Identification and expression analysis of long noncoding RNAs in embryogenesis and larval metamorphosis of Ciona savignyi

Long noncoding RNAs (lncRNAs) play important roles in diverse developmental and pathological processes through chromatin reprogramming, cis regulation and posttranscriptional modification. They have been extensively studied in both vertebrates and invertebrates. However, the information of lncRNAs in urochordate is still lacking. In this study, we used the RNA-Seq data from three developmental stages (18, 21 and 42 hours post fertilization, hpf) of embryos and larvae in Ciona savignyi to identify candidate lncRNAs and analyze their expression profiles. A total of 29,944 unigenes were predicted as lncRNAs, five of which had hits with lncRNAs in NONCODE database. The acquired lncRNAs had an average length of 466 nt. The peaks of length, GC content and minimum free energy of the lncRNAs were significantly lower than that of the message RNAs (mRNAs). The average expression levels of lncRNAs were also lower than those of mRNAs. Among the three developmental stages, highly expressed lncRNAs concentrated in 18 hpf embryos. While, for those lncRNAs specifically up-regulated in 21 hpf embryos, their co-expressed mRNAs were enriched in GO terms of membrane, indicating these lncRNAs are involved in the regulation of luminal membrane biogenesis, and extracellular matrix secretion through membrane localized proteins during Ciona notochord tubulogenesis. The lncRNAs in 42 hpf larvae were distinct from those in 18 and 21 hpf embryos. This result is associated with the fact that swimming larvae are transiting into metamorphic juveniles at this stage, indicating lncRNAs are involved in the regulation of larval metamorphosis. Overall, our study identified a large number of lncRNAs in C. savignyi and revealed their expression characteristics and dynamics during Ciona embryogenesis and larval metamorphosis. The results will help to further understand the function of lncRNAs in chordate development and the evolution of lncRNAs.