Experimental animals

In October 2012, animals were sampled from the coastal area of Bebuwan Bay (108°30′-108°50′E, 20°70′-20°90′N), which belongs to the South China Sea, under the jurisdiction of Guangxi province, China. The local fisheries authority enforces a fishing moratorium between June 1 and August 1 to conserve fisheries resources. After the fishing off season, the fishermen were allowed to resume operation in that area. The sampling process does not involve endangered or protected animals. They were purchased from Dijiao Wharf market in Beihai (109.086576°E, 21.486342°N) near the Beibu Gulf, China. The scallops used were 6.8–7.5 cm in shell length and cultured in the aquarium at Lab of Marine Pearl Culture. Two mantle tissue branches of each individual (a total of 10 individuals) were separately dissected from red (R) and white valve (W).

RNA extraction

Total RNAs of ten mantle tissues were respectively extracted using Trizol reagent (Invitrogen) according to the manufacturer’s protocol. RNA integrity and quantity were evaluated through lab-on-chip analysis using a 2100 bioanalyzer (Agilent Technologies). In the current study, two samples had RNA integrity number values of 7.9 and 7.8. Then, equal amounts of mRNA (each of 2μg total RNA) from five left branches were pooled for a “red valve-secreting tissue”, as well as five right branches for a“white valve-secreting tissue” sample.

Library construction

The cDNA library was constructed according to the manufacturer’s instructions (Illumina/Hiseq-2000 RNA-seq). Poly(A)⁺ RNA was purified using Sera-mag Magnetic Oligo (dT) beads from total RNA samples. The collected mRNAs were firstly cleaved into fragments. And the prepared buffers containing dNTPs, RNaseH, and DNA polymerase I were used to reverse transcript these fragments to second-strand cDNA purified by QiaQuick PCR extraction kit (Qiagen). After adapter connection, the cDNA fragments (200±25 bp) were purified and sequenced in BGI-Shenzhen via Illumina/Hiseq-2000 RNA-seq.

Transcriptome analysis

Transcriptome analysis used de novo assembly bioinformatics analysis. Primary sequencing data (or raw reads) produced by the Illumina/Hiseq-2000 platform were evaluated by the quality control (QC) to determine if a re-sequencing step is required. After QC, raw reads are filtered as clean reads, which will be used in Trinity software [29] to assemble unigenes (i.e., R-unigene and W-unigene). Multiple samples from the same species were sequenced, and then the unigenes were obtained from the assembly of each sample. These unigenes were further processed by sequence splicing and redundancy removal to produce the longest possible non-redundant unigene (All-unigene). Finally, the All-unigene was obtained from each sample assembly. All-unigene sequences were first aligned by Blastx to protein databases, such as Nr, SwissPro, KEGG, and COG, with E-value <10⁻⁵. In addition, the function of All-unigenes was assigned by their corresponding best-hit function-known proteins from each database. The algorithm of reads per kilobase of unigene per million mapped reads (RPKM) [30] was utilized to calculate the expression levels of all unigenes in each sample. And then the differentially expressed genes and performed gene ontology (GO) and pathway enrichment analyses were identified. P-value corresponds to the results of differential gene expression test. False discovery rate (FDR) is a method that determines the P-value threshold in multiple tests. The threshold (FDR≤0.001 [31] and log₂ Ratio≥1 absolute value) was used to assess the significance of gene expression differences.

Validation of RNA-Seq analysis by real-time quantitative PCR

Real-time quantitative PCR (RT-qPCR) was designed to verify the differences in gene expression of selected target gene observed during RNA-Seq analysis. The mantle tissues of A. Pleuronectes (Linneus) for RT-qPCR were collected from 5 individuals. Both sides (red and white) of mantle were separately collected. The cDNA was synthesized using M-MLV First Strand cDNA Synthesis Kit (Invitrogen). Primers designed for each gene were present in S1 Table. The qRT-PCR was performed using DyNAmoColorFlash SYBR Green qPCR Kit (Thermo Scientific, USA) according to the manufacturer’s protocol and done on the 7500 Real-time PCR system (ABI Applied Bisosystems, USA). After amplification, fluorescent data was converted to threshold cycle values (CT). The concentration of the template in the sample was determined by relating the CT value to the standard curve. Target gene transcript levels were normalized against reference gene transcripts levels. GAPDH was used as the reference gene. Statistical analysis Quantitative data was expressed as mean ± S.E.M.

