Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, People's Republic of China.
Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, People's Republic of China.
BMC Genomics. 2018 May 29;19(1):406. doi: 10.1186/s12864-018-4662-5.
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 sensing were differentially expressed between gill and lung tissues. Three miRNAs were differentially expressed between the lungs of larvae and lungs of adults.
This 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.
中国大鲵（Andrias davidianus）在从水生幼体到陆地成体的变态过程中，呼吸从鳃转移到肺，在此之前发生变态。对这两种组织以及皮肤进行采样，以鉴定差异表达的 miRNA。
从变态幼体的鳃、肺和皮肤组织以及成体的肺组织中生成了高覆盖率的参考转录组：获得了 86,282 个全长约 77,275,634bp，N50 为 1732bp 的基因，其中 13,246 个基因被分配到 288 条途径中。为了确定 miRNA 可能参与呼吸转变，对小 RNA 文库进行了测序；鉴定出 282 个 miRNA，其中 65 个是已知的，217 个是新的。基于层次聚类分析，使用差异表达的 miRNA 将 12 个研究样本分为三大类。我们使用 qPCR 验证了 10 个差异表达的 miRNA 及其部分相关靶基因。这些结果与转录组和 miRNA 分析的结果基本一致。最后，构建了 miRNA-基因网络。其中，两个具有与氧感应相关靶基因的 miRNA 在鳃和肺组织之间差异表达。3 个 miRNA 在幼体肺和成体肺之间差异表达。
本研究首次提供了中国大鲵从鳃到肺呼吸转变过程中大规模 miRNA 表达谱概述。在皮肤、鳃和肺组织中鉴定到 5 个差异表达的 miRNA 和它们的靶基因。这些结果表明，呼吸组织中的 miRNA 谱在呼吸转变的调节中发挥重要作用。
