Integrated analysis of RNA-seq and microRNA-seq depicts miRNA–mRNA networks involved in stripe patterns of Botia superciliaris skin

Zhou, Jian; Zhao, Han; Zhang, Lu; Liu, Can; Feng, Siyuan; Ma, Jideng; Li, Qiang; Ke, Hongyu; Wang, Xinyu; Liu, Lingyan; Liu, Chao; Su, Xutao; Liu, Yingkai; Yang, Song

doi:10.1007/s10142-019-00683-2

Cited by 11 publications

(7 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Melaninbased coloration was associated with aggressiveness, immune function, antibiotic activity, and oxidative stress (Slominski et al, 2004;Ducrest et al, 2008). Melanin-related pathways, namely Wnt and MAPK signaling pathways, were enriched in the present study and participated in the body color formation and melanin biosynthesis (Kelsh, 2004;Jiang et al, 2014;Zhou et al, 2019). Wen et al (2022) also reported that the signal transduction Wnt and MAKP signaling pathway involved in the body color formation of P. leopardus.…”

Section: Melanin Synthesissupporting

confidence: 52%

“…Fish often display captivating color patterns that are crucial for multiple biological processes for adaptation and survival in the environment, such as predator avoidance, species identifi cation, photoreception, structural support, thermoregulation, microbial resistance, and selective mating (Kelsh, 2004;Hubbard et al, 2010;Zhou et al, 2019). However, the underlying mechanism of these adaptation consequences is still unclear.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Analysis of body color formation of leopard coral grouper Plectropomus leopardus

et al. 2022

View full text Add to dashboard Cite

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.

show abstract

Section: Melanin Synthesissupporting

confidence: 52%

Section: Introductionmentioning

confidence: 99%

Analysis of body color formation of leopard coral grouper Plectropomus leopardus

et al. 2022

View full text Add to dashboard Cite

show abstract

“…SLC24A5, found in the zebrafish and known to be responsible for lighter pigmentation caused by hypopigmentation of melanocytes in the skin and the retinal pigment epithelium, was also expressed very little in the A. baenschi albino-type compared with in the wild-type (Lamason et al, 2005). Also, MATP (SLC45A2) and MLPH involved in the transport of melanocytes of inorganic ions and charged and uncharged organic molecules were less expressed in the albino group, showing the same expression pattern as the one observed in the Japanese flounder albinism and the crimson snapper (Zhang Y.-P. et al, 2015;Wang et al, 2017).…”

Section: Discussionmentioning

confidence: 76%

Comprehensive RNA-seq Analysis to Evaluate the Pigmentation-Related Genes Involved in Albinism of Cichlid Fish, Aulonocara baenschi

Lee

2020

Front. Mar. Sci.

View full text Add to dashboard Cite

The Nkhomo-benga peacock, Aulonocara baenschi is a species inhabiting Lake Malawi and its population has decreased by over 70% over the past 10 years. Since 2018, the species has been included in the IUCN Red list and its status has been set to the critically endangered (CR) level. And the fish is known to have rare but naturally occurring albino strain. Despite that, little has been done to develop its genetic resources such as sequence-based data and expression patterns of genes. Accordingly, this study performed high-throughput sequencing on the caudal fin of the two different-colored A. baenschi in order to identify their pigment-related genes and analyze the expression patterns of the genes on the transcriptome level. Through the Illumina sequencing platform, we obtained 77,035,702 and 88,689,756 reads from the caudal fin of the wildtype and the albino-type, respectively. In addition to that, using de novo assembly and various annotation databases, a total of 141,116 contigs, including 129,369 unigenes were obtained. In the comparative analysis of differentially expressed genes between the wild-type and the albino-type in terms of melanogenesis, the tyrosinase gene family involved in melanin synthesis tended to be less expressed in the albino-type than the wild-type. However, the expression of the critical proteins involved in the pigment synthesis of xanthophore was higher in the albino-type than in the wild-type. In addition, the yellow-orange pigment was more apparently expressed in the caudal fin of the albino-type than of the wild-type. This indicates that the external characteristics of the fish were in accordance with the analysis results on the transcriptome level. The results of this study will be the foundation of research on expression characteristics and gene networking analysis of the pigmentation-related genes of fish.

