Comparative transcriptome and miRNA analysis of skin pigmentation during embryonic development of Chinese soft-shelled turtle (Pelodiscus sinensis)

Pei Wang; Gang Xiong; Dan Zeng; Jianguo Zhang; Lingrui Ge; Li Liu; Xiaoqing Wang; Yazhou Hu

doi:10.1186/s12864-022-09029-y

Comparative transcriptome and miRNA analysis of skin pigmentation during embryonic development of Chinese soft-shelled turtle (Pelodiscus sinensis)

BMC Genomics. 2022 Dec 5;23(1):801. doi: 10.1186/s12864-022-09029-y.

Authors

Pei Wang¹, Gang Xiong², Dan Zeng³, Jianguo Zhang⁴, Lingrui Ge^{1

2}, Li Liu⁵, Xiaoqing Wang⁶, Yazhou Hu⁷

Affiliations

¹ College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China.
² Hunan Biological and Electromechanical Polytechnic, Changsha, 410127, Hunan, China.
³ College of Life and Environmental Science, Hunan University of Arts and Science, Changde, 415000, Hunan, China.
⁴ Hunan Biological and Electromechanical Polytechnic, Changsha, 410127, Hunan, China. jgz1969@126.com.
⁵ School of Medical Technology, Shaoyang University, Shaoyang, 422000, Hunan, China.
⁶ College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China. wangxiao8258@126.com.
⁷ College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China. huyazhou@hunau.edu.cn.

Abstract

Background: Aquatic animals show diverse body coloration, and the formation of animal body colour is a complicated process. Increasing evidence has shown that microRNAs (miRNAs) play important regulatory roles in many life processes. The role of miRNAs in pigmentation has been investigated in some species. However, the regulatory patterns of miRNAs in reptile pigmentation remain to be elucidated. In this study, we performed an integrated analysis of miRNA and mRNA expression profiles to explore corresponding regulatory patterns in embryonic body colour formation in the soft-shelled turtle Pelodiscus sinensis.

Results: We identified 8 866 novel genes and 9 061 mature miRNAs in the skin of Chinese soft-shelled turtles in three embryonic stages (initial period: IP, middle period: MP, final period: FP). A total of 16 563 target genes of the miRNAs were identified. Furthermore, we identified 2 867, 1 840 and 4 290 different expression genes (DEGs) and 227, 158 and 678 different expression miRNAs (DEMs) in IP vs. MP, MP vs. FP, and IP vs. FP, respectively. Among which 72 genes and 25 miRNAs may be related to turtle pigmentation in embryonic development. Further analysis of the novel miRNA families revealed that some novel miRNAs related to pigmentation belong to the miR-7386, miR-138, miR-19 and miR-129 families. Novel_miR_2622 and novel_miR_2173 belong to the miR-19 family and target Kit and Gpnmb, respectively. The quantification of novel_miR_2622 and Kit revealed negative regulation, indicating that novel_miR_2622 may participate in embryonic pigmentation in P. sinensis by negatively regulating the expression of Kit.

Conclusions: miRNA act as master regulators of biological processes by controlling the expression of mRNAs. Considering their importance, the identified miRNAs and their target genes in Chinese soft-shelled turtle might be useful for investigating the molecular processes involved in pigmentation. All the results of this study may aid in the improvement of P. sinensis breeding traits for aquaculture.

Keywords: Embryonic development; Melanogenesis; Pelodiscus sinensis; Transcriptome; microRNA.

MeSH terms

Animals
China
Embryonic Development / genetics
MicroRNAs* / genetics
Skin Pigmentation / genetics
Transcriptome
Turtles* / genetics

Substances

MicroRNAs