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Identification of genes potentially involved in pearl formation by expressed sequence tag analysis of mantle from freshwater pearl mussel (Hyriopsis cumingii Lea).

ABSTRACT The triangle sail mussel (Hyriopsis cumingii Lea) is the most important mussel species exploited for commercial freshwater pearl production in China. However, little is known about the genes that are involved in pearl formation. A complementary DNA library from mantle tissue of Hyriopsis cumingii was constructed to identify the genes required for pearl formation. A total of 5,019 expressed sequence tags (ESTs) were sequenced, which resulted in the identification of 620 contigs and 1,151 singletons. BLAST analysis showed that nearly half (44.7%) of these unigenes were homologous to the known genes and 55.3% were genes with unknown functions. Based on the sequence similarities, 29 genes were putatively involved in pearl formation. These EST data provide the basis for future studies of the molecular mechanisms underlying pearl formation.

KEY WORDS: freshwater pearl mussel, expressed sequence tag, pearl formation, mantle

INTRODUCTION

Biominerals, including pearls, are organic-inorganic composites with exceptional toughness, strength, and hardness. The mechanical design of biominerals is intriguing, and scientists have been exploring it for many years (Stephen 2001). The mollusc shell, especially the nacre, is a masterpiece of natural design. It is composed of 2 layers: noncalcified and calcified. The noncalcified layer is called "periostracum," which is made from the organic materials secreted from the mantle. The main component of the calcified layer is calcium carbonate, calcite, or aragonite (Lowenstaum & Weiner 1989). Growth of the crystals is strictly regulated throughout the developmental stages in which the specific shell formation is based on the genetic background of the species. Although calcium carbonate accounts for more than 95% of the nacre weight, unlike inorganic calcium carbonate it is arranged in a highly functional and strictly controlled way under the instructions of many organic macromolecules secreted from the mantle tissues or elsewhere (Stephen 2001).

The extracellular matrix is an integrated system regulating protein--mineral, protein--protein, and feedback interactions between biominerals and the calcifying epithelium that synthesizes them (Gong et al. 2008). Thus, the molluscan matrix may be a source of bioactive molecules, and provides interesting insight into pearl formation and biomineralization. However, the organic layer is so thin that it has not been studied well because of the difficulty in obtaining materials from this layer. Heretofore, only a few matrix proteins have been identified from the nacre or the prismatic layer of molluscan shell (Zhang et al. 2006b).

The mantle is a thin organ lining the surface of the inner shell. It is composed of a layer of epithelium covering the mantle surface, muscle, connective tissue, and nerve fibers (Hiroshi et al. 2002). The extrapallial fluid, enclosed between the outer mantle epithelium and the inner shell surface, is a complex mixture of a large number of inorganic and organic substances. The mantle is positively involved in the regulation and maintenance of the extrapallial fluid, where calcium carbonate is crystallized, suggesting that synthesis of matrix proteins present in the calcified layer of the shell is dependent on the mantle (Gong et al. 2008). The importance of the mantle in shell formation is also evident from pearl cultivation, in which the quality of the mantle used greatly affects the surface microstructure of the oyster pearls, which are equivalent to the nacreous layer of the shell. The triangle sail mussel (Hyriopsis cumingii Lea), an endemic species in China, is mainly present in large lakes and rivers (Liu 1979). Since artificial propagation of H. cumingii was achieved in 1979, the species has become the most important mussel for commercial freshwater pearl production. Currently, the annual production of freshwater pearl has reached 1,800 metric tonnes in China, accounting for more than 95% of the total world output (Li et al. 2005). More than 90% of Chinese freshwater pearls were produced by the triangle sail mussel (Wang et al. 2006). However, little is known with regard to the molecular mechanisms underlying pearl formation.

Expressed sequence tags (ESTs) are single-pass, partial sequences of complementary DNA (cDNA) and have been used extensively for gene discovery and for studying gene expression profiles (Adams et al. 1991, Smith et al. 1996, Suzuki et al. 2004, Nair et al. 2005). In this study, we sequenced and analyzed 5,019 ESTs from a mantle cDNA library and identified 29 genes that are potentially involved in pearl formation in mussels. This information could facilitate understanding the molecular mechanisms of pearl formation and biomineralization.