show abstract

“…MiRNAs can regulate gene transcription by restraining the 3 untranslated regions (3 UTRs) of messenger RNAs (mRNAs) to participate in BPs, such as cell development, transcription, translation, and occurrence of diseases (Hobert, 2008). At present, miRNA research in teleost fishes mainly focuses on growth and body development (Gan et al, 2016;Zhang et al, 2016;Zhao et al, 2017;Lan et al, 2019;Zhou et al, 2019). In addition, the competing endogenous RNA (ceRNA) theory has revealed a complex interacting mechanism between RNAs (Salmena et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Identification of lncRNA-miRNA-mRNA Network Involved in Sexual Size Dimorphism of Chinese Tongue Sole (Cynoglossus semilaevis)

Wang

Yang

et al. 2022

Front. Mar. Sci.

View full text Add to dashboard Cite

Chinese tongue sole (Cynoglossus semilaevis) is a flatfish species unique to Northeast Asia, exhibiting the typical female-biased sexual size dimorphism (SSD). To explore the possible regulatory roles of non-coding RNAs (ncRNAs) on this phenomenon, whole transcriptomic analysis was performed by using female, male, and pseudomale C. semilaevis to identify differentially expressed (DE) long ncRNAs (DE lncRNAs), microRNA (DE miRNAs), and differentially expressed genes (DEGs) from the brain, gonad, liver, and muscle tissues. Most of them were concentrated in the gonad and muscle, and the gene expression patterns of pseudomale individuals were similar to male individuals. The association of DE lncRNAs and target messenger RNAs (mRNAs) was predicted based on antisense, cis-, and trans-regulatory mechanisms, with enriched protein digestion and absorption, cyclic adenosine monophosphate (cAMP) signaling pathway, sulfur metabolism, cell cycle, and splicesome (p < 0.05). Furthermore, weighted gene co-expression network analysis (WGCNA) was employed to cluster the expression patterns of DE lncRNA, and two modules (greenyellow and blue) had the highest positive and negative correlations with growth traits, respectively. Importantly, the female-biased expression in the greenyellow module and the male- and pseudomale-biased expression in the blue module were observed in the gonad. The target gene analysis for DE miRNA revealed 3,034 mRNA-miRNA pairs with the opposite expression patterns. Finally, the lncRNA-miRNA-mRNA network, including 385 DE lncRNAs, 138 DE miRNAs, and 456 DEGs, was constructed. Among which, 78 DE lncRNAs, 12 DE miRNAs, and 13 DEGs involved in cell growth and death pathway were related to the SSD of C. semilaevis. This study described the lncRNA-miRNA-mRNA regulatory network in the SSD of C. semilaevis for the first time. The functional prediction analysis suggested that these DE lncRNAs and DE miRNAs might be involved in flatfish SSD by regulating several potential growth-related pathways (e.g., cell cycle, cAMP signaling, and Rap1 signaling). Further studies related to these ncRNAs will enlarge our understanding of the regulatory effects of ncRNAs on fish SSD.

show abstract

Integrated analysis of RNA-seq and microRNA-seq depicts miRNA–mRNA networks involved in stripe patterns of Botia superciliaris skin

Cited by 11 publications

References 38 publications

Analysis of body color formation of leopard coral grouper Plectropomus leopardus

Analysis of body color formation of leopard coral grouper Plectropomus leopardus

Comprehensive RNA-seq Analysis to Evaluate the Pigmentation-Related Genes Involved in Albinism of Cichlid Fish, Aulonocara baenschi

Identification of lncRNA-miRNA-mRNA Network Involved in Sexual Size Dimorphism of Chinese Tongue Sole (Cynoglossus semilaevis)

Contact Info

Product

Resources

About