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http://dx.doi.org/10.9710/kjm.2012.28.4.377

Expressed sequence tag analysis of Meretrix lusoria (Veneridae) in Korea  

Kang, Jung-Ha (Biotechnology Research Division, NFRDI)
Jeong, Ji Eun (Department of Parasitology, College of Medicine and UHRC, Inje University)
Kim, Bong Seok (Biotechnology Research Division, NFRDI)
An, Chel-Min (Biotechnology Research Division, NFRDI)
Kang, Hyun-Sook (Biotechnology Research Division, NFRDI)
Kang, Se-Won (Department of Parasitology, College of Medicine and UHRC, Inje University)
Hwang, Hee Ju (Department of Parasitology, College of Medicine and UHRC, Inje University)
Han, Yeon Soo (Department of Agricultural Biology, Chonnam National University)
Chae, Sung-Hwa (Research Institute, GnC Bio Co., LTD.)
Ko, Hyun-Sook (Department of Biological Science, Silla University)
Lee, Jun-Sang (Division of Life Sciences, College of Natural Sciences, Kangwon National University)
Lee, Yong Seok (Department of Parasitology, College of Medicine and UHRC, Inje University)
Publication Information
The Korean Journal of Malacology / v.28, no.4, 2012 , pp. 377-384 More about this Journal
Abstract
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.
Keywords
Meretrix lusoria; EST sequence; Molecular phylogenetic Study;
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1 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.   DOI   ScienceOn
2 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.   DOI   ScienceOn
3 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.   DOI   ScienceOn
4 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.   DOI
5 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.   DOI   ScienceOn
6 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.   DOI   ScienceOn
7 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.   DOI
8 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.
9 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.
10 Blandin, S., and Levashina, E.A. (2004) Thioestercontaining proteins and insect immunity. Molecular Immunology, 40: 903-908.   DOI   ScienceOn
11 Cambi, A., and Figdor, C. (2009) Necrosis: C-type lectins sense cell death. Current Biology, 19: R375-378.   DOI   ScienceOn
12 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.   DOI
13 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.   DOI
14 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.   DOI
15 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.
16 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.   DOI
17 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.
18 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.
19 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.
20 Drickamer, K. (1999) C-type lectin-like domains. Current Opinion Structural Biology, 9: 585-590.   DOI   ScienceOn
21 Ewing, B., and Green, P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Research, 8: 186-194.   DOI
22 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.   DOI   ScienceOn
23 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.
24 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.
25 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.   DOI   ScienceOn
26 Kim, A.Y. (1971) Ecological studies on the propagation of Saxidomus purpuratus (Sowerby). Journal of The Korean Fisheries Society, 4: 92-98.
27 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.
28 Kwon, O.K., Park, K.M., and Lee, J.S. (1993) Coloured Shells of Korea. Coloured Shells of Korea, : 371.
29 Lee, B.D. (1956) The catalogue of Molluscan Shell of Korea. Bulletin of Pusan Fisheries College., 1: 53-100.
30 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.   DOI
31 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.
32 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.
33 Loosanoff, V.L., and Davis, H.C. (1963) Rearing of bivalve molluscus. Advanced Marine Biology, 1: 1-136.   DOI
34 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.   DOI   ScienceOn
35 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.   DOI   ScienceOn
36 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.   DOI   ScienceOn
37 Min, D.K., Lee, J.S., Koh, D.B., and Je, J.K. (2004) Mollusks in Korea. Min Molluscan Research Institutte
38 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.   DOI   ScienceOn
39 Rice, P., Longden, I., and Bleasby, A. (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics, 16: 276-277.   DOI   ScienceOn
40 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.   DOI   ScienceOn
41 Shiba, N. (1934) A catalogue of the mollusca in Chosen(Corea). Journal of the Chosen Natural History, 18: 6-31.
42 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.