MATERIALS AND METHODS

Mussel Tissue Sample

Live individuals of freshwater pearl mussel were collected from the Wangjiajing pearl farm, Zhuji City, Zhejiang Province, China. The mussels have been under mass selection since 2000 and reached the third selected generation in 2006. Nine-month-old mussels have been used for culturing pearls since March 2007. We chose mussels that can produce high-quality pearls, collected the mantle tissues, and stored the tissues at liquid nitrogen for future experiments.

eDNA Library Construction and Sequencing

Total RNA was extracted from the pearl mussel mantle using Unizol reagent (Biostar Genechip Inc., Shanghai, China). Messenger RNA (mRNA) was purified from total RNA using the Oligotex mRNA mini kit (Qiagen, Valencia, CA). First-strand cDNA was obtained by reverse transcription of mRNA and, subsequently, double-strand cDNA was synthesized. After end repair, adapter attachment, and digestion, these cDNAs were inserted into pBluescript lI SK (+) Vector (Stratagene, La Jolla, CA) and was subsequently transformed into Electro-MAXTM DH10BTM cells (Invitrogen, Carlsbad, CA). Individual colonies were randomly picked and grown in LB medium containing 100 [micro]g/mL ampicillin for 18 h at 37[degrees]C. Plasmids were extracted from each bacterial culture using the alkaline lysis method and were stored at -20[degrees]C until use. DNA sequencing was performed using the DYEnamic ET Terminator (GE Healthcare, Waukesha, WI) in the 5' direction (T3 primer: 5'-AATTAACCCTCACTAAAG-3') and the 3730XL DNA analyzer (Applied Biosystems, Foster City, CA).

Assembling and Bio-informatic Analysis

The raw data were "base called" using the Phred program (Ewing et al. 1998a, Ewing et al. 1998b). Vector sequences were screened by the Cross-Match program (University of Washington, Seattle, WA), and the linker sequences were trimmed manually. High-quality ESTs (>100 bp) were assembled and clustered into contiguous sequences (contigs) with the Phrap program (available at http://www.phrap.org). A Consed assembly viewer was used to remove misassembles from the contigs (Gordon et al. 1998). Unique sequences from contigs and singletons were recognized as unigenes. BLASTX and BLASTN were used to compare the sequences of unigenes with the National Center for Biotechnology Information (NCBI) nonredundant protein (nr) (E value [less than or equal to] 1.0 x [10.sup.5]) and nucleotide (nt) (E value [less than or equal to] 1.0 x [10.sup.-10]) databases for annotation (Altschul et al. 1990, Altschul et al. 1997). Sequences with no significant match to the nr or nt databases were partially identified by the InterProScan (Zdobnov & Apweiler 2001) (The sequence which translated protein length in six frames is no less than 30 amino acids were under InterProScan.), and the best-matched items were extracted as reliable results. Gene Ontology (GO) annotation (Ashburner et al. 2000) was based on BLASTX searching of the updated Universal Protein Resource (Uniprot) database (E value [less than or equal to] 1.0 x [10.sup.-5]). GO terms were assigned to all the well-annotated unigenes by performing Uniprot2GO (PERL script was written by ourselves). These terms were further classified and mapped at the second level to 3 GO categories. We also submitted the unigenes to the Kyoto Encyclopedia of Genes and Genomes (KEGG) online server (http://www.genome.jp/kaas-bin/kaas_main?mode=est_b) to acquire concrete metabolic pathway information.

RESULTS

EST Sequencing and General Characteristics

Pearl mussel mantle was used to generate a nonnormalized, directional cDNA library, as described in Materials and Methods. A total of 7,024 single colonies were randomly selected from the library for sequencing from the 5' end. After vector sequences were eliminated, 5,019 ESTs that were longer than 100 bp were characterized. All the ESTs have been deposited to GenBank with continuous accession numbers (GW691652-GW696670). In total, 1,771 unigenes consisting of 620 contigs and 1,151 singletons were assembled (Table 1). Approximately 12.5% of the contigs were composed of 2 EST sequences and nearly 4.6% of the contigs were constructed by more than 10 ESTs (Fig. 1). A large number of the sequences ranged from 500-700 bp (Fig. 2), and average GC content of these ESTs was 41.5%, with 90.3% between 31% and 50% (Fig. 3).

