Comparative Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Characterized by Shell Colors: Identification of Genetic Bases Potentially Involved in Pigmentation

Mapping Genetic Loci for Quantitative Traits of Golden Shell Color, Mineral Element Contents, and Growth-Related Traits in Pacific Oyster (Crassostrea gigas)

Golden shell color and mineral content are important economic traits of Pacific oyster (Crassostrea gigas). In this study, we mapped a series of quantitative trait loci (QTLs) that control zinc (Zn) and magnesium (Mg) content, shell color and growth performance to two sex-averaged linkage maps from the FAM-A and FAM-B families. In total, ten QTLs were identified in seven linkage groups (LGs) in the FAM-B family, and seven QTLs were identified in four linkage groups in the FAM-A family. Two QTLs affecting the trait of golden shell color were identified in LG8 of the FAM-A and LG10 of the FAM-B families, which could explain 20.2 and 10.5% of the phenotypic variations, respectively. Two QTLs for Zn content were identified that could contribute to 17.9 and 34.44% of the phenotypic variations in FAM-A. Six QTLs for Zn and Mg contents were identified in four LGs (LG1, LG2, LG5, and LG9) in FAM-B, which explained 13.5-26.7% of the phenotypic variations. In addition, seven QTLs related to oyster growth were recognized in both FAM-A and FAM-B families accounting for 14.6-36.7% of the phenotypic variations. All of the DNA markers in QTL regions were blasted and 14 genes associated with above traits were identified. The mRNA expression of these genes was determined by quantitative RT-PCR. These QTLs and candidate genes could be used as potential targets for marker-assisted selection in C. gigas breeding.

Comparison of Two Pearl Sacs Formed in the Same Recipient Oyster with Different Genetic Background Involved in Yellow Pigmentation in Pinctada fucata

Color is one of the most important factors determining the commercial value of pearls. Pinctada fucata is a well-known pearl oyster producing high-quality Akoya pearls. Phenotypic variation in amount of yellow pigmentation produces white and yellowish pearls. It has been reported that polymorphism of yellow pigmentation of Akoya pearls is genetically regulated, but the responsible gene(s) has remained unknown. Here, we prepared pearl sac pairs formed in the same recipient oyster but coming from donor oysters that differ in their color. These two pearl sacs produced pearls with different yellowness even in the same recipient oyster. Yellow tone of produced pearls was consistent with shell nacre color of donor oysters from which mantle grafts were prepared, indicating that donor oysters strongly contribute to the yellow coloration of Akoya pearls. We also conducted comparative RNA-seq analysis and retrieved several candidate genes involved in the pearl coloration. Whole gene expression patterns of pair sacs were not grouped by pearl color they produced, but grouped by recipient oysters in which they were grown, suggesting that the number of genes involved in the yellow coloration is quite small, and that recipient oyster affects gene expression of the majority of genes in the pearl sac.

Comparative transcriptome analysis of Paphia undulata with different foot colors

Foot color is an important trait in Paphia undulata that influences consumer selection. To elucidate the molecular basis of foot color, six transcriptome libraries of P. undulata with different foot colors were constructed: white (L2, L3 and L4) and orange (D2, D3, D4). There is a significant difference in color index (L^⁎, a^⁎, b^⁎) between the two groups (P < 0.05). These six paired-end libraries were sequenced using the Illumina HiSeq 2500 platform. In total, 48.22 Gb of clean data were obtained and de novo assembled into 58,159 unigenes with a mean length of 889.51 bp and N50 of 1461 bp. A total of 19,070 unigenes were significantly matched to known unique proteins. The Gene Ontology (GO) annotation and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to determine metabolic pathways and candidate genes associated with foot color traits. Compared with white P. undulate, a total of 107 transcripts were identified as differentially expressed genes (DEGs) in orange samples using Cuffdiff, including 74 up-regulated and 33 down-regulated genes. Of these differentially expressed genes, many were involved in the synthesis and transport of carotenoids and pigment biosynthesis. Additionally, results of the transcriptome analysis were verified by quantitative real-time PCR (qRT-PCR). Overall, this experiment discovered several potential foot coloration genes and related molecular mechanisms using RNA-seq, which paves the way for further functional elucidation of color-related genes and assists selective breeding practices in P. undulata.

