated that the lncRNAs of S. japonicum have synteny conservation with S. mansoni lncRNAs, even when there is a lack of sequence conservation. Pegueroles et al [28] analyses of lncRNAs sequence or synteny conservation between the Caenorhabditis spp. also identified a much higher number of lncRNAs with synteny conservation than with sequence conservation [28].…”

“…Pegueroles et al [28] analyses of lncRNAs sequence or synteny conservation between the Caenorhabditis spp. also identified a much higher number of lncRNAs with synteny conservation than with sequence conservation [28].…”

Microsyntenic Clusters Reveal Conservation of lncRNAs in Chordates Despite Absence of Sequence Conservation

“…Searches of lncRNAs conserved between amphioxus and vertebrates based on sequence similarity have been unsuccessful [14,15], probably due to the long evolutionary distance that separates these lineages [16]. Recently, however, a strategy to identify conserved intergenic lncRNAs (lincRNAs) by means of syntenic analyses has been successfully attempted, but limited to closely related species [17,18].…”

Genomic and Transcriptomic Analysis Identified Novel Putative Cassava lncRNAs Involved in Cold and Drought Stress

“…Recently, syntenic lncRNAs have been reported in several organisms, including plants [68][69][70]. The conservation of genomic positions of lncRNAs and their target genes across related species has been investigated to consolidate their interactions [70].…”