Identification and Profiling of MicroRNAs During Embryogenesis in the Red Claw Crayfish Cherax quadricarinatus.

Yan Wang,Lei Wang,Mengqiang Wang,Keyong Jiang,Baojie Wang,Mei Liu,Xuqing Shao

doi:10.3389/fphys.2020.00878

Abstract

MicroRNAs (miRNAs) are endogenous small non-coding RNAs that constitute a broad layer of gene regulation at both transcriptional and post-transcriptional levels from prokaryotes to eukaryotes. In embryonic development, they regulate the complex gene expression associated with the complexity of embryogenesis. There is little information about miRNAs in the red claw crayfish (Cherax quadricarinatus), an important commercial species and a potential biological model. In the present study, miRNAs and their target genes were identified during three embryonic developmental stages of C. quadricarinatus. Nineteen known miRNAs and 331 novel ones belonging to 50 miRNA families were obtained. A total of 113 differentially expressed miRNAs were identified, and 2,575 target genes were predicted, of which 1,257 were annotated. Additionally, 63 target genes of 9 miRNAs in C. quadricarinatus were found to be related to embryonic development. For example, miR-10 and its target genes may regulate the nervous system development and body segmentation and miR-2788 may regulate cell proliferation to impact embryonic development. Moreover, miR-28 (target gene tutl), miR-50 (target gene fbx5), and miR-1260b (target gene sif) may co-regulate eye development of embryonic C. quadricarinatus. These miRNAs together with their target genes constitute a network for regulating the development of tissues and organs in the embryo of C. quadricarinatus. Our results lay a foundation for further study on the fundamental molecular and developmental mechanism of crustacean embryogenesis.

Highlights

Since Crick proposed the central dogma of molecular biology in 1958, research on genetic information has mainly focused on DNA and proteins
6ftp://ftp.ncbi.nih.gov/blast/db/ 7http://www.uniprot.org/ 8http://geneontology.org/ 9http://www.genome.jp/kegg/ 10http://www.ncbi.nlm.nih.gov/Clusters of Orthologous Groups (COG)/ 11http://www.ncbi.nlm.nih.gov/KOG/ 12http://pfam.xfam.org/ 13http://eggnog.embl.de size range for small RNAs generated by DICER
An annotated genome was lacking in C. quadricarinatus to identify miRNAs, the transcriptome of embryogenesis contributed to miRNAs recognition in this study

Summary

Introduction

Since Crick proposed the central dogma of molecular biology in 1958, research on genetic information has mainly focused on DNA and proteins. This is because the former acts as both storage and carrier of genetic information, while the latter is the expresser and executor of genetic information. A considerable portion of the genetic information transmitted by DNA does not reach proteins and is only used by non-coding RNA, which means that a large amount of genetic information needs to be processed and transmitted after transcription and before translation. The regulation of gene expression at the post-transcriptional level of microRNAs (miRNAs) requires further research, since they are the most important post-transcriptional regulators discovered in recent years (Bartel, 2004). MiRNAs are essential for the normal development of plants and animals (Ebert and Sharp, 2012), and have a role in a wide variety of biological processes, including embryo formation, developmental patterning, cell proliferation, cell apoptosis, cell differentiation, and viral infection (Rhoades et al, 2002; Pernaute et al, 2011; Nguyen et al, 2017; Chen et al, 2018; Liang et al, 2018; Peng et al, 2018)

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