Sequencing and assembly

Poly(A)⁺-enriched mRNA from RS and WS of A. pleuronectes were sequenced using Illumina/Hiseq-2000 to obtain 54,361,178 and 50,796,780 clean reads, respectively. Detailed GC content, Q20, and unknown bases are shown in S2A Table. Data were archived at the NCBI Sequence Read Archive (SRA) under accession SRA297257. Assembly of the reads produced Trinity_original and unigenes, which could be clustered into two databases. A total of 159,521 All-unigenes were obtained, which ranged from 200 bp to 23,337 bp in size. Furthermore, All-unigene N50 was 979 bp (S2B Table). Gap distribution was below 5% (S2C Table). These results showed that the obtained unigenes were suitable for further annotation.

Functional annotation of unigenes

For the annotation of assembled All-unigenes, a sequence similarity examination was conducted against the NCBI Nr and Swiss–Prot protein databases using BLASTx software [32] with a cutoff E-value of 1e-5. A total of 48,597 All-unigenes had significant similarities to known protein databases, of which 46,837 and 41,974 unigenes shared homologous proteins from the Nr and Swiss-Prot databases. Moreover, E-value and similarity distributions of best hits in the Nr and Swiss–Prot databases were analyzed. According to the Nr result, unigenes with significant homology (E-value<1e-50) and high identity (greater than 80%) accounted for 27.94% and 6.43% of all matched ones (Fig 1A and 1C). In the Swiss-Prot result, unigenes with significant homology and high identity accounted for 29.17% and 7.84% of all matches (Fig 1B and 1D).

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Fig 1. The annotation of assembled All-unigenes.

The results of sequence similarity examination conducted against the NCBI Nr (A and B) and Swiss–Prot protein databases (C and D) were shown, respectively. The legend in the middle of A and B represents the E-value and the one between C and D represents the percentage of different identity.

https://doi.org/10.1371/journal.pone.0141390.g001

The GO database is a major bioinformatics innovation that aims to standardize the representation of gene and gene product attributes across species and databases. As shown in the annotation results, 14,738 unigenes were assigned to one or more GO terms. In total, 94,147 GO assignments were obtained: 43,523 were assigned to biological process, 17,524 were assigned to molecular function, and 33,100 were assigned to cellular component (Fig 2). Under the biological process category, cellular process (8,293; 18.93%) was the largest group, which was followed by metabolic process (6,513; 14.96%), biological regulation (3,523; 8.09%), and biological process regulation (3,091; 7.10%). Under the cellular component category, 8,113 (46.30%) unigenes were assigned to cell or cell part, followed by organelle (5,449; 31.09%) and membrane (3,144; 17.94%). For the molecular function category, binding (8,093; 24.29%) was the largest group, which was followed by catalytic activity (6,431; 19.43%), transporter activity (954; 2.88%), and molecular transducer activity (535; 1.62%).

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Fig 2. Gene ontology of genes annotated with GO terms.

https://doi.org/10.1371/journal.pone.0141390.g002

The protein database of clusters of orthologous groups (COGs) aims to systematically classify complete complement of proteins (both predicted and characterized) encoded by complete genomes or transcriptome. In this research, 46,276 All-unigenes were assigned to COG terms. For COG functional classification, general function prediction was predominant (16.90%), followed by translation, ribosomal structure, and biogenesis (6.63%). Extracellular structures (0.09%) and nuclear structures (0.017%) were the least represented COG terms (Fig 3).

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Fig 3. Clusters of orthologous groups annotated with COG terms.

https://doi.org/10.1371/journal.pone.0141390.g003

KEGG and GO enrichment analyses of differential expression genes in red (RS) and white (WS) valve-secreting tissues

Left and right mantles secrete red and white valves in A. pleuronectes. Genes showing differential expression between the two samples were identified using an algorithm developed by Audic et al.. [33] The edgeR software was used to identify the DGEs with critical thresholds (P-value <0.05, fold >2, FDR<0.05). The results suggested that 6,131 genes were significantly highly expressed in RS, while 3,064 genes were lowly expressed, compared with that in WS. In RS, 1,105 specific expressed unigenes were observed, but only 337 of them were observed in WS. These specific expressed unigenes were analyzed based on KEGG cluster analysis. The red shell-specific pathways (93 specific pathways, data not shown) were higher than the white shell-specific pathways [e.g., non-homologous end-joining, cell adhesion molecules (CAMs), fat digestion and absorption, fatty acid metabolism, sulfur metabolism, and MAPK signaling pathway]. In addition, KEGG metabolic pathway analysis indicated that differentially expressed genes were involved in 228 signaling pathways, and 43 genes revealed significant differences (P<0.01). Among these pathways, the ribosome was the most significantly enriched pathway (P-value 3.24e-49), which was followed by oxidative phosphorylation (P-value 2.30e-14).

