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ACOMS+ 및 학술지 리포지터리 설명회

  • 한국과학기술정보연구원(KISTI) 서울분원 대회의실(별관 3층)
  • 2024년 07월 03일(수) 13:30
 

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연체동물 유전체 연구현황

Current Status of Genome Research in Phylum Mollusks

Abstract

The availability of fast and inexpensive sequencing technology has enabled researchers around the world to conduct many genome sequencing and expressed sequence tag (EST) projects of diverse organisms. In recent years, whole genome projects have been undertaken to sequence ten species from the phylum Mollusca. These include Aplysia californica, Lottia gigantea, Crassostrea virginica, Spisula solidissima, Mytilus californianus, Biomphalaria glabrata, Crepidula fornicata, Elysia chlorotica, Lottia scutum and Radix balthica. Additionally, complete mitochondrial genomes of 91 mollusks have been reported. In Korea, EST projects have been conducted in nine mollusk species that include Nesiohelix samarangae, Pisidium (Neopisidium) coreanum, Physa acuta, Incilaria fruhstorferi, Meretrix lusoria, Ruditapes philippinarum, Nordotis gigantea, Crassostrea gigas and Laternula elliptica. Finally, the mitochondrial genome projects from the Pacific Oyster (Crassostrea gigas) and the rock shell (Thais clavigera) have been conducted and reported. However, no systemic mollusk genome project has so far been conducted in Korea. In this report, the current status and research trends in mollusk genome study in Korea will be discussed.

keywords
Mollusks, Genome, EST

참고문헌

1.

Akasaki, T., Nikaido, M., Tsuchiya, K., Segawa, S., Hasegawa, M., and Okada, N. (2006) Extensive mitochondrial gene arrangements in coleoid Cephalopoda and their phylogenetic implications. Mol. Phylogenet Evol., 38: 648-658.

2.

Bandyopadhyay, P.K., Stevenson, B.J., Cady, M.T., Olivera, B.M., and Wolstenholme, D.R. (2006) Complete mitochondrial DNA sequence of a Conoidean gastropod, Lophiotoma (Xenuroturris) cerithiformis: gene order and gastropod phylogeny. Toxicon., 48: 29-43.

3.

Boore, J.L. (2006) The complete sequence of the mitochondrial genome of Nautilus macromphalus (Mollusca: Cephalopoda). BMC Genomics, 7: 182.

4.

Boore, J.L., and Brown, W.M. (1994) Complete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicata. Genetics, 138: 423-443.

5.

Boore, J.L., Medina, M., and Rosenberg, L.A. (2004) Complete sequences of the highly rearranged molluscan mitochondrial genomes of the Scaphopod Graptacme eborea and the bivalve Mytilus edulis. Mol. Biol. Evol., 21: 1492-1503.

6.

Breton, S., Beaupre, H.D., Stewart,D.T., Piontkivska, H., Karmakar, M., Bogan, A.E., Blier, P.U., and Hoeh, W.R. (2009) Comparative mitochondrial genomics of freshwater mussels (Bivalvia:Unionoida) with doubly uniparental inheritance of mtDNA: gender-specific open reading frames and putative origins of replication. Genetics, 183:1575-1589.

7.

Breton, S., Burger, G., Stewart, D.T., and Blier, P.U. (2006) Comparative analysis of gender-associated complete mitochondrial genomes in marine mussels (Mytilus spp.). Genetics, 172: 1107-1119.

8.

Burki, F., Shalchian-Tabrizi, K., and Pawlowski, J. (2008) Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes. Biol. Lett., 4: 366-369.

9.

Cao, L., Kenchington, E., Zouros, E., and Rodakis, G.C. (2004) Evidence that the large noncoding sequence is the main control region of maternally and paternally transmitted mitochondrial genomes of the marine mussel (Mytilus spp.). Genetics, 167:835-850.

10.

Cunha, R.L., Grande, C., and Zardoya, R. (2009) Neogastropod phylogenetic relationships based on entire mitochondrial genomes. BMC Evol. Biol., 9:210.

11.

DeJong, R.J., Emery, A.M., and Adema, C.M. (2004) The mitochondrial genome of Biomphalaria glabrata (Gastropoda: Basommatophora), intermediate host of Schistosoma mansoni. J. Parasitol., 90: 991-997.

12.

Dreyer, H., and Steiner, G. (2004) The complete sequence and gene organization of the mitochondrial genome of the gadilid scaphopod Siphonondentalium lobatum (Mollusca). Mol. Phylogenet Evol., 31:605-617.

13.

Dreyer, H., and Steiner, G. (2006) The complete sequences and gene organisation of the mitochondrial genomes of the heterodont bivalves Acanthocardia tuberculata and Hiatella arctica--and the first record for a putative Atpase subunit 8 gene in marine bivalves. Front Zool., 3: 13.

14.

