Comparative microRNA-seq Analysis Depicts Candidate miRNAs Involved in Skin Color Differentiation in Red Tilapia

Wang, Lanmei; Zhu, Wenbin; Dong, Zaijie; Song, Fei; Dong, Juanjuan; Fu, Jianjun

doi:10.3390/ijms19041209

Cited by 47 publications

(14 citation statements)

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“…Thus, in the present work we explored the molecular mechanisms of pigmentation regulation and evolution to facilitate improving coloration and ornamental value [ 43 ]. Increasing evidence suggests that miRNAs play a vital role in skin pigmentation by controlling the expression of a vast number of genes [ 44 , 45 ]. Herein, we generated miRNA transcriptome data from black, white, and red skin samples of Koi carp using a deep sequencing approach, and the findings provide a foundation for future skin pigmentation studies.…”

Section: Discussionmentioning

confidence: 99%

Identification and characterization of skin color microRNAs in Koi carp (Cyprinus carpio L.) by Illumina sequencing

et al. 2018

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BackgroundMicroRNAs (miRNAs) are endogenous, small (21–25 nucleotide), non-coding RNAs that play important roles in numerous biological processes. Koi carp exhibit diverse color patterns, making it an ideal subject for studying the genetics of pigmentation. However, the influence of miRNAs on skin color regulation and variation in Koi carp is poorly understood.ResultsHerein, we performed small RNA (sRNA) analysis of the three main skin colors in Koi carp by Illumina sequencing. The results revealed 330, 397, and 335 conserved miRNAs (belonging to 81 families) and 340, 353, and 351 candidate miRNAs in black, red, and white libraries, respectively. A total of 164 differentially expressed miRNAs (DEMs) and 14 overlapping DEMs were identified, including miR-196a, miR-125b, miR-202, miR-205-5p, miR-200b, and etc. Target prediction and functional analysis of color-related miRNAs such as miR-200b, miR-206, and miR-196a highlighted putative target genes, including Mitf, Mc1r, Foxd3, and Sox10 that are potentially related to pigmentation. Determination of reference miRNAs for relative quantification showed that let-7a was the most abundant single reference gene, and let-7a and miR-26b was the most abundant combination.ConclusionsThe findings provide novel insight into the molecular mechanisms determining skin color differentiation in Koi carp, and serve as a valuable reference for future studies on tissue-specific miRNA abundance in Koi carp.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5189-5) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Identification and characterization of skin color microRNAs in Koi carp (Cyprinus carpio L.) by Illumina sequencing

et al. 2018

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“…At present, some studies have illustrated that miRNAs are essential for skin colour pigmentation and differentiation processes. For instance, miRNA‐508‐3p regulated melanin production of alpaca by targeted to the Mitf mRNA (Zhang et al., 2017), miR‐21a‐5p inhibited Sox gene expression level and regulated the melanin deposition in mouse skin (Wang, Zhao, Fan, Chen, & Dong, 2016), miR‐429 regulated the skin pigmentation of tilapia and common carp through targeting the foxd3 gene (Yan et al., 2013), and miR‐138‐5p and miR‐722 were predicted to play important roles in tilapia skin pigmentation (Wang et al., 2018). Therefore, it is necessary to further explore the crosstalk between miRNA and mRNA function on skin colour differentiation and pigmentation in koi carp.…”

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miR‐196a regulates the skin pigmentation of koi carp (Cyprinus carpioL.) by targeting transcription factormitfa

Yin

Luo

et al. 2020

Aquac. Res.

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Body colour of fish is an important phenotypic trait that closely related to its survival and reproduction, which involved in many biological processes such as mimicry, courtship, camouflage and environmental adaptation (Kelsh, 2004; Protas & Patel, 2008). Compared with mammals and birds, fish are ideal models for skin colour differentiation and pigmentation research, which possess various pigment cells including melanophores (black), xanthophores (yellow), erythrophores (red), iridophores (iridescent, blue, silver or gold) and leucophores (dull, whitish) (Braasch, Schartl, & Volff, 2007). Koi carp (Cyprinus carpio L.) is an ornamental fish selected from the common carp (C. carpio) with several colour variants including Kohaku, Taisho sanke and Showa sanshoku, thus provides good materials for the researches related to fish skin colour (De Kock & Gomelsky, 2015). To date, a series of genes have been identified in the differentiation and pigmentation in koi carp, such as melanogenesis pathway genes including tyrosinase (tyr), tyrosinase-related protein 1 (tyrp1), dopachrome tautomerase (dct), melanocortin 1 receptor (mc1r), agouti signalling protein (asip) and microphthalmia-associated transcription factor a (mitfa). Among them, mitfa is an important member of the mitf gene family that located in the centre of gene regulatory networks in which act as a 'master regulator', and its product has a basic/

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“…168 Via Illumina sequencing, Wang et al169 discovered that miR-107b, miR-138-5p, miR-141-3p and miR-27d were up-regulated in pink/black and pink/red skin compared to whole pink skin, suggesting that differentially expressed miRNAs (DEMs) may play a role in the red tilapia skin pigmentation process.Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed membrane, pigment cell development, cAMP signalling, melanogenesis and tyrosine metabolism F I G U R E 3 Schematic diagram of putative signal pathways for melanin biosynthesis in fish modified according to Ref 25,47,171,192. …”

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Fish pigmentation and coloration: Molecular mechanisms and aquaculture perspectives

Luo

Yin

et al. 2021

Reviews in Aquaculture

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Pigmentation is one of the most diverse characters in vertebrates, with a broad variety of colour phenotypes and colour patterns found in different species, populations and individuals. 1 The diversity and fascinating skin colours and pigment patterns are observed in fish (Figure 1), which coloration widely distributed in the hypodermis of the body as well as the epidermis of scales and fins. 2,3 According to the FAO, global fish production in 2018 was projected to be around 179 million tonnes, with a total first-sale value estimated at USD 401 billion, of which 82 million tonnes from aquaculture and the rest from capture production, and approximately 88 per cent of total fish production was used for direct human consumption, with the remaining 12 per cent going to non-food purposes such as fish oil, fishmeal and ornamental fish. 4 Body colour is an interesting economic feature in aquatic animals, for example fish and shellfish, and the global exports of ornamental fish increased from USD 177.7 million in 2000 to a peak of USD 347.5 million in 2014. 5 The global market for ornamental fish is currently competitive, with a relatively high demand for aquarium fish around the world, and more than

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Comparative microRNA-seq Analysis Depicts Candidate miRNAs Involved in Skin Color Differentiation in Red Tilapia

Cited by 47 publications

References 45 publications

Identification and characterization of skin color microRNAs in Koi carp (Cyprinus carpio L.) by Illumina sequencing

Identification and characterization of skin color microRNAs in Koi carp (Cyprinus carpio L.) by Illumina sequencing

miR‐196a regulates the skin pigmentation of koi carp (Cyprinus carpioL.) by targeting transcription factormitfa

Fish pigmentation and coloration: Molecular mechanisms and aquaculture perspectives

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