Abstract
BackgroundChinese giant salamander (Andrias davidianus) undergoes a metamorphosis from aquatic larvae to terrestrial adults, with concomitant transfer of respiration from gills to lungs prior to metamorphosis. These two tissues, as well as skin, were sampled to identify the differentially expressed miRNAs.ResultsHigh-coverage reference transcriptome was generated from combined gill, lung and skin tissues of metamorphosing juveniles, and lung tissue of adults: 86,282 unigenes with total length of approximately 77,275,634 bp and N50 of 1732 bp were obtained. Among these, 13,246 unigenes were assigned to 288 pathways. To determine the possible involvement of miRNAs in the respiratory transition, small RNA libraries were sequenced; 282 miRNAs were identified, 65 among which were known and 217 novel. Based on the hierarchical clustering analysis, the twelve studied samples were classified into three major clusters using differentially expressed miRNAs. We have validated ten differentially expressed miRNAs and some of their related target genes using qPCR. These results largely corroborated the results of transcriptomic and miRNA analyses. Finally, an miRNA-gene-network was constructed. Among them, two miRNAs with target genes related to oxygen sensing were differentially expressed between gill and lung tissues. Three miRNAs were differentially expressed between the lungs of larvae and lungs of adults.ConclusionsThis study provides the first large-scale miRNA expression profile overview during the respiration transition from gills to lungs in Chinese giant salamander. Five differentially expressed miRNAs and their target genes were identified among skin, gill and lung tissues. These results suggest that miRNA profiles in respiratory tissues play an important role in the regulation of respiratory transition.
Highlights
Chinese giant salamander (Andrias davidianus) undergoes a metamorphosis from aquatic larvae to terrestrial adults, with concomitant transfer of respiration from gills to lungs prior to metamorphosis
In order to unveil the role of miRNAs in the adjustment of respiratory system to the transition from water to land, we have studied the expression of miRNAs and their corresponding target genes in metamorphosing larvae of the Chinese giant salamander
And annotation of Andrias davidianus transcriptome To obtain a reference transcriptome for the study of microRNA regulation patterns during the transition from gill respiration to lung respiration, samples from individuals which only had lung tissue and from those possessing both gill and lung tissues at the same time were used for RNA-Seq analysis
Summary
Chinese giant salamander (Andrias davidianus) undergoes a metamorphosis from aquatic larvae to terrestrial adults, with concomitant transfer of respiration from gills to lungs prior to metamorphosis These two tissues, as well as skin, were sampled to identify the differentially expressed miRNAs. The endangered Chinese giant salamander (Andrias davidianus, Cryptobranchidae family), endemic to China, is the world’s largest amphibian. Assunta et al (2016) studied the water-land transition from the perspective of gene expression patterns; they used lungfish transcriptome sequence (which is a time-effective and economical method [10,11,12,13]) and phylogenetic relationship analysis [14] They identified 226 concatenated protein sequences in all vertebrates and 59, 951 informative amino acid positions in both lungfish/tetrapod and the coelacanth/ lungfish + tetrapod nodes. Misexpression of some miRNAs can contribute towards neurodevelopmental disorders, which can affect the lung ventilation [26]
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