De novo assembly transcriptome analysis reveals the genes associated with body color formation in the freshwater ornamental shrimps Neocaridina denticulate sinensis

Huang, Yongyu; Zhang, Lili; Wang, Guodong; Huang, Shi-Yu

doi:10.1016/j.gene.2021.145929

Cited by 17 publications

(6 citation statements)

References 102 publications

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“…A-G SNP in β,β-carotene 15,15′-dioxygenase causes isoleucine-to-valine non-synonymous amino acid substitution. Transcriptome analysis identifies retinol dehydrogenase-12 as a candidate gene regulating body-color formation in ornamental shrimp [ 50 ]. Carotenoids can serve as exogenous antioxidants to prevent cell oxidative damage, and these pigments inhibit lipid peroxidation and hemoglobin oxidation in human erythrocytes [ 51 ].…”

Section: Discussionmentioning

confidence: 99%

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Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout

Ahmed

Ali

Al-Tobasei

et al. 2022

Genes

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The visual appearance of the fish fillet is a significant determinant of consumers’ purchase decisions. Depending on the rainbow trout diet, a uniform bright white or reddish/pink fillet color is desirable. Factors affecting fillet color are complex, ranging from the ability of live fish to accumulate carotenoids in the muscle to preharvest environmental conditions, early postmortem muscle metabolism, and storage conditions. Identifying genetic markers of fillet color is a desirable goal but a challenging task for the aquaculture industry. This study used weighted, single-step GWAS to explore the genetic basis of fillet color variation in rainbow trout. We identified several SNP windows explaining up to 3.5%, 2.5%, and 1.6% of the additive genetic variance for fillet redness, yellowness, and whiteness, respectively. SNPs are located within genes implicated in carotenoid metabolism (β,β-carotene 15,15′-dioxygenase, retinol dehydrogenase) and myoglobin homeostasis (ATP synthase subunit β, mitochondrial (ATP5F1B)). These genes are involved in processes that influence muscle pigmentation and postmortem flesh coloration. Other identified genes are involved in the maintenance of muscle structural integrity (kelch protein 41b (klh41b), collagen α-1(XXVIII) chain (COL28A1), and cathepsin K (CTSK)) and protection against lipid oxidation (peroxiredoxin, superoxide dismutase 2 (SOD2), sestrin-1, Ubiquitin carboxyl-terminal hydrolase-10 (USP10)). A-to-G single-nucleotide polymorphism in β,β-carotene 15,15′-dioxygenase, and USP10 result in isoleucine-to-valine and proline-to-leucine non-synonymous amino acid substitutions, respectively. Our observation confirms that fillet color is a complex trait regulated by many genes involved in carotenoid metabolism, myoglobin homeostasis, protection against lipid oxidation, and maintenance of muscle structural integrity. The significant SNPs identified in this study could be prioritized via genomic selection in breeding programs to improve fillet color in rainbow trout.

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Section: Discussionmentioning

confidence: 99%

“…This gene may play a role in the interconversion of three myoglobin forms, thereby influencing fillet coloration. The cytochrome c oxidase subunit II gene was a differentially expressed gene between red and chocolate ornamental shrimp [ 50 ].…”

Section: Discussionmentioning

confidence: 99%

Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout

Ahmed

Ali

Al-Tobasei

et al. 2022

Genes

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“…The process involves several biological stages such as absorption, oxidation, transportation, deposition, and degradation (Figure 3). Carotenoid absorption relies on transport molecules, including scavenger receptor class B type 1 (SR-B1) [108], cluster of differentiation 36 (CD36) [109], and ATP-binding cassette transporters [110]. After being absorbed, carotenoids undergo oxidation via ketolases before being assimilated by the organism.…”

Section: Accumulation Of Pigments and Body Color Differencesmentioning

confidence: 99%

Harnessing Hue: Advances and Applications of Fish Skin Pigmentation Genetics in Aquaculture

Liu,

Yin,

et al. 2024

Fishes

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Fish exhibit a broad spectrum of colors and patterns facilitated by specialized cells known as chromatophores. The vibrant coloration of fish, controlled by complex genetic and environmental interactions, serves critical roles in ecological functions such as mating, predation, and camouflage. This diversity not only makes fish an invaluable model for exploring the molecular mechanisms of pigmentation but also significantly impacts their economic value within the aquaculture industry, where color traits can drive marketability and breeding choices. This review delves into the sophisticated biological processes governing fish pigmentation and discusses their applications in enhancing aquaculture practices. By exploring the intersection of genetic regulation, environmental influences, and advanced breeding techniques, this review highlights both the scientific understanding and practical applications of fish coloration, providing a bridge between basic biological research and its application in commercial aquaculture.

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“…These two studies showed an elegant example of convergence evolution of cytochrome p450 to produce astaxanthin. More recently, homologs of CYP2J19 or CYP384A1 genes have been searched in orange-red decapods such as Halocaridina rubra (Weaver et al, 2020), Neocaridina denticulata sinensis (Huang et al, 2022), and Exopalaemon carinicauda (Jin et al, 2021), as well as in the copepod Acartia fossae (Mojib et al, 2014). They did not succeed in pointing to such homologs, but suggested other putative cytochrome p450 candidates.…”

Section: Perspectives and Implications To Monitor Aquatic Ecosystems ...mentioning

confidence: 99%

Copepods' true colors: astaxanthin pigmentation as an indicator of fitness

et al. 2023

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Pigmentation is often overlooked in zooplankton, since these organisms are mostly colorless to fit the translucid water medium. However, one of the dominant zooplankton taxa in aquatic ecosystems—copepods—often show a bright red‐orange or blue coloration owing to the accumulation of carotenoid pigments in some parts of their bodies. Even though there are many functional traits describing copepod's performance (e.g., size, feeding, and reproductive modes), it is surprising that the role of such a simple and visible trait as coloration has not been studied in a coherent manner yet. Here, by reviewing 95 studies, we demonstrate that carotenoid‐based pigmentation (mainly caused by astaxanthin molecules) is a widespread functional trait in freshwater and marine copepods. We propose a way to disentangle the complex and thus intriguing patterns of pigment expression along latitudinal and altitudinal gradients, addressing its relationship to diet quality and quantity, temperature, ultraviolet radiation stress, predation pressure, lipid metabolism, and reproduction. We show that large‐scale variations in pigmentation are difficult to tackle because of the fundamental plasticity of this trait at short time scales (i.e., hours, days), and the most recent information about carotenoid bioconversion are addressed (genes and enzyme identification, and influence of microbiota). From this literature review, we hypothesize that pigments play a “Swiss‐army knife” role for copepod's fitness, useful in various ecosystem conditions owing to the strong antioxidant power and the finely‐tuned metabolism of astaxanthin. With larger antioxidant capacities (survival), higher metabolisms (growth), and more offspring in better condition (reproduction), red morphs appear more successful than their uncolored siblings. Also, the potential camouflage strategies allowed by red and blue pigmentation are discussed. We finally formulate new directions and future research fields from molecular to ecosystem scales. Routine quantifications of copepod's pigmentation through trait‐based approaches could be useful (1) to obtain an accurate copepod fitness indicator and (2) to better estimate the transfer of antioxidant to higher trophic levels in ecosystems, including humans.

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De novo assembly transcriptome analysis reveals the genes associated with body color formation in the freshwater ornamental shrimps Neocaridina denticulate sinensis

Cited by 17 publications

References 102 publications

Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout

Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout

Harnessing Hue: Advances and Applications of Fish Skin Pigmentation Genetics in Aquaculture

Copepods' true colors: astaxanthin pigmentation as an indicator of fitness

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