Selection of reference genes for quantitative real-time PCR in Octopus minor (Cephalopoda: Octopoda) under acute ammonia stress

High concentration of ammonia is a common issue in the aquaculture industry and often causes detrimental effects to aquatic products. Exploring expression regulation of genes involved in acute ammonia stress can help to understand the molecular mechanisms of ammonia response. Quantitative real-time PCR (qRT-PCR) with proper reference genes is an effective way to normalize the expression of target genes. To identify the most suitable reference genes for Octopus minor (Mollusca: Cephalopoda: Octopoda) under acute ammonia stress and the normal culturing, nine candidate genes were selected for the validation: OD, RPS18b, RPL29, RPS5, EF-1α, RPL6, AA4, ACT, TUB. The results showed that the stability of candidate genes varied considerably in gill, digestive gland, brain and hemolymph. Thus, the reference genes were determined separately in different tissues. RPS5 and RPL6 showed relatively high stability in gill, while RPL6, TUB, RPL29 and OD were four suitable reference genes in digestive gland. EF-1α, TUB and RPL6 were the best combination in brain and EF-1α and RPS18b were the most appropriate reference genes in hemolymph.

Integrative analysis of genome-wide lncRNA and mRNA expression in newly synthesized Brassica hexaploids

Polyploidization, as a significant evolution force, has been considered to facilitate plant diversity. The expression levels of lncRNAs and how they control the expression of protein-coding genes in allopolyploids remain largely unknown. In this study, lncRNA expression profiles were compared between Brassica hexaploid and its parents using a high-throughput sequencing approach. A total of 2,725, 1,672, and 2,810 lncRNAs were discovered in Brassica rapa, Brassica carinata, and Brassica hexaploid, respectively. It was also discovered that 725 lncRNAs were differentially expressed between Brassica hexaploid and its parents, and 379 lncRNAs were nonadditively expressed in this hexaploid. LncRNAs have multiple expression patterns between Brassica hexaploid and its parents and show paternal parent-biased expression. These lncRNAs were found to implement regulatory functions directly in the long-chain form, and acted as precursors or targets of miRNAs. According to the prediction of the targets of differentially expressed lncRNAs, 109 lncRNAs were annotated, and their target genes were involved in the metabolic process, pigmentation, reproduction, exposure to stimulus, biological regulation, and so on. Compared with the paternal parent, differentially expressed lncRNAs between Brassica hexaploid and its maternal parent participated in more regulation pathways. Additionally, 61 lncRNAs were identified as putative targets of known miRNAs, and 15 other lncRNAs worked as precursors of miRNAs. Some conservative motifs of lncRNAs from different groups were detected, which indicated that these motifs could be responsible for their regulatory roles. Our findings may provide a reference for the further study of the function and action mechanisms of lncRNAs during plant evolution.

Identification of a tyrosinase gene and its functional analysis in melanin synthesis of Pteria penguin

Tyrosinase is a key rate-limiting enzyme in melanin synthesis. In this study, a new tyrosinase gene (Tyr) was identified from Pteria penguin and its effect on melanin synthesis was deliberated by RNA interference (RNAi). The cDNA of PpTyr was 1728 bp long, containing a 5'untranslated region (UTR) of 11 bp, a 3'UTR of 295 bp, and an open reading fragment of 1422 bp encoding 473 amino acids. Amino acid alignment showed PpTyr had the highest (50%) identity to tyrosinase-like protein 1 from Pinctada fucata. Phylogenetic tree analysis classified PpTyr into α-subclass of type-3 copper protein. Tissue expression analysis indicated that PpTyr was highly expressed in mantle, a nacre formation related tissue. After PpTyr RNA interference, PpTyr mRNA was significantly inhibited by 71.0% (P < 0.05). For other melanin-related genes, PpCreb2 and PpPax3 expression showed no significant change, but PpBcl2 was obviously increased. By liquid chromatograph-tandem mass spectrometer (LC-MS/MS) analysis, the total content of PDCA (pyrrole-2, 3-dicarboxylic acid) and PTCA (pyrrole-2,3,5-tricarboxylic acid), as main markers for eumelanin, was sharply decreased by 66.6% after PpTyr RNAi (P < 0.05). The percentage of PDCA was also obviously decreased from 20.1% to 13.9%. This indicated that tyrosinase played a key role in melanin synthesis and color formation of P. penguin.