BLASTX was performed to compare the unigenes with the NCBI nr database with a cutoff E value of [10.sup.-5]. Sequences without a reliable match (E value > [10.sup.-5]) were subsequently compared with the NCBI nt database by performing BLASTN for annotation. With these 2 alignment algorithms, 791 unigenes were annotated. The distribution tendency of the E values upon the annotated unigenes is displayed in Figure 4. More than 85.5% of the annotated unigenes had an E value less than [10.sup.-10]; 239 unigenes (13.5%) matched the known genes with an E value of less than [10.sup.-50] indicating that the annotation is reliable and valid. A total of 980 nonannotated unigenes (55.3%) representing genes with unknown functions were identified in the pearl mussel mantle. These nonannotated sequences were partially identified by means of InterProScan searching. The query results showed that 296 sequences hit to "Epidermal Growth Factor (EGF) like region, conserved site," followed by 124 and 102 unigenes that match the genes encoding "2Fe-2S ferredoxin, iron-sulfur binding site," and "thiolase," respectively (Table 2).

Unigene Functional Category

We constructed a gene expression profile for the mantle tissue of pearl mussel based on GO. In this ontology, 30.2% (534 of 1,771 unigenes) of the unigenes identified in this study were classified into 3 functional categories: biological process, cellular component, and molecular process. The GO assignment details are available in the appendix. Some unigenes were classified into more than 1 subcategory, which resulted in the sum of the unigene ratio in each subcategory exceeding 100%. Among the unigenes categorized as cellular components, 64.2% were classified as cell, 45.3% as organelle, and 38.2% as macromolecular complex. The majority (47.2%) of the unigenes categorized as molecular functions was associated with binding, followed by those involved in catalytic activity (37.1%). The unigenes categorized as biological process were classified into metabolic processes and cellular processes, comprising 61.0% and 59.4%, respectively, of the total unigenes in this category. An overview of the classification is shown in Figure 5. A total of 417 unigenes (23.5%) were assigned specific pathways based on KEGG. Approximately 43% of these unigenes were involved in metabolic processes, including energy metabolism, carbohydrate metabolism, and glycan biosynthesis and metabolism. The remaining unigenes were assigned to pathways associated with genetic information processing (33%), cellular processes (11%), human diseases (7%), and environmental information processing (6%; Table 3).

[FIGURE 1 OMITTED]

Identification of Genes Potentially Involved in Pearl Formation

Twenty-nine unigenes showed significant similarities to genes that may be involved in the formation of pearls. These unigenes were classified into 3 broad groups according to the predicted functions (Table 4). Calcium carbonate is the main component of the pearl; thus, calcium metabolism plays an important role in pearl formation. We identified unigenes encoding 5 proteins that were involved in calcium metabolism. We also identified 12 unigenes encoding extracellular matrix proteins and 12 unigenes encoding cytoskeleton proteins, both protein types that are potentially involved in the regulation of pearl formation.

DISCUSSION

A total of 5,019 ESTs were sequenced, resulting in the identification of 620 contigs and 1,15l singletons. BLAST analysis showed that less than half (44.7%) of these unigenes were homotogues of known genes, whereas 55.3% belong to unknown identities. Potentially novel genes may be functionally important in an evolutionary context (Chistiakov et al. 2008). The level of homology between different aquaculture species is generally low (Chu et al. 2006, Dong & Xiang 2007, Zhao et al. 2009). Thus, genome research on these species has lagged behind that of other taxa. Because the technology for DNA sequencing is steadily improving and getting less expensive, EST resources have been recently developed for economically important aquaculture species, such as half-smooth tongue sole (Cynoglossus semilaevis) (Wang et al. 2009); Atlantic salmon: the gilthead seabream (Sparus aurata) (Senger et al. 2006, Sarropoulou et al. 2007); bay scallop (Argopecten irradians irradians) (Song et al. 2006); pacific oyster (Crassostrea gigas) (Gueguen et al. 2003), Mytilus edulis, Ruditapes decussates, and Bathymodiolus azoricus (Tanguy et al. 2008); and the chinese mitten crab (Eriocheir sinensis) (Zhao et al. 2009).