Among the enriched gene sets of GO in these comparisons, 3,440 of 9,195 genes belonged to GO biological process, 2,007 of 9,195 genes belonged to GO cellular component, and 1,337 of 9,195 genes belonged to GO molecular function in RS-vs-WS. Among these genes, ribonucleoprotein complex, ribosomal subunit, small ribosomal subunit, macromolecular complex, large ribosomal subunit of cellular component, structural molecule activity, cytokine activity of molecular function and gene expression of biological process revealed significant differences (corrected P<0.01) in RS than those in WS (data not shown).

Identification of genes involved in organic pigmentation

In higher animals, the deposition or aggregation of coloring matter in an organism, tissue, or cell are systematically dissected by a pigment cell called melanocyte, which is an ideal system for genetic, molecular, and cellular analysis. [34–36] A total of 37 identified genes were involved in pigmentation (GO: 0043473), however, only one gene, transcription factor abd-b, showed significantly higher expression in RS than in WS. The melanogenesis signal pathway contains 53 genes with significant differences in A. pleuronectes, of which 32 genes exhibited significantly higher expression in RS than in RS. The number of other crucial enzymes was limited during melanin formation in higher animal cells, e.g., tyrosinase-related protein 1 [EC:1.14.18.-] and dopachrome tautomerase [EC:5.3.3.12]. These results suggested the possibility of another available pigmentation mechanism in lower animals. In insect cuticle sclerotization [37] and mollusk shell periostracum, [38,39] the quinone process mainly catalyzed by tyrosinase(TYR) is believed to be a process that embeds pigments into the conchyolin of the shell. TYRs in some mollusk species have been recently reported to be related to crystal shell structures (data shown below). [40]

The presence of Carotenoids is related to body colors that appear in tissues of many aquatic animals. [41–43] Mollusk shell contains various pigments, which are commonly carotenoids and porphyrins. However, mollusks are unable to synthesize carotenoids. Therefore, carotenoids are absorbed from food and modified to other forms during accumulation. [18] The carrier, storage, and lipid transfer protein (LLTP) superfamily of pigments mediate the intracellular uptake of lipids, proteins, vitamins, and carotenoids, which include the large cytosolic subunit of the microsomal triglyceride transfer protein (MTP), vertebrate apolipoprotein B (apoB), vitellogenin (Vg), and insect apolipophorin II/I precursor (apoLp-II/I). [44] 47 genes were found, including MTP, Vtg, and apoLp. Notably, we found 33 expressed Vg genes (S3 Table, S1 Fig), of which 20 showed significantly different expression between RS and WS. Moreover, 19 of these genes presented higher expression level in RS (S3 Table, Fig 4A).

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Fig 4. Crystal formation-related genes differently expressed in the RS and WS.

The macromorphology of white shell (left) and red shell (right) was shown in F. And the different expressed genes between RS and WS involved in organic pigment transportor (A), framework macromolecules (B), crystal nucleation (C), Ca2+ level regulators (D) and relative signal pathways (E) were represented respectively.

https://doi.org/10.1371/journal.pone.0141390.g004

Biomineralization-related genes

There are fewer reports on shell forming-relevant genes in A. pleuronectes. In this work, the unigenes were compared with the biomineralization-related (BMR) genes from the GenBank database. A total of 687 unigenes were identified, of which 144 were significantly differentially expressed (S3 Table). According to Mann’s shell organic matrix model, two major categories of those shell matrix molecules are defined as framework macromolecules, including insoluble or poorly soluble proteins, polysaccharides or mucopolysaccharide, and soluble acid molecules. These macromolecules regulate the nucleation, orientation, growth, and termination of the CaCO₃ crystal. [45] However, apart from those well-known organic matrices in shells, upstream signal factors [46] and transporters of minerals [47] should be considered.

