Comparative miRNA-seq analysis revealed molecular mechanisms of red color formation in the early developmental stages of Plectropomus leopardus

Xi Liu; Mouyan Jiang; Mouyan Jiang; Mouyan Jiang; Simin Wen; Kaixiang Zhang; Yucong Hong; Kaihui Sun; Xianwu Deng; Yang Huang; Yang Huang; Yang Huang; Gang Shi; Gang Shi; Gang Shi; Changxu Tian; Changxu Tian; Changxu Tian; Huapu Chen; Huapu Chen; Huapu Chen; Guangli Li; Guangli Li; Guangli Li; Chunhua Zhu; Chunhua Zhu; Chunhua Zhu; Chunhua Zhu

doi:10.3389/fmars.2023.1321196

Frontiers in Marine Science (Dec 2023)

Comparative miRNA-seq analysis revealed molecular mechanisms of red color formation in the early developmental stages of Plectropomus leopardus

Xi Liu,
Mouyan Jiang,
Mouyan Jiang,
Mouyan Jiang,
Simin Wen,
Kaixiang Zhang,
Yucong Hong,
Kaihui Sun,
Xianwu Deng,
Yang Huang,
Yang Huang,
Yang Huang,
Gang Shi,
Gang Shi,
Gang Shi,
Changxu Tian,
Changxu Tian,
Changxu Tian,
Huapu Chen,
Huapu Chen,
Huapu Chen,
Guangli Li,
Guangli Li,
Guangli Li,
Chunhua Zhu,
Chunhua Zhu,
Chunhua Zhu,
Chunhua Zhu

Affiliations

Xi Liu: Fisheries College, Guangdong Ocean University, Zhanjiang, China
Mouyan Jiang: Fisheries College, Guangdong Ocean University, Zhanjiang, China
Mouyan Jiang: Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Ocean University, Zhanjiang, China
Mouyan Jiang: Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Ocean University, Zhanjiang, China
Simin Wen: Fisheries College, Guangdong Ocean University, Zhanjiang, China
Kaixiang Zhang: Fisheries College, Guangdong Ocean University, Zhanjiang, China
Yucong Hong: Guangdong Provincial Key Laboratory of Aquatic Larvae Feed, Guangdong Yuequn Biotechnology Co., Ltd., Jieyang, Guangdong, China
Kaihui Sun: Guangdong Provincial Key Laboratory of Aquatic Larvae Feed, Guangdong Yuequn Biotechnology Co., Ltd., Jieyang, Guangdong, China
Xianwu Deng: Fisheries College, Guangdong Ocean University, Zhanjiang, China
Yang Huang: Fisheries College, Guangdong Ocean University, Zhanjiang, China
Yang Huang: Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Ocean University, Zhanjiang, China
Yang Huang: Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Ocean University, Zhanjiang, China
Gang Shi: Fisheries College, Guangdong Ocean University, Zhanjiang, China
Gang Shi: Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Ocean University, Zhanjiang, China
Gang Shi: Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Ocean University, Zhanjiang, China
Changxu Tian: Fisheries College, Guangdong Ocean University, Zhanjiang, China
Changxu Tian: Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Ocean University, Zhanjiang, China
Changxu Tian: Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Ocean University, Zhanjiang, China
Huapu Chen: Fisheries College, Guangdong Ocean University, Zhanjiang, China
Huapu Chen: Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Ocean University, Zhanjiang, China
Huapu Chen: Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Ocean University, Zhanjiang, China
Guangli Li: Fisheries College, Guangdong Ocean University, Zhanjiang, China
Guangli Li: Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Ocean University, Zhanjiang, China
Guangli Li: Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Ocean University, Zhanjiang, China
Chunhua Zhu: Fisheries College, Guangdong Ocean University, Zhanjiang, China
Chunhua Zhu: Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Ocean University, Zhanjiang, China
Chunhua Zhu: Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Ocean University, Zhanjiang, China
Chunhua Zhu: Development and Research Center for Biological Marine Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China

DOI: https://doi.org/10.3389/fmars.2023.1321196
Journal volume & issue: Vol. 10

Abstract

Read online

MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play important roles in several biological processes, including the regulation of body color. Leopard coral grouper (Plectropomus leopardus) is a valuable marine aquaculture fish; however, at present, there are no published reports on its early body color development. The skin color of P. leopardus undergoes a transition from transparent to red from 26 days post-hatching (dph) to 30 dph. In this study, we performed miRNA sequencing on 26 dph (Transparent, PT) and 30 dph (Red, PR) skin samples of P. leopardus to explore the molecular mechanism underlying red color formation. A total of 44.31 M and 37.55 M clean tags were obtained from PT and PR group, respectively. Among these tags, 981 miRNAs were identified, including 493 known and 488 novel miRNAs. A total of 106 differentially expressed miRNAs (DEMs) were identified in PT vs. PR, with 43 up-regulated and 63 down-regulated miRNAs in the PR group, compared to the PT group (|fold change| > 2 and p-value < 0.05). A miRNA-mRNA network based on 18 candidate miRNAs and 53 target genes related to pigmentation, and KEGG enrichment analysis of the target genes of all DEMs, revealed that miRNAs involved in the formation of red skin color were mainly related to: 1) the inhibition of melanin synthesis (miR-141-z, miR-206-z, miR-206-y, miR-27-z, miR-137-y, miR-204-x, miR-204-y, miR-211-x, miR-211-z); 2) chromatophore development (miR-206-z, miR-206-y, miR-499-y, miR-1-z, miR-2188-x, miR-423-x); and 3) carotenoid metabolism (miR-204-x, miR-204-y, miR-499-y). This study demonstrates the potential role of miRNAs in red color formation and lays the foundation for the molecular mechanism of body color polymorphism in P. leopardus.

Published in Frontiers in Marine Science

ISSN: 2296-7745 (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Science: Natural history (General): General. Including nature conservation, geographical distribution
Website: https://www.frontiersin.org/journals/marine-science

About the journal

Abstract

Keywords