Transcriptional profiling of long non-coding RNAs in mantle of Crassostrea gigas and their association with shell pigmentation

Long non-coding RNAs (lncRNAs) play crucial roles in diverse biological processes and have drawn extensive attention in the past few years. However, lncRNAs remain poorly understood about expression and roles in Crassostrea gigas, a potential model organism for marine molluscan studies. Here, we systematically identified lncRNAs in the mantles of C. gigas from four full-sib families characterized by white, black, golden, and partially pigmented shell. Using poly(A)-independent and strand-specific RNA-seq, a total of 441,205,852 clean reads and 12,243 lncRNA transcripts were obtained. LncRNA transcripts were relatively short with few exons and low levels of expression in comparison to protein coding mRNA transcripts. A total of 427 lncRNAs and 349 mRNAs were identified to differentially express among six pairwise groups, mainly involving in biomineralization and pigmentation through functional enrichment. Furthermore, a total of 6 mRNAs and their cis-acting lncRNAs were predicted to involve in synthesis of melanin, carotenoid, tetrapyrrole, or ommochrome. Of them, chorion peroxidase and its cis-acting lincRNA TCONS_00951105 are implicated in playing an essential role in the melanin synthetic pathway. Our studies provided the first systematic characterization of lncRNAs catalog expressed in oyster mantle, which may facilitate understanding the molecular regulation of shell colour diversity and provide new insights into future selective breeding of C. gigas for aquaculture.

Comparative transcriptome analysis provides clues to molecular mechanisms underlying blue-green eggshell color in the Jinding duck (Anas platyrhynchos)

BACKGROUND

In birds, blue-green eggshell color (BGEC) is caused by biliverdin, a bile pigment derived from the degradation of heme and secreted in the eggshell by the shell gland. Functionally, BGEC might promote the paternal investment of males in the nest and eggs. However, little is known about its formation mechanisms. Jinding ducks (Anas platyrhynchos) are an ideal breed for research into the mechanisms, in which major birds lay BGEC eggs with minor individuals laying white eggs. Using this breed, this study aimed to provide insight into the mechanisms via comparative transcriptome analysis.

RESULTS

Blue-shelled ducks (BSD) and white-shelled ducks (WSD) were selected from two populations, forming 4 groups (3 ducks/group): BSD1 and WSD1 from population 1 and BSD2 and WSD2 from population 2. Twelve libraries from shell glands were sequenced using the Illumina RNA-seq platform, generating an average of 41 million clean reads per library, of which 55.9% were mapped to the duck reference genome and assembled into 31,542 transcripts. Expression levels of 11,698 genes were successfully compared between all pairs of 4 groups. Of these, 464 candidate genes were differentially expressed between cross-phenotype groups, but not for between same-phenotype groups. Gene Ontology (GO) annotation showed that 390 candidate genes were annotated with 2234 GO terms. No candidate genes were directly involved in biosynthesis or transport of biliverdin. However, the integral components of membrane, metal ion transport, cholesterol biosynthesis, signal transduction, skeletal system development, and chemotaxis were significantly (P < 0.05) overrepresented by candidate genes.

CONCLUSIONS

This study identified 464 candidate genes associated with duck BGEC, providing valuable information for a better understanding of the mechanisms underlying this trait. Given the involvement of membrane cholesterol contents, ions and ATP levels in modulating the transport activity of bile pigment transporters, the data suggest a potential association between duck BGEC and the transport activity of the related transporters.

A Preliminary Study on the Pattern, the Physiological Bases and the Molecular Mechanism of the Adductor Muscle Scar Pigmentation in Pacific Oyster Crassostrea gigas

The melanin pigmentation of the adductor muscle scar and the outer surface of the shell are among attractive features and their pigmentation patterns and mechanism still remains unknown in the Pacific oyster Crassostrea gigas. To study these pigmentation patterns, the colors of the adductor muscle scar vs. the outer surface of the shell on the same side were compared. No relevance was found between the colors of the adductor muscle scars and the corresponding outer surface of the shells, suggesting that their pigmentation processes were independent. Interestingly, a relationship between the color of the adductor muscle scars and the dried soft-body weight of Pacific oysters was found, which could be explained by the high hydroxyl free radical scavenging capacity of the muscle attached to the black adductor muscle scar. After the transcriptomes of pigmented and unpigmented adductor muscles and mantles were studied by RNAseq and compared, it was found that the retinol metabolism pathway were likely to be involved in melanin deposition on the adductor muscle scar and the outer surface of the shell, and that the different members of the tyrosinase or Cytochrome P450 gene families could play a role in the independent pigmentation of different organs.

