ISSN : 1225-3480
The importance of biological resources has been gradually increasing, and mollusks have been utilized as main fishery resources in terrestrial ecosystems. But little is known about genomic and transcriptional analysis in mollusks. This is the first report on the transcriptomic profile of Meretrix lusoria. In this study, we constructed cDNA library and determined 542 of distinct EST sequences composed of 284 singletons and 95 contigs. At first, we identified 180 of EST sequences that have significant hits on protein sequences of the exclusive Mollusks database through BLASTX program and 343 of EST sequences that have significant hits on NCBI NR database. We also found that 211 of putative sequences through local BLAST (blastx, E < e-10) search against KOG database were classified into 16 functional categories. Some kinds of immune response related genes encoding allograft inflammatory factor 1 (AIF-1), B-cell translocation gene 1 (BTG1), C-type lectin A, thioester-containing protein and 26S proteasome regulatory complex were identified. To determine phylogenetic relationship, we identified partial sequences of four genes (COX1, COX2, 12S rRNA and NADH dehydrogenase) that significantly matched with the mitochondrial genomes of 3 species-Ml (Meretrix lusoria), Mp (Meretrix petechialis) and Mm (Meretrix meretrix). As a result, we found that there was a little bit of a difference between sequences of Korean isolates and other known isolates. This study will be useful to develop breeding technology and might also be helpful to establish a classification system.
Altschul, S.F., Gish, W., Miller, W., Meyers, E.W., and Lipman, D.J. (1990) Basic Local Alignment Search Tool. Journal of Molecular Biology, 215: 403-410.
Anderson, G.J. (1982) Comments of the settlement of Manila clam spats (Trapes philippinarum) at Filucy Bay, Washigton. USA. Journal of Shellfish Research, 2: 115.
Bang, I.S., Han, Y.S., Lee, J.-S., and Lee, Y.S. (2010) Current Status of Genome Research in Phylum Mollusks. The Korean Journal of Malacology, 26: 317-326.
Blandin, S., and Levashina, E.A. (2004) Thioestercontaining proteins and insect immunity. Molecular Immunology, 40: 903-908.
Cambi, A., and Figdor, C. (2009) Necrosis: C-type lectins sense cell death. Current Biology, 19: R375-378.
Canapa, A., Marota, I., Rollo, F., and Olmo, E. (1996) Phylogenetic analysis of Veneridae (Bivalvia): comparison of molecular and palaeontological data. Journal of Molecular Evolution, 43: 517-522.
Canapa, A., Marota, I., Rollo, F., and Olmo, E. (1999) The small-subunit rRNA gene sequences of venerids and the phylogeny of bivalvia. Journal of Molecular Evolution, 48: 463-468.
Canapa, A., Schiaparelli, S., Marota, I., and Barucca, M. (2003) Molecular data from the 16S rRNA gene for the phylogeny of Veneridae (Mollusca: Bivalvia). Marine Biology, 142: 1125-1130.
Chen, A.-h., Li, Z.-x., and Feng, G.-n. (2009) Phylogenetic Relationships of the Genus Meretrix (Mollusca:Veneridae) Based on Mitochondrial COI Gene Sequences. Zoological Research, 30: 233-239.
Cheng, H.L., Xia, D.Q., Wu, T.T., Meng, X.P., Ji, H.J., and Dong, Z.G. (2006) Study on sequences of ribosomal DNA internal transcribed spacers of clams belonging to the Veneridae family (Mollusca: Bivalvia). Yi Chuan Xue Bao, 33: 702-710.
Choi, K.C. (1971) Ecological studies of the clams , Meretrix lusoria and Cyclina sinenis for increasing seed clam yield. Korean Journal of Limnology, 4: 1-10.
Choi, S.S. (1975) Comparative studies on the early embryonic development and growth of Meretrix lusoria and Cyclina sinensis. Journal of The Korean Fisheries Society 8: 185-195.
Choi, S.S., and Song, Y.K. (1975) Studies on the artificial fertilization and development of Cyclina sinensis. Journal of The Korean Fisheries Society, 8: 185-195.
Drickamer, K. (1999) C-type lectin-like domains. Current Opinion Structural Biology, 9: 585-590.
Ewing, B., and Green, P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Research, 8: 186-194.
Ewing, B., Hillier, L., Wendl, M.C., and Green, P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Research, 8: 175-185.
Jung, H.T., Kim, J., and Choi, S.D. (2004) Phylogenetic relationship of the five Korean Veneridae clams, Bivalviam, Veneroida according to morphological characters. Journal of Aquaculture, 17: 197-208.
Kappner, I., and Bieler, R. (2006) Phylogeny of venus clams (Bivalvia: Venerinae) as inferred from nuclear and mitochondrial gene sequences. Molecular Phylogenetics and Evolution, 40: 317-331.
Kim, A.Y. (1971) Ecological studies on the propagation of Saxidomus purpuratus (Sowerby). Journal of The Korean Fisheries Society, 4: 92-98.