Droege, M., and Hill, B. (2008) The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. J. Biotechnol., 136: 3-10.

15.

Grande, C., Templado, J., Cervera, J.L., and Zardoya, R. (2002) The complete mitochondrial genome of the nudibranch Roboastra europaea (Mollusca:Gastropoda) supports the monophyly of opisthobranchs. Mol. Biol. Evol., 19: 1672-1685.

16.

Grande, C., Templado, J., Cervera, J.L., and Zardoya, R. (2004) Molecular phylogeny of euthyneura (mollusca: gastropoda). Mol. Biol. Evol., 21: 303-313.

17.

Grande, C., Templado, J., Cervera, J.L., and Zardoya, R. (2004) Phylogenetic relationships among Opisthobranchia (Mollusca: Gastropoda) based on mitochondrial cox 1, trnV, and rrnL genes. Mol. Phylogenet Evol., 33: 378-388.

18.

Grande, C., Templado, J., and Zardoya, R. (2008) Evolution of gastropod mitochondrial genome arrangements. BMC Evol. Biol., 8: 61.

19.

Hatzoglou, E., Rodakis, G.C., and Lecanidou, R. (1995) Complete sequence and gene organization of the mitochondrial genome of the land snail Albinaria coerulea. Genetics, 140: 1353-1366.

20.

Hoffmann, R.J., Boore, J.L., and Brown, W.M. (1992) A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics, 131: 397-412.

21.

Knudsen, B., Kohn, A.B., Nahir, B., McFadden, C.S., and Moroz, L.L. (2006) Complete DNA sequence of the mitochondrial genome of the sea-slug, Aplysia californica: conservation of the gene order in Euthyneura. Mol. Phylogenet Evol., 38: 459-469.

22.

Kurabayashi, A., and Ueshima, R. (2000) Complete sequence of the mitochondrial DNA ofthe primitive opisthobranch gastropod Pupa strigosa: systematic implication of the genome organization. Mol. Biol. Evol., 17: 266-277.

23.

La Roche, J., Snyder, M., Cook, D.I., Fuller, K., and Zouros, E. (1990) Molecular characterization of a repeat element causing large-scale size variation in the mitochondrial DNA of the sea scallop Placopecten magellanicus. Mol. Biol. Evol., 7: 45-64.

24.

Liolios, K., Chen, I.M., Mavromatis, K., Tavernarakis, N., Hugenholtz, P., Markowitz, V.M., and Kyrpides, N.C. (2010) The Genomes OnLine Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res., 38: D346-354.

25.

Maynard, B.T., Kerr, L.J., McKiernan, J.M., Jansen, E.S., and Hanna, P.J. (2005) Mitochondrial DNA sequence and gene organization in the [corrected] Australian blacklip [corrected] abalone Haliotis rubra (leach). Mar. Biotechnol. (NY), 7: 645-658.

26.

McComish, B.J., Hills, S.F., Biggs, P.J., and Penny, D. (2010) Index-free de novo assembly and deconvolution of mixed mitochondrial genomes. Genome. Biol. Evol., 2: 410-424.

27.

Milbury, C.A., and Gaffney, P.M. (2005) Complete mitochondrial DNA sequence of the eastern oyster Crassostrea virginica. Mar. Biotechnol. (NY), 7:697-712.

28.

Mizi, A., Zouros, E., Moschonas, N., and Rodakis, G.C. (2005) The complete maternal and paternal mitochondrial genomes of the Mediterranean mussel Mytilus galloprovincialis: implications for the doubly uniparental inheritance mode of mtDNA. Mol. Biol. Evol., 22: 952-967.

29.

Morozova, O., and Marra, M.A. (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics, 92: 255-264.

30.

NCBI, (http://www.ncbi.nlm.nih.gov) The National Center for Biotechnology Information, NIH

31.

Ratnasingham, S., and Hebert, P.D. (2007) bold: The Barcode of Life Data System (http://www.barcodinglife.org). Mol. Ecol Notes, 7:355-364.

32.

Rawlings, T.A., MacInnis, M.J., Bieler, R., Boore, J.L., and Collins, T.M. (2010) Sessile snails, dynamic genomes: gene rearrangements within the mitochondrial genome of afamily of caenogastropod molluscs. BMC Genomics, 11: 440.

33.

Ren, J., Liu, X., Zhang, G., Liu, B., and Guo, X. (2009) "Tandem duplication-random loss" is not a real feature of oyster mitochondrial genomes. BMC Genomics, 10: 84.

34.

Ren, J., Shen, X., Jiang, F., and Liu, B. (2010) The mitochondrial genomes of two scallops, Argopecten irradians and Chlamys farreri (Mollusca: Bivalvia):the most highly rearranged gene order in the family Pectinidae. J. Mol. Evol., 70: 57-68.

35.

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.

36.