Identification of conserved proteins from diverse shell matrix proteome in Crassostrea gigas: characterization of genetic bases regulating shell formation

The calcifying shell is an excellent model for studying biomineralization and evolution. However, the molecular mechanisms of shell formation are only beginning to be elucidated in Mollusca. It is known that shell matrix proteins (SMPs) play important roles in shell formation. With increasing data of shell matrix proteomes from various species, we carried out a BLASTp bioinformatics analysis using the shell matrix proteome from Crassostrea gigas against 443 SMPs from nine other species. The highly conserved tyrosinase and chitin related proteins were identified in bivalve. In addition, the relatively conserved proteins containing domains of carbonic anhydrase, Sushi, Von Willebrand factor type A, and chitin binding, were identified from all the ten species. Moreover, 25 genes encoding SMPs were annotated and characterized that are involved in CaCO3 crystallization and represent chitin related or ECM related proteins. Together, data from these analyses provide new knowledge underlying the molecular mechanism of shell formation in C.gigas, supporting a refined shell formation model including chitin and ECM-related proteins.

Comparative transcriptome and potential antiviral signaling pathways analysis of the gills in the red swamp crayfish, Procambarus clarkii infected with White Spot Syndrome Virus (WSSV)

Red swamp crayfish is an important model organism for research of the invertebrate innate immunity mechanism. Its excellent disease resistance against bacteria, fungi, and viruses is well-known. However, the antiviral mechanisms of crayfish remain unclear. In this study, we obtained high-quality sequence reads from normal and white spot syndrome virus (WSSV)-challenged crayfish gills. For group normal (GN), 39,390,280 high-quality clean reads were randomly assembled to produce 172,591 contigs; whereas, 34,011,488 high-quality clean reads were randomly assembled to produce 182,176 contigs for group WSSV-challenged (GW). After GO annotations analysis, a total of 35,539 (90.01%), 14,931 (37.82%), 28,221 (71.48%), 25,290 (64.05%), 15,595 (39.50%), and 13,848 (35.07%) unigenes had significant matches with sequences in the Nr, Nt, Swiss-Prot, KEGG, COG and GO databases, respectively. Through the comparative analysis between GN and GW, 12,868 genes were identified as differentially up-regulated DEGs, and 9,194 genes were identified as differentially down-regulated DEGs. Ultimately, these DEGs were mapped into different signaling pathways, including three important signaling pathways related to innate immunity responses. These results could provide new insights into crayfish antiviral immunity mechanism.

In-depth comparative transcriptome analysis of intestines of red swamp crayfish, Procambarus clarkii, infected with WSSV

Crayfish has become one of the most important farmed aquatic species in China due to its excellent disease resistance against bacteria and viruses. However, the antiviral mechanism of crayfish is still not very clear. In the present study, many high-quality sequence reads from crayfish intestine were obtained using Illumina-based transcriptome sequencing. For the normal group (GN), 44,600,142 high-quality clean reads were randomly assembled to produce 125,394 contigs. For the WSSV-challenged group (GW), 47,790,746 high-quality clean reads were randomly assembled to produce 148,983 contigs. After GO annotation, 39,482 unigenes were annotated into three ontologies: biological processes, cellular components, and molecular functions. In addition, 15,959 unigenes were mapped to 25 different COG categories. Moreover, 7,000 DEGs were screened out after a comparative analysis between the GN and GW samples, which were mapped into 250 KEGG pathways. Among these pathways, 36 were obviously changed (P-values < 0.05) and 28 pathways were extremely significantly changed (P-values < 0.01). Finally, five key DEGs involved in the JAK-STAT signaling pathway were chosen for qRT-PCR. The results showed that these five DEGs were obviously up-regulated at 36 h post WSSV infection in crayfish intestine. These results provide new insight into crayfish antiviral immunity mechanisms.