Kim, H.J., and Zhang, C.I. (1999) A Population Ecological Study of Short necked Clam, Tapes philippinarum in the Adjacent Waters of Jinhae. Journal of The Korean Fisheries Society, 2: 32-43.
Kim, J.J., Kim, S.C., and Hong, H.C. (2004) Molecular Phylogeny of Veneridae (Bivalvia: Heteroconchia) on the Basis of Partial Sequences of Mitochondrial Cytochrome Oxidase I. Korean Journal of Malacology, 20: 171-181.
Kwon, O.K., Park, K.M., and Lee, J.S. (1993) Coloured Shells of Korea. Coloured Shells of Korea, : 371.
Lee, B.D. (1956) The catalogue of Molluscan Shell of Korea. Bulletin of Pusan Fisheries College., 1: 53-100.
Lee, H., Cha, S., Lee, M.-S., Cho, G.J., Choi, W.S., and Suk, K. (2003) Role of Antiproliferative B Cell Translocation Gene-1 as an Apoptotic Sensitizer in Activation-Induced Cell Death of Brain Microglia. The Journal of Immunology, 171: 5802-5811.
Lee, J.Y., and Kim, Y.G. (1991) Environmental survey on the cultivation ground in the West coast of Korea. 3. Environmental conditions for Hard clam farm in Puan. Journal of Aquaculture, 4: 111-128.
Lee, Y.S., Jo, Y.H., Kim, D.S., Kim, D.W., Kim, M.Y., Choi, S.H., Yon, J.O., Byun, I.S., Kang, B.R., Jeong, K.H., and Park, H.S. (2004) Construction of BLAST Server for Mollusks. Korean Journal of Malacology, 20: 165-169
Loosanoff, V.L., and Davis, H.C. (1963) Rearing of bivalve molluscus. Advanced Marine Biology, 1: 1-136.
Low, P., Bussell, K., Dawson, S.P., Billett, M.A., Mayer, R.J., and Reynolds, S.E. (1997) Expression of a 26S proteasome ATPase subunit, MS73, in muscles that undergo developmentally programmed cell death, and its control by ecdysteroid hormones in the insect Manduca sexta. FEBS Letters 400: 345-349.
Mikkelsen, P.M., Bieler, R., Kappner, I., and Rawlings, T.A. (2006) Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules.Zoological Journal of the Linnean Society, 148: 439-521.
Min, D.K., Lee, J.S., Koh, D.B., and Je, J.K. (2004) Mollusks in Korea. Min Molluscan Research Institutte
Pertea, G., Huang, X., Liang, F., Antonescu, V., Sultana, R., Karamycheva, S., Lee, Y., White, J., Cheung, F., Parvizi, B., Tsai, J., and Quackenbush, J. (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics, 19: 651-652.
Ren, J., Shen, X., Sun, M., Jiang, F., Yu, Y., Chi, Z., and Liu, B. (2009) The complete mitochondrial genome of the clam Meretrix petechialis (Mollusca: Bivalvia: Veneridae). Mitochondrial DNA, 20: 78-87.
Rice, P., Longden, I., and Bleasby, A. (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics, 16: 276-277.
Salvi, D., and Mariottini, P. (2012) Molecular phylogenetics in 2D: ITS2 rRNA evolution and sequence-structure barcode from Veneridae to Bivalvia. Molecular Phylogenetics and Evolution, 65: 792-798.
Shiba, N. (1934) A catalogue of the mollusca in Chosen(Corea). Journal of the Chosen Natural History, 18: 6-31.
Tamura, K., and Nei, M. (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10: 512-526.
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28: 2731-2739.
Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., Koonin, E.V., Krylov, D.M., Mazumder, R., Mekhedov, S.L., Nikolskaya, A.N., Rao, B.S., Smirnov, S., Sverdlov, A.V., Vasudevan, S., Wolf, Y.I., Yin, J.J., and Natale, D.A. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4: 41.
Wang, H., Zhang, S., Li, Y., and Liu, B. (2010) Complete mtDNA of Meretrix lusoria (Bivalvia: Veneridae) reveals the presence of an atp8 gene, length variation and heteroplasmy in the control region. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 5: 256-264.
Xu, X., Wu, X., and Yu, Z. (2010) The mitogenome of Paphia euglypta (Bivalvia: Veneridae) and comparative mitogenomic analyses of three venerids. Genome, 53: 1041-1052.
Yang, Z.F., Ho, D.W., Lau, C.K., Lam, C.T., Lum, C.T., Poon, R.T., and Fan, S.T. (2005) Allograft inflammatory factor-1 (AIF-1) is crucial for the survival and pro-inflammatory activity of macrophages. International Immunology, 17: 1391-1397.
Yue, X., Liu, B., Sun, L., and Tang, B. (2011) Cloning and characterization of a hsp70 gene from Asiatic hard clam Meretrix meretrix which is involved in the immune response against bacterial infection. Fish & Shellfish Immunology, 30: 791-799.