[FIGURE 2 OMITTED]

[FIGURE 3 OMITTED]

Based on the sequence similarities, we identified 29 genes that were putatively involved in pearl formation. Pearl, as well as mollusc shell, is the biomineralization product of calcium carbonate crystals, matrix proteins, and other biopolymers. Initially, insoluble matrix proteins form a framework structure and provide a nucleation sheet for the first nucleation of highly oriented crystals. Then, calcium ions are assembled by water-soluble matrix proteins and finally deposited in orderly arrays on the nucleation sites of the framework (Mann 1988). In the current study, genes potentially involved in the pearl information were classified into 3 functional groups: calcium metabolism, extracellular matrix, and cytoskeleton.

[FIGURE 4 OMITTED]

Calcium ions are not only a regulatory molecule involved in many physiological processes in bivalves, but they also are the primary cation participating in the formation of shell structures (Gong et al. 2008). During the process of shell formation, large amounts of calcium ions are continuously depositing onto the framework formed by matrix proteins. The mechanisms of calcium metabolism, such as [Ca.sup.2+] uptake, accumulation, transport, incorporation, and the particular regulators involved during these processes remain an attractive field for further studies. In the current study, 5 proteins involved in calcium metabolism were identified. One of them, calmodulin (CAM), is a multifunctional calcium sensor protein that participates in several cellular processes, such as secretion and metabolism of calcium (Kretschmer & Fritzsche 2004). As a pivotal regulator of calcium metabolism, CaM regulates many calcium metabolism-related proteins, including cyclic nucleotide phosphodiesterase, adenylate cyclase, [Ca.sup.2+]-adenosine triphosphatase (ATPase), as well as [Ca.sup.2+] channel and [Ca.sup.2+] release channel proteins (Ashby & Tepikin 2002, Saimi & Kung 2002). It has also been demonstrated that the calcium stores in Drosophila are regulated by CaM (Arnon et al. 1997). In marine bivalves, calcium is taken up by the gill from the external medium and transported to the mantle epithelium. During this process, CaM has been thought to play a regulatory role in the membrane [Ca.sup.2+]-ATPase system or act as a "calcium sink," and be involved in the ciliary arrest of calcium (Stommel et al. 1982, Stommel & Stephens 1985). In addition, calcium ions can also be transported by the calcium pump directly across the mantle surface into the extrapallial space for the formation of shells (Richardson et al. 1981). In recent years, L-type [Ca.sup.2+] channels, which are regulated by CaM, have been suggested to be involved in the calcium transport and calcification in some marine invertebrates (Zoccola et al. 1999). Because CaM is an essential subunit of calcium channels and a crucial regulator of [Ca.sup.2+]-ATPase in nearly all organisms, we propose that CaM plays an important role in the regulation of the uptake and transport of calcium for pearl formation. The molecular mechanisms of the regulation of pearl formation by CaM remain for future studies.

[FIGURE 5 OMITTED]

Previous studies have demonstrated that extracellular matrix proteins regulate the formation of pearls. For example, several shell matrix proteins from Pinctata fucata, and the related congeneric species were involved in calcium carbonate crystal and framework formation (Zhang et al. 2003a, Zhang et al. 2003b, Li et al. 2004, Zhang et al. 2006a, Zhang et al. 2006c). Identification of these shell matrix proteins makes P. fucata a useful model organism for the study of pearl formation and shell biomineralization. In this study, 12 extracellular matrix protein genes were identified (Table 4). Chitin is one of the key players in the complex pools of extracellular proteins and polysaccharides, because chitin contributes to the framework for implementation of biological hierarchy into the calcified biomineral. In brachiopod and mollusc shells, an alignment between the orientation of chitin fibers and the crystallographic axes of the mineral phase was observed both in vivo (Falini & Fermani 2004) and in vitro (Falini et al. 2002). This implies that chitin is functionally important for the guidance of mineral deposition in the mollusc shell. However, little is known with regard to the composition of the enzyme complex responsible for chitin deposition in the mollusc shells. Identification of genes encoding chitinase, chitin deacetylase and chitin binding protein in the current study will facilitate understanding the mechanisms of chitin deposition. Collagen proteins have been found in the extracellular spaces of all Metazoa. In teleostian fish, a collagen is observed to be located in the saccular otolithic organ (Davis et al. 1995). This suggests the hypothesis that collagenlike molecules are secreted into extrapallial fluid from the mantle and are involved in the regulation of shell formation.

