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

Insights into the mechanism of color formation of the freshwater prawn (Macrobrachium rosenbergii) revealed by de novo assembly transcriptome analysis

Body color is an important visual indicator of crustacean quality and plays a major role in consumer acceptability, perceived quality, and the market price of crustaceans. The freshwater prawn (Macrobrachium rosenbergii) has two distinct phenotypic variations, characterized by dark blue and light yellow body colors. However, the underlying mechanisms regulating the body color of M. rosenbergii remain unclear. In this study, the composition of shell color parameters and pigment cells of raw and cooked dark blue and light yellow M. rosenbergii was investigated and the mechanisms associated with body color were elucidated by transcriptome analysis. The results showed significant differences in the raw shells of the dark blue and light yellow M. rosenbergii (L: 26.20 ± 0.53 vs. 29.25 ± 0.45; a: -0.88 ± 0.19 vs. 0.35 ± 0.18; b: 1.73 ± 0.20 vs. 3.46 ± 0.37; dE: 70.33 ± 0.53 vs. 67.34 ± 0.45, respectively, p = 0.000) as well as the cooked shells (L: 58.14 ± 0.81 vs. 55.78 ± 0.55; a: 19.30 ± 0.56 vs. 16.42 ± 0.40; b: 23.60 ± 0.66 vs. 20.30 ± 0.40, respectively, p < 0.05). Transcriptome differential gene analysis obtained 39.02 Gb of raw data and 158,026 unigenes. Comprehensive searches of the SwissProt, Nr, KEGG, Pfam, and KOG databases resulted in successful annotations of 23,902 (33 %), 40,436 (25.59 %), 32,015 (20.26 %), 26,139 (16.54 %), and 22,155 (14.02 %) proteins, respectively. By KEGG pathway analysis, numerous differentially expressed genes were related to pigmentation-related pathways (MAPK signaling pathway, Wnt signaling pathway, melanin production, tyrosine metabolism, and cell-cell communication process). Candidate DEGs that may be involved in body color included apolipoprotein D, crustacyanin, cytochrome P450, and tyrosinase, as verified by quantitative real-time PCR. The results of this study provide useful references to further elucidate the molecular mechanisms of color formation of M. rosenbergii and other crustaceans.

The comparison of morphology and transcriptome in the inner membrane reveals the potential mechanism of the heritable carapace color of the Chinese mitten crab Eriocheir sinensis

Carapace color plays an important role in the communication, reproduction, and self-defense of crustaceans, which is also related to their economic value. Chinese mitten crab (Eriocheir sinensis) is an important aquaculture species in China, and there are different strains with heritable carapace colors, i.e. Green, White, and Red. However, there is a lack of research on the formation mechanism of carapace color of this species. This study was conducted to compare the histology and transcriptome in the inner membrane of three carapace color strains of E. sinensis. Histological comparisons revealed that the inner membrane of green and red carapace crabs contained more melanin, appearing in clusters, and had a higher presence of yellow or orange pigments. In contrast, the inner membrane of white carapace crabs had smaller and fewer melanin particles, as well as a lower presence of yellow or orange pigments. Observation under an electron microscope showed that the inner membrane of E. sinensis contained a large number of collagen fibers and various types of cells, including fibroblasts, melanocytes, and other tissue cells, which exhibited different levels of activity. Transcriptome analysis showed that the Green, Red, and White strains of E. sinensis had approximately 80.3 K, 81.6 K and 80.3 K expressed unigenes in their inner membranes, respectively. When comparing Green and Red crabs, there were 2, 850 upregulated genes and 2, 240 downregulated genes. In the comparison between Red and White crabs, there were 2, 853 upregulated genes and 2, 583 downregulated genes. Furthermore, there were 2, 336 upregulated genes and 2, 738 downregulated genes in the inner membranes between White and Green crabs. Among these genes, some members of the solute carriers family, which are involved in carotenoid transportation, showed differential expression among the three carapace color strains. Additionally, significant differences were observed in the expression of genes related to melanin synthesis, including wingless/integrate, tyrosinase, guanine nucleotide-binding protein inhibitory subunit, cell adhesion molecule, adenylyl cyclase, and creb-binding protein. there were no differences in the gene expression levels of the crustacyanin family. In conclusion, this study identified several candidate genes associated with carapace color in the inner membrane of E. sinensis, suggesting a close relationship between the heritable carapace colors and the transport of the carotenoids as well as the synthesis of melanin.

Transcriptome analysis of growth and shell color between two genetic variants of Corbicula fluminea with different shell colors

To clarify the molecular mechanism of the black and yellow shell coloration, we performed a transcriptome analysis of whole tissue of Corbicula fluminea in Hongze Lake (Jiangsu Province, China). After assembly, 335,247 unigenes were obtained, and 136,804 unigenes were functionally identified using public databases (NR, GO, KEGG, eggnog, and Swissprot). 1567 differentially expressed genes (DEGs) were detected through pairwise comparisons, of which 941 DEGs were up-regulated and 626 were down-regulated in the black-shelled clam. We compared the DEGs between two clams and identified some coloration-related genes. Notably, the black-shelled clam was larger than the yellow-shelled. We speculated that higher digestion and anabolic ability of black-shelled clam might lead to this phenomenon. In contrast, the yellow-shelled clam appeared to be more sensitive to environmental stress. The metabolic energy of the yellow-shelled clam was depleted to maintain or recover from stress, and provide less energy for growth. In summary, our finding provides a theoretical basis for the molecular mechanism of pigmentation and the difference of somatotype in bivalve, as well as promotes the future breeding of more elite varieties.