Rumpho, M.E., Worful, J.M., Lee, J., Kannan, K., Tyler, M.S., Bhattacharya, D., Moustafa, A., and Manhart, J.R. (2008) Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. Proc. Natl. Acad. Sci. USA, 105: 17867-17871.

37.

Sasuga, J., Yokobori, S., Kaifu, M., Ueda, T., Nishikawa, K., and Watanabe, K. (1999) Gene contents and organization of a mitochondrial DNA segment of the squid Loligo bleekeri. J. Mol. Evol., 48: 692-702.

38.

Sato, M., and Nagashima, K. (2001) Molecular characterization of a mitochondrial DNA segment from the Japanese scallop (Patinopecten yessoensis):demonstration of a region showing sequence polymorphism in the population. Mar. Biotechnol. (NY), 3: 370-379.

39.

Serb, J.M., and Lydeard, C. (2003) Complete mtDNA sequence of the North American freshwater mussel, Lampsilis ornata (Unionidae): an examinationof the evolution and phylogenetic utility of mitochondrial genome organization in Bivalvia (Mollusca). Mol. Biol. Evol., 20: 1854-1866.

40.

Simison, W.B., Lindberg, D.R., and Boore, J.L. (2006) Rolling circle amplification of metazoan mitochondrial genomes. Mol. Phylogenet. Evol., 39: 562-567.

41.

Terrett, J.A., Miles, S., and Thomas, R.H. (1996) Complete DNA sequence of the mitochondrial genome of Cepaea nemoralis (Gastropoda:Pulmonata). J. Mol. Evol., 42: 160-168.

42.

Timmermans, M.J., Dodsworth, S., Culverwell, C.L., Bocak, L., Ahrens, D., Littlewood, D.T., Pons, J., and Vogler, A.P. (2010) Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics. Nucleic Acids Res., 38: e197.

43.

Tomita, K., Ueda, T., and Watanabe, K. (1998) 7-Methylguanosine at the anticodon wobble position of squid mitochondrial tRNA(Ser)GCU: molecular basis for assignment of AGA/AGG codons as serine in invertebrate mitochondria. Biochim. Biophys. Acta., 1399: 78-82.

44.

Tomita, K., Yokobori, S., Oshima, T., Ueda, T., and Watanabe, K. (2002) The cephalopod Loligo bleekeri mitochondrial genome: multiplied noncoding regions and transposition of tRNA genes. J. Mol. Evol., 54:486-500.

45.

Wagele, H., Deusch, O., Handeler, K., Martin, R., Schmitt, V., Christa, G., Pinzger, B., Gould, S.B., Dagan, T., Klussmann-Kolb, A., and Martin, W. (2011) Transcriptomic Evidence That Longevity of Acquired Plastids in the Photosynthetic Slugs Elysia timida and Plakobranchus ocellatus Does Not Entail Lateral Transfer of Algal Nuclear Genes. Mol. Biol. Evol., 28: 699-706.

46.

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. Comp Biochem Physiol. Part. D. Genomics Proteomics, 5: 256-264.

47.

Weber, M., Teeling, H., Huang, S., Waldmann, J., Kassabgy, M., Fuchs, B.M., Klindworth, A., Klockow, C., Wichels, A., Gerdts, G., Amann, R., and Glockner, F.O. (2010) Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics. ISME J

48.

Wu, X., Xu, X., Yu, Z., Wei, Z., and Xia, J. (2010) Comparison of seven Crassostrea mitogenomes and phylogenetic analyses. Mol. Phylogenet Evol., 57:448-454.

49.

Yamazaki, N., Ueshima, R., Terrett, J.A., Yokobori, S., Kaifu, M., Segawa, R., Kobayashi, T., Numachi, K., Ueda, T., Nishikawa, K., Watanabe, K., and Thomas, R.H. (1997) Evolution of pulmonate gastropod mitochondrial genomes: comparisons of gene organizations of Euhadra, Cepaea and Albinaria and implications of unusual tRNA secondary structures. Genetics, 145: 749-758.

50.

Yang, R., Guo, X., Yang, J., Jiang, Y., Pang, B., Chen, C., Yao, Y., Qin, J., and Li, Q. (2009) Genomic research for important pathogenic bacteria in China. Sci. China C. Life Sci., 52: 50-63.

51.

Yokobori, S., Fukuda, N., Nakamura, M., Aoyama, T., and Oshima, T. (2004) Long-term conservation of six duplicated structural genes in cephalopod mitochondrial genomes. Mol. Biol. Evol., 21:2034-2046.

52.

Yokobori, S., Lindsay, D.J., Yoshida, M., Tsuchiya, K., Yamagishi, A., Maruyama, T., and Oshima, T. (2007) Mitochondrial genome structure and evolution in the living fossil vampire squid, Vampyroteuthis infernalis, and extant cephalopods. Mol. Phylogenet Evol., 44: 898-910.

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