Cytoskeleton proteins form a framework structure that is essential to create special microenvironments to accommodate the growing minerals and to supply a specific surface for the organic-inorganic molecular reorganization (Marin et al. 2008). Among the proteins belonging to the cytoskeleton category, we found general cytoskeletal factors such as actin, myosin, tubulin, and capping protein. Capping protein is a ubiquitous actin binding protein that regulates actin assembly and cell motility (Hart et al. 1997, Hart et al. 2000), suggesting that capping protein might be involved in the regulation of pearl formation.

In addition to known sequences, we have also identified many novel cDNA sequences. Further functional characterization of the genes isolated in this study will undoubtedly increase our understanding of pearl formation and calcification in mussel. Gene transcription profiling is one important step toward identifying genes that underlie important traits (Vasemagi & Primmer 2005). Transcription profiling has been successful in unraveling the genetic basis of calcification in phytoplankton (Fujiwara et al. 2007). To validate the role of candidate genes played in pearl formation, we may first examine the difference in expression of all the candidate genes between mussels producing high- and low-quality pearls. Pearl quality traits are complex genetic traits, with multiple genetic and environmental variables contributing to the observed phenotype. The variants of 1 gene generally have only a modest effect. Genetic association studies may be an effective approach in detecting the effects of common variants with modest effects (Newton-Cheh & Hirschhorn 2005). With the explosion in single nucleotide polymorphism discovery and genotyping technologies, large-scale association studies have become feasible, and small-scale association studies have become plentiful (Kim & Misra 2007). Therefore, future work may include examining whether there is genetic variation in any of the candidate genes that might be associated with pearl quality.
APPENDIX
The GO assignment results of the pearl mussel mantle cDNA library

                                                   No. of     Percent
GO Level 1    GO Level 2                          Unigenes   Unigene *

Cellular      Cell                                     343        64.2
  component   Envelope                                  28         5.2
              Extracellular matrix                       8         1.5
              Extracellular matrix part                  6         1.1
              Extracellular region                      34         6.4
              Extracellular region part                 13         2.4
              Macromolecular complex                   204        38.2
              Membrane-enclosed lumen                    5         0.9
              Organelle                                242        45.3
              Organelle part                           101        18.9
              Synapse                                    1         0.2
Molecular     Antioxidant activity                       3         0.6
  function    Binding                                  252        47.2
              Catalytic activity                       198        37.1
              Enzyme regulator activity                 38         7.1
              Molecular transducer activity             15         2.8
              Motor activity                            23         4.3
              Structural molecule activity             150        28.1
              Transcription regulator                    6         1.1

              Translation regulator activity            11         2.1
              Transporter activity                      50         9.4
Biological    Biological adhesion                        4         0.7
  process     Biological regulation                     39         7.3
              Cellular process                         317        59.4
              Developmental process                     14         2.6
              Establishment of localization             75        14.0
              Gene expression                          152        28.5
              Growth                                     2         0.4
              Immune system process                      2         0.4
              Localization                              75        14.0
              Metabolic process                        326        61.0
              Multiorganism process                      1         0.2
              Multicellular organismal process          13         2.4
              Reproduction                               3         0.6
              Reproductive process                       1         0.2
              Response to stimulus                      16         3.0

* Of a total of 1,771,534 unigenes were classified by GO.


ACKNOWLEDGMENTS

This study was supported by the Prophase Program of the Key Project of Chinese National Programs for Fundamental Research and Development (973 program; 2009CB126000), the National Natural Science Foundation of China (30871923), the Construction Project of Provincial University for Promoting Research Ability (08390510100) from Science and Technology Commission of the Shanghai Municipal Government, the Shanghai Leading Academic Discipline Project (Y1101), and the "Chen Guang" project (2008CG56) supported by Shanghai Municipal Education Commission and Shanghai Education Development Foundation.