Framework macromolecules in shell matrix are considered to play a vital role in biomineralization. The dynamic balance of the chitin framework seems to be pursued by the moon oyster, which is similar to other shelled mollusks and crustaceans. [48] Although 37 chitin synthesis- and degradation-related genes were identified, all differentially expressed genes (nine genes) had higher levels in RS than that in WS (S3 Table, Fig 4B). A similar expression pattern was observed in tyrosinases (TYRs), and seven among 18 patterns were annotated (S3 Table, Fig 4B). Aguilera [40] reported that the TYR gene family has expanded independently in pearl oysters and the Pacific oyster; in addition, their markedly different expression profiles indicate their shell formation function. Zhang also found that TYR may participate in shell matrix maturation by oxidation in the Pacific oyster. [24] Meanwhile, 26 C-lectin genes were annotated (S3 Table). Interestingly, among the seven differentially expressed genes, two genes were similar to Apis mellifera (Unigene129630) and Plutella xylostella (Unigene124011), which presented higher levels in RS; however, the remaining genes were homologs of mollusk species (S3 Table, Fig 4B). Previous studies indicated that the C-lectin domain is critical for mineralization, but the functional nature of C-lectin and its related genes have not been elucidated. They generally align with other functional domains, which make them as novel genes of mineralization matrix proteins, similar to the echinoderm endoskeleton matrix protein SM50 [49] and abalone shell matrix protein perlucin. [50] Two perlucins were identified: one was similar to Haliotis diversicolor, while the other was homologous to Mytilus galloprovincialis. These perlucins presented different expression patterns (S3 Table, Fig 4B). In addition to this, nine matrilin genes in A.Pleuronectes were identified, and five of them had markedly different expression levels (S3 Table, Fig 4B). In higher animals, matrilin supports matrix assembly by connecting fibrillar components and mediating interactions in the cartilage. [51] In the present study, the fibronectin gene family, which is an important shell matrix in some mollusk species, [23,24] was annotated, but apparent differential expression was not detected between the two samples. Moreover, four members of 17 annotated cement genes presented dominant expression levels in WS (S3 Table, Fig 4B). Cement in A. pleuronectes is serine-rich, which is similar to Phragmatopoma californica but in contrast to those found in pearl oyster (i.e., serine, glycine, and glutamine-rich proteins). [23] The expression level of two dermatopontin genes in WS was 5 to 60 times than that in RS (S3 Table, Fig 4B). In some mollusk species, dermatopontin is suggested to function during shell matrix assembly. [52,53] From the aforementioned results, scallop may select mineralization framework matrix proteins to be dominant in its two different valves or at least secrete different ECMs using the two branches of mantle. Chitin and macromolecules were catalyzed by TYRs for the red valve, whereas C-type lectin, matrilin, cement, and dermatopontin were catalyzed for the white valve. This arrangement may possibly contribute to shell coloring; chitin easily adsorbs pigments and has been applied to food engineering applications. [54]

A total of 146 potential genes directly related to crystal nucleation and growth were identified (S3 Table). There were 99 dentin sialophosphoprotein-like genes in A.pleuronectes (ApDSPPs) that have been annotated, and 12 of these genes were differentially expressed (S3 Table, Fig 4C). One ApDSPP (Unigene68675) presented the highest expression level (RPKM = 208.541), which contains abundant serine and aspartic acid composition similar to DSPPs in mammals. DSPP (N-linked glycoprotein) and its cleaved products, namely, dentin phosphoprotein (DPP) and dentin sialoprotein (DSP), in mammals are essential for dentin mineralization. Mutation in/or knockout of the DSPP gene results in mineralization defects in dentin and/or bone. [55,56] This large group of DSPP-like genes presented in A. pleuronectes show that some common features during biomineralization are shared by this mollusk species and higher animals. Another glycoprotein, called PIF, also undergoes proteolytical process, which forms two products, i.e., Pif97 and Pif80; these products have different functions in shell nacre layer formation. [57] All four of 12 PIF annotated genes were remarkably highly expressed in RS (S3 Table, Fig 4C). Meanwhile, eight carbonic anhydrase (CA) genes and one nacrein gene were identified (S3 Table). Among these genes, five CA genes were highly expressed in RS, whereas nacrein presented lower levels in RS (S3 Table, Fig 4C). Nacrein was reported to be a rapid evolutionary product of CA, which specifically supplied the essential element HCO₃^- of crystal nucleation through CO₂ catalysis in mineralization. [58] Uncoordinated expression of nacrein and other CAs indicated their differential biological functions in A.pleuronectes. The result of this project showed that BMSP, shell matrix proteins, and perlucin were highly expressed in RS (S3 Table, Fig 4C), which have been reported to directly participate in crystal formation. [50,59,60] In summary, DSPP homologs utilized by moon oyster require further investigation. Those mollusk-specific genes, such as PIF, BMSP, and shell matrix proteins, share a common feature, that is, aspartic acid is believed to be directly involved in crystal nucleation. Their high expression level in RS indicated that the reinforced crystal formation capability should easily stock more macromolecules, such as framework elements and pigments in the shell.

