Analysis of body color formation of leopard coral grouper Plectropomus leopardus

Abstract

Body color is an essential ecological phenotypic trait determining the ability of aquatic animals to adapt to or survive in a treacherous environment. However, researches regarding its underlying molecular mechanism in leopard coral groupers has been limited. Therefore, mRNAs, metabolites, and miRNAs of different-colored leopard coral grouper (Plectropomus leopardus) were sequenced to investigate the body color formation mechanism. The transcriptome analysis identified 1236 genes as differentially expressed genes (DEGs), of which 579 were up-regulated and 657 were down-regulated in the red-colored group compared with the brown-colored group (FDR < 0.01 and |log2FC| > 1). Metabolome analysis revealed 439 and 84 SDMs in POS and NEG of liquid chromatography-mass spectrometry, respectively (VIP > 1 and P < 0.05). The miRNA analysis exhibited 149 (120 up-regulated and 29 down-regulated) differentially expressed miRNAs (DEMs) in the analysis of the brown-colored vs. red-colored groups (P < 0.05 and |log2FC| > 1), including miR-144, miR-185, miR-192, miR-2188, miR-6316, novel-m0015, and novel-m0040. Integrated analysis of multiple omics exhibited that carotenoid metabolism, immune response, lipid metabolism, and amino acid metabolism were involved in the body color formation and adaptation to the environment. Therefore, the present multiomics research prepared a foundation for bright body color formation and promoted the process of preferred body-color breeding.

The circular RNA expression landscape across tissues implicates their functional roles in the marine gastropod Rapana venosa

“…1). This observation aligns with previous ndings of intergenic circRNAs (Zhang et al 2013), which have been extensively documented across various taxa including marine invertebrates (Hao et al 2023), sh (Cai et al 2023), birds and mammals (Wu et al 2020). However, we cannot rule out the possibility that some of these circRNAs originated from non-annotated protein-coding genes in the genome or transcriptional noises.…”

“…Numerous studies have elucidated the regulatory roles of circRNAs in gene expression and their involvement in many fundamental pathways such as cell proliferation, cellular homeostasis, immunity and disease pathogenesis (Zhou et Within marine invertebrates, genome-wide circRNA pro ling has been conducted only in a limited number of species. For instance, a previous study performed circRNA pro ling and investigated their regulatory roles in determining the body coloration of leopard corals (Hao et al 2023). Additionally, Farhadi et al…”

Comparative transcriptome analysis of skin color-associated genes in leopard coral grouper (Plectropomus leopardus)

“…Besides, gene regulation associated with skin color is also a critical factor. Candidate carotenoid-related genes, including BCO2, LRP11, ANGPTLs, ALAS, PDIL, MED12, SOX, FAX, FATP, SCD, and LDLRA, were involved in carotenoid metabolism and significantly linked to the skin coloration of leopard coral grouper [5,22,27,28]. Several miRNAs including miR-215, miR-2188, miR-194, miR-122, and novel-m0118 may also play a potential role in regulating skin color in the red-colored leopard coral groupers [29].…”

LncRNA–miRNA–mRNA ceRNA network of different body colors in Plectropomus leopardus

“…affecting human consumption and preference (Vissio et al, 2021). The pigmentation process is affected by multiple factors, including genes, such as forkhead box D3, tyrosinase (TYR), and tyrosinaserelated protein 1 (TYRP1); miRNAs, such as miR-2188, miR-122, novel-m0118, miR-194, and miR-215; and metabolites, such as tyrosine, PGG2, PGH2, and traumatic acid (Braasch et al, 2009;Curran et al, 2009;Zhu et al, 2021;Hao et al, 2022a;Hao et al, 2022b). However, the underlying mechanisms regulating body color formation are still incompletely understood.…”

“…Plectropomus leopardus, as an important member of the genus Plectropomus, is characterized by different body colors, which determine its economic and ornamental values (Maoka et al, 2017;Zhou et al, 2020). Recent studies on aquatic organisms' body color formation mainly focus on miRNAs or mRNAs, and many related genes and miRNAs associated with pigmentation or color variation were characterized in P. leopardus (Wang et al, 2015;Yang et al, 2020;Zhu et al, 2021;Hao et al, 2022a;Hao et al, 2022b). However, the regulatory mechanisms of ceRNA in coral grouper P. leopardus remain unclear.…”