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ZHIYI BAI, (1) YUXIN YIN, (2,3) SONGNIAN HU, (2) GUILING WANG, (1) XIAOWEI ZHANG (2) AND JIALE LI (1) *

(1) Key Laboratory of Aquatic Genetic Resources and Utilization Certificated by Ministry of Agriculture, E-Institute of Shanghai Universities, Shanghai Ocean University, Shanghai 201306, China; (2) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China; (3) Graduate School of Chinese Academy of Sciences, Beijing 100049, China

* Corresponding author. E-mail: jlli@shou.edu.cn
TABLE 1.
A summary of the properties of cDNA library clones.

Description                                 No.

Total cDNAs sequenced                      7,024
Total analyzed cDNAs                       5,019
Average EST size (bp after trimming)         547
Total no. of unigenes                      1,771
No. of contigs                               620
No. of orphan sequences (singletons)       1,151
Matched known genes, n (%)                   791 (44.7%)
No database match, n (%)                     980 (55.3%)

TABLE 2.
Protein families and functional domains in the cDNA library.

IPR No.      Annotation                          No. of Unigenes

IPRO13032    EGF-like region, conserved site          296
IPR006058    2Fe-2S ferredoxin, iron-sulfur           124
               binding site
IPR002155    Thiolase                                 102
IPR000020    Anaphylatoxin/fibulin                     19
IPR001007    von Willebrand factor, type C             15
IPR001778    Pollen allergen Poa pIX/Phl pVl,          14
               C-terminal
IPR001450    4Fe-4S ferredoxin, iron-sulfur             6
               binding
IPR004051    Potassium channel, voltage                 3
               dependent, Kv1A
IPR007899    CHAD                                       3
IPR000217    Tubulin                                    2
1PRO15812    Integrin beta subunit                      2
IPR000104    Antifreeze protein, type I                 2
IPR006081    Alpha defensin                             2
IPR011142    Spider toxin CSTX, conserved site          1
IPR001316    Peptidase SIA, streptogrisin               1
IPR002049    EGF-like, laminin                          1

EGF, epidermal growth factor; CHAD, Chondroadherin; CSTX,
Cupiennius salei toxin.

TABLE 3.
KEGG classification of the unigenes from pearl mussel mantle

                              No. of                     No. of KEGG
Category                     Unigenes    Percentage    Pathways Mapped

Metabolism                                   43
  Carbohydrate                  30                           15
  metabolism
  Energy metabolism             47                            6
  Lipid metabolism              18                           10
  Nucleotide metabolism          6                            2
  Amino acid metabolism         18                           10
  Metabolism of other           11                            4
    amino acids
  Glycan biosynthesis           24                            9
    and metabolism
  Metabolism of cofactors        9                            4
    and vitamins
  Biosynthesis of                2                            2
    secondary metabolites
  Xenobiotic                    16                            8
    biodegradation and
    metabolism
Genetic information                          33
  processing
  Transcription                  3                            1
  Translation                  115                            2
  Folding, sorting, and         20                            6
    degradation
Environmental                                 6
  information processing
  Membrane transport             1                            1
  Signal transduction           16                            7
  Signaling molecules            6                            2
    and interaction
Cellular processes                           11
  Cell motility                  7                            1
  Cell growth and death          7                            4
  Cell communication            14                            4
  Endocrine system               9                            6
  Immune system                  7                            3
  Nervous system                 1                            1
  Sensory system                 1                            1
Human diseases                                7
  Cancers                        9                            6
  Neurodegenerative             16                            6
    diseases
  Infectious diseases            4                            2

TABLE 4.
The ESTS that showed similarity to genes potentially involved
in pearl formation.

