Genome-Wide Identification and Transcriptomic Analysis of MicroRNAs Across Various Amphioxus Organs Using Deep Sequencing

Frontiers in Genetics

Qian-Hua Zhu¹  Lin-Feng Yang¹  Jun-Yuan Chen²  Qi-Lin Zhang³  Hideaki Morikawa⁴  Yi-Min Li⁵  Yu-Jun Wang⁵  Hong Wang⁵  Xiao-Xue Wang⁵ 

[1] BGI Genomics, BGI-Shenzhen, Shenzhen, China;Evo-devo Institute, School of Life Sciences, Nanjing University, Nanjing, China;Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China;Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano, Japan;Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Ocean College, Beibu Gulf University, Qinzhou, China;

关键词: Branchiostoma belcheri;    organ transcriptomics;    microRNAs;    deep sequencing;    qRT-PCR;   

DOI  :  10.3389/fgene.2019.00877

来源: DOAJ

【 摘 要 】

Amphioxus is the closest living invertebrate proxy of the vertebrate ancestor. Systematic gene identification and expression profile analysis of amphioxus organs are thus important for clarifying the molecular mechanisms of organ function formation and further understanding the evolutionary origin of organs and genes in vertebrates. The precise regulation of microRNAs (miRNAs) is crucial for the functional specification and differentiation of organs. In particular, those miRNAs that are expressed specifically in organs (OSMs) play key roles in organ identity, differentiation, and function. In this study, the genome-wide miRNA transcriptome was analyzed in eight organs of adult amphioxus Branchiostoma belcheri using deep sequencing. A total of 167 known miRNAs and 23 novel miRNAs (named novel_mir), including 139 conserved miRNAs, were discovered, and 79 of these were identified as OSMs. Additionally, analyses of the expression patterns of eight randomly selected known miRNAs demonstrated the accuracy of the miRNA deep sequencing that was used in this study. Furthermore, potentially OSM-regulated genes were predicted for each organ type. Functional enrichment of these predicted targets, as well as further functional analyses of known OSMs, was conducted. We found that the OSMs were potentially to be involved in organ-specific functions, such as epidermis development, gonad development, muscle cell development, proteolysis, lipid metabolism, and generation of neurons. Moreover, OSMs with non–organ-specific functions were detected and primarily include those related to innate immunity and response to stimuli. These findings provide insights into the regulatory roles of OSMs in various amphioxus organs.

【 授权许可】

Unknown