Molecular characterization and functional analysis of peroxiredoxin 3 (NdPrx3) from Neocaridina denticulata sinensis

Peroxiredoxins (Prxs) widely exist in organisms and can prevent oxidative damage. Here, the characterization and biological function of NdPrx3 from Neocaridina denticulata sinensis were analyzed. The coding sequence of NdPrx3 consists of 684 bp open reading frame (ORF), encoding 227 amino acids with a predicted molecular weight of 24.7 kDa and theoretical pI 6.49. Multiple sequence alignments showed that the conserved domains of NdPrx3, including catalytic triad, dimer interface, decamer interface, peroxidatic, and resolving cysteines, were similar to those of other organisms. The phylogenetic relationship demonstrated that NdPrx3 clustered in the Prx3 class. The highest relative expression of NdPrx3 mRNA was confirmed in gill among the nine tissues from healthy shrimp. The transcript level of NdPrx3 was significantly upregulated from 0 h to 48 h and decreased in 72 h under copper challenge, indicating that NdPrx3 may play an important role in the copper challenge of N. denticulata sinensis. In addition, NdPrx3 was recombinantly expressed in E. coli and purified to one band on SDS-PAGE. The DNA protection of rNdPrx3 was verified. The enzymatic assay of the recombinant NdPrx3 indicated that it had the oxidoreductase function and was stable at a low temperature (10-30 °C).

Ovarian transcriptome and metabolic responses of RNAi-mediated farnesyl pyrophosphate synthase knockdown in Neocaridina denticulata sinensis

Methyl farnesoate (MF) is considered the equivalent of JH in crustaceans and plays an essential role in many crucial physiological processes. It is believed that farnesyl pyrophosphate synthase (FPPS) plays an essential role in the biosynthesis of mevalonate, which is a branch of the JH/MF pathway. The full-length cDNA of FPPS (NdFPPS) from Neocaridina denticulata sinensis was isolated and characterized, and the deduced amino acid of NdFPPS contained a polyprenyl_synt domain. In addition to its ubiquitous tissue expression, NdFPPS was significantly expressed in the ovary. In vivo gene silencing with dsRNA interference was performed to further investigate the function of NdFPPS. An ovarian transcriptomic analysis of dsNdFPPS experimental and control groups was used to compare, annotate, and classify differentially expressed genes (DEGs). A total of 9230 DEGs were identified in the experimental and control groups based on FPKM values, of which 5082 were up-regulated genes and 4148 were down-regulated genes. 761 GO terms and 102 KEGG pathways were enriched for the DEGs. Our results suggest that NdFPPS might play an important role in ovarian development, however, further functional study is needed to elucidate physiological role of NdFPPS in reproduction.

Functional analysis of ABCG2 gene in pigment transport of Neocaridina denticulata sinensis

Many strains of Neocaridina denticulata sinensis (cherry shrimp) possess vivid body colors.However, the molecular underpinnings of these various body colors are scarcely understood. To study the role of the ABCG2 gene in the pigmentation of cherry shrimp, four strains (red, yellow, blue, and wild strains) were sampled. The sequence and expression pattern of ABCG2in tissues and embryos were analyzed, and the distribution of ABCG2 was also explored via WFISH (whole mount flurescence in situ hybridization). And further, RNA interference (RNAi) was used to explore the role of ABCG2 in body color deposition. The results showed that the ABCG2 sequence contained the conserved motif of Walker A, Walker B, Q-loop, d-loop, and H-loop. In tissues, ABCG2 was highly expressed in the epidermis of the four strains. During development stages, it was first expressed at the cleavage stage, then decreased at the gastrula stage, with the lowest expression at the pre-nauplius stage. From the metanauplius stage, its expression level was significantly upregulated until it reached the highest level at the membrane-zoea stage. WFISH showed that ABCG2 was first expressed at the cleavage stage in all four strains, and its distribution was similar from the cleavage stage to the before-zoea stage. The strongest positive signals were observed at the membrane-zoea stage, which was consistent with the qPCR results. Moreover, at the membrane-zoea stage, the positive signals of the four strains were mainly distributed in the compound eye and appendages. RNAi knockdown of ABCG2 encumbered the development of compound eye pigment cells (CEPCs) and erythrophores. It had effects on the expressions of other genes related to body color. These results suggest that ABCG2 is involved in the development of compound eye and the proliferation of erythrophores. This study provides new ideas for the cultivation of novel body colors in cherry shrimp at the molecular level.

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

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.