                                       GenBank
                                      Accession
Putative Function                        No.     Redundancy   E Value

Extracellular matrix
  67-kD Laminin receptor precursor    GW695570        54     3.00E-78
  Chitin deacetylase 1                GW695655         2     2.00E-20
  Chitinase                           GW694969         1     9.00E-55
  Fasciclinlike protein               GW695476         4     2.00E-32
  Peritrophic membrane chitin         GW693632         1     3.00E-31
    binding protein
  Keratinocyte-associated             GW694171         1     9.00E-38
    protein 2
  Matrilin 2                          GW695726         1     7.00E-06
  Papilin                             GW695162         3     2.00E-12
  Primary mesenchyme specific         GW692983         1     3.00E-16
    protein MSP 130-related-2
  Tuftelin-interacting protein 11     GW696610         1     4.00E-27
  Uncharacterized conserved
    secreted protein                  GW692379         2     6.00E-32
  Collagen pro alpha-chain            GW695250         7     8.00E-16
Cytoskeleton
  Actin                               GW695333         5     0
  Actin 2                             GW695890        16     1.00E-88
  Beta tubulin                        GW693210        10     8.00E-79
  Capping protein (actin filament)    GW695934         1     2.00E-32
    muscle Z-line
  Cytoplasmic dynein light chain      GW693259         2     2.00E-46
  Fibrinogenlike protein 1            GW695346         1     8.00E-18
  Myosin                              GW695809        14     2.00E-54
  Paramyosin                          GW693466       131     2.00E-95
  Tubulin, alpha 2 isoform 2          GW693966         5     1.00E-146

  Tubulin, alpha 3d                   GW692043         1     1.00E-102
  Actin-related protein 2/3           GW695716         1     9.00E-41
    complex subunit 2
  Tropomyosin                         GW692578         3     1.00E-32
Calcium metabolism
  Hypothetical protein CaO19.6835     GW691712         1     4.00E-14
  Calmodulin variant 3                GW692024         1     6.00E-73
  Metal-binding protein               GW693606         4     2.00E-12
  Sarcoplasmic calcium-binding        GW693092         1     3.00E-69
    protein
  Stanniocalcinlike protein           GW692635         1     1.00E-12

                                       Organism with Highest
Putative Function                         Similar Sequence

Extracellular matrix
  67-kD Laminin receptor precursor    Pinctada fucata
  Chitin deacetylase 1                Tribolium castaneum
  Chitinase                           Mus musculus
  Fasciclinlike protein               Aplysia californica
  Peritrophic membrane chitin         Culex quinquefasciatus
    binding protein
  Keratinocyte-associated             Monodelphis domestica
    protein 2
  Matrilin 2                          Gallusgallus
  Papilin                             Acyrthosiphon pisum
  Primary mesenchyme specific         Strongylocentrotus
    protein MSP 130-related-2           purpuratus
  Tuftelin-interacting protein 11     Xenopus tropicales
  Uncharacterized conserved
    secreted protein                  Idimrtarina baltica
  Collagen pro alpha-chain            Haliotis discus
Cytoskeleton
  Actin                               Pinctada fucata
  Actin 2                             Crassostrea gigas
  Beta tubulin                        Monosiga bre vicollis
  Capping protein (actin filament)    Danio rerio
    muscle Z-line
  Cytoplasmic dynein light chain      Aedes aegtpti
  Fibrinogenlike protein 1            Mus musculus
  Myosin                              Mytilusgalloprovincialis
  Paramyosin                          Mytilusgalloprovincialis
  Tubulin, alpha 2 isoform 2          Strongylocentrotats
                                        purpuratus
  Tubulin, alpha 3d                   Egous caballos
  Actin-related protein 2/3           Taeniopygia guttata
    complex subunit 2
  Tropomyosin                         Balanus rostrums
Calcium metabolism
  Hypothetical protein CaO19.6835     Candida albicans
  Calmodulin variant 3                Taeniopygia guttata
  Metal-binding protein               Adineta vaga
  Sarcoplasmic calcium-binding        Meretrix lusoria
    protein
  Stanniocalcinlike protein           Haliotis diversicolor

When more than 1 clone matched the same gene, only the highest
scoring clone is listed and the total number of clone (i.e.,
including the listed one) is  indicated in the Redundancy column.
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Article Details
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Author:Bai, Zhiyi; Yin, Yuxin; Hu, Songnian; Wang, Guiling; Zhang, Xiaowei; Li, Jiale
Publication:Journal of Shellfish Research
Article Type:Report
Geographic Code:9CHIN
Date:Aug 1, 2010
Words:5908
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