Comparative expression analysis identifies the respiratory transition-related miRNAs and their target genes in tissues of metamorphosing Chinese giant salamander (Andrias davidianus)

BMC Genomics
Shengyan SuYulin Zhou

Abstract

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. High-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 sens...Continue Reading

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Methods Mentioned

BETA
RNA Assay
Assay
PCR
RNA-seq

Software Mentioned

HMMER
RSEM
TargetScan
blast2go
Trinity
TransDecoder
Trans
DESeq
RNA hybrid
BLASTX

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