Shells of bivalve animals are calcium metabolism products. The most widely discussed modes of ion uptake for mineralization purposes involve ion transporters and channels located in membranes, a pathway within a cell, and at the mineralization site. A total of 80 Ca²⁺ transport-related genes (CTRs), especially from membrane channels, are found in A. pleuronectes (S3 Table). Ca exchangers (Calx) in moon scallop were more active in the red valve-secreting branch of mantle. Two of these exchangers were highly similar to that in mammal species (Nr E-value>1E-80) (S3 Table, Fig 4D). Cells expel Ca²⁺ with ATP-driven pumps and Na-Ca exchangers. [61] Interestingly, seven Ca channels homologous to Lymnaea stagnalis had higher expression in WS; by contrast, one channel that was highly similar to Loligo bleekeri (Nr E-value = 1E-125) presented the highest level in RS (S3 Table, Fig 4D). Despite their differential expression, all had high calcium-buffering capacity in neurons, [62,63] which was distributed in the mantle margins of scallop species. [64] Salmodulin (CaM) is another important constituent of cellular Ca²⁺ regulation, and previous studies showed its close relationship with biomineralization. [65,66] Despite large CaM group members, the mollusk homologous CaM found in A. pleuronectes presented no difference in expression in RS and WS (S3 Table, Fig 4D). Twelve alkaline phosphatases (APs) were identified, of which four showed higher expression level in RS (S3 Table, Fig 4D). All APs in A. pleuronectes were highly similar to PFAP in pearl oyster, Pinctada fucata (martensii), which may participate in calcium transportation; this result was based from sequence analysis, in situ hybridization, and in vivo studies. [67]

Finally, signal pathways related to mineralization, especially growth factors (GFs) and their receptors, despite the limitations of studies on invertebrate species, were studied in this project. Limited information about these cellular regulators during mineralization has been obtained from sequence analysis, [68] genomic survey, [69] and in vivo and in vitro studies. [70] However, these analogues were hypothesized to have a potential use in the regeneration of living bone for potential clinical use. Notably, 125 genes in the tumor necrosis factor (TNF) signal pathway were detected, including TNF, TNF receptor-associated factor, TNF receptor, and TNF-induced proteins (S3 Table, S2 Fig). The only TNF gene that was highly similar to TNF in human (E-value = 1E119) was detected and significantly expressed in RS (S3 Table, Fig 4E). TNF in higher animals is a potent substance in bone remodeling [46], and several studies suggested that TNF played immunity function in mollusk [71]. The TNF signal pathway may participate in defense systems that trigger inflammatory reaction, which initiates ECM crossing-linking. Furthermore, 54 members of EGF-like substances were identified, one of which was highly similar to Brugia malayi (E-value = 1E-148), which showed significantly higher level in RS (FDR = 3.81E-213) (S3 Table, Fig 4E). Only one bone morphogenetic protein (BMP) was identified at high levels in RS. BMP members are reported to play a crucial role in the formation of the shell nacre and prismatic layer; the result was evidenced by expression profiling and RNA interference technology. [72,73]

To validation the authenticity and functions of those genes mentioned above, ten genes were selected randomly for performing the qRT-PCR. The different expression between RS and WS was in union with the RNA-seq data, which demonstrated the accuracy of RNA-seq analysis (S3 Fig).

The identification of Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNPs)

Misa [74] was applied to screen 159,521 unigene sequences with total size of 106.6Mb, and 15,252 SSRs were detected, which were located in 13,299 unigenes. Among them, 1,632 unigenes contained more than 1 SSRs. Among the distribution of SSR types, the number of Mono-nucleotide is the highest, followed by the Di-nucleotide type, specially, AT/AT type is notable more than others (S4 Fig). 60,167 SNPs and 33,257 Indels were totally identified by using SOAPsnp between RS and WS. These results may provide valuable resource for further analysis, e.g. genetic diversity analysis, genetic linkage and QTL analysis.