메뉴 건너뛰기




Volumn 6, Issue , 2016, Pages

Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions

Author keywords

[No Author keywords available]

Indexed keywords

TOLL LIKE RECEPTOR;

EID: 84964917300     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep25211     Document Type: Article
Times cited : (54)

References (68)
  • 1
    • 84966372768 scopus 로고    scopus 로고
    • Alternative adaptive immunity strategies: Coelacanth, cod and shark immunity
    • Buonocore, F. & Gerdol, M. Alternative adaptive immunity strategies: coelacanth, cod and shark immunity. Mol Immunol, doi: 10.1016/j.molimm.2015.09.003 (2015).
    • (2015) Mol Immunol
    • Buonocore, F.1    Gerdol, M.2
  • 2
    • 85028097860 scopus 로고    scopus 로고
    • Advances in research of fsh immune-relevant genes: A comparative overview of innate and adaptive immunity in teleosts
    • Zhu, L. Y., Nie, L., Zhu, G., Xiang, L. X. & Shao, J. Z. Advances in research of fsh immune-relevant genes: a comparative overview of innate and adaptive immunity in teleosts. Dev Comp Immunol 39, 39-62, doi: 10.1016/j.dci.2012.04.001 (2013).
    • (2013) Dev Comp Immunol , vol.39 , pp. 39-62
    • Zhu, L.Y.1    Nie, L.2    Zhu, G.3    Xiang, L.X.4    Shao, J.Z.5
  • 3
    • 22844435410 scopus 로고    scopus 로고
    • Innate immunity of fsh (overview)
    • Magnadottir, B. Innate immunity of fsh (overview). Fish Shellfsh Immunol 20, 137-151, doi: 10.1016/j.fsi.2004.09.006 (2006).
    • (2006) Fish Shellfsh Immunol , vol.20 , pp. 137-151
    • Magnadottir, B.1
  • 4
    • 77950343791 scopus 로고    scopus 로고
    • Pattern recognition receptors and infammation
    • Takeuchi, O. & Akira, S. Pattern recognition receptors and infammation. Cell 140, 805-820, doi: 10.1016/j.cell.2010.01.022 (2010).
    • (2010) Cell , vol.140 , pp. 805-820
    • Takeuchi, O.1    Akira, S.2
  • 5
    • 84918564833 scopus 로고    scopus 로고
    • Toll-like receptor signaling pathways
    • Kawasaki, T. & Kawai, T. Toll-like receptor signaling pathways. Frontiers in immunology 5, 461, doi: 10.3389/fmmu.2014.00461 (2014).
    • (2014) Frontiers in Immunology , vol.5 , pp. 461
    • Kawasaki, T.1    Kawai, T.2
  • 6
    • 84874046317 scopus 로고    scopus 로고
    • Toll-like receptors of deuterostome invertebrates
    • Satake, H. & Sekiguchi, T. Toll-like receptors of deuterostome invertebrates. Frontiers in immunology 3, 34, doi: 10.3389/fmmu.2012.00034 (2012).
    • (2012) Frontiers in Immunology , vol.3 , pp. 34
    • Satake, H.1    Sekiguchi, T.2
  • 7
    • 80455168991 scopus 로고    scopus 로고
    • Toll-like receptors in bony fish: From genomics to function
    • Palti, Y. Toll-like receptors in bony fish: from genomics to function. Dev Comp Immunol 35, 1263-1272, doi: 10.1016/j. dci.2011.03.006 (2011).
    • (2011) Dev Comp Immunol , vol.35 , pp. 1263-1272
    • Palti, Y.1
  • 8
    • 22144452520 scopus 로고    scopus 로고
    • The evolution of vertebrate Toll-like receptors
    • Roach, J. C. et al. The evolution of vertebrate Toll-like receptors. Proc Natl Acad Sci USA 102, 9577-9582, doi: 10.1073/pnas.0502272102 (2005).
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 9577-9582
    • Roach, J.C.1
  • 9
    • 84890368964 scopus 로고    scopus 로고
    • Toll-like receptors (TLRs) in aquatic animals: Signaling pathways, expressions and immune responses
    • Rauta, P. R., Samanta, M., Dash, H. R., Nayak, B. & Das, S. Toll-like receptors (TLRs) in aquatic animals: signaling pathways, expressions and immune responses. Immunol Lett 158, 14-24, doi: 10.1016/j.imlet.2013.11.013 (2014).
    • (2014) Immunol Lett , vol.158 , pp. 14-24
    • Rauta, P.R.1    Samanta, M.2    Dash, H.R.3    Nayak, B.4    Das, S.5
  • 10
    • 84906272537 scopus 로고    scopus 로고
    • Origin and evolution of adaptive immunity
    • Boehm, T. & Swann, J. B. Origin and evolution of adaptive immunity. Annual review of animal biosciences 2, 259-283, doi: 10.1146/annurev-animal-022513-114201 (2014).
    • (2014) Annual Review of Animal Biosciences , vol.2 , pp. 259-283
    • Boehm, T.1    Swann, J.B.2
  • 11
    • 84859407338 scopus 로고    scopus 로고
    • VLR-based adaptive immunity
    • Boehm, T. et al. VLR-based adaptive immunity. Annu Rev Immunol 30, 203-220, doi: 10.1146/annurev-immunol-020711-075038 (2012).
    • (2012) Annu Rev Immunol , vol.30 , pp. 203-220
    • Boehm, T.1
  • 13
    • 80052606169 scopus 로고    scopus 로고
    • The genome sequence of Atlantic cod reveals a unique immune system
    • Star, B. et al. The genome sequence of Atlantic cod reveals a unique immune system. Nature 477, 207-210, doi: 10.1038/nature10342 (2011).
    • (2011) Nature , vol.477 , pp. 207-210
    • Star, B.1
  • 14
    • 84883407340 scopus 로고    scopus 로고
    • Unraveling the evolution of the Atlantic cod's (Gadus morhua L.) alternative immune strategy
    • Malmstrom, M., Jentof, S., Gregers, T. F. & Jakobsen, K. S. Unraveling the evolution of the Atlantic cod's (Gadus morhua L.) alternative immune strategy. PLoS One 8, e74004, doi: 10.1371/journal.pone.0074004 (2013).
    • (2013) PLoS One , vol.8 , pp. e74004
    • Malmstrom, M.1    Jentof, S.2    Gregers, T.F.3    Jakobsen, K.S.4
  • 15
    • 84863876490 scopus 로고    scopus 로고
    • Why does the immune system of Atlantic cod lack MHC II?
    • Star, B. & Jentof, S. Why does the immune system of Atlantic cod lack MHC II? Bioessays 34, 648-651, doi: 10.1002/bies.201200005 (2012).
    • (2012) Bioessays , vol.34 , pp. 648-651
    • Star, B.1    Jentof, S.2
  • 16
    • 80052146101 scopus 로고    scopus 로고
    • The machinery of Nod-like receptors: Refning the paths to immunity and cell death
    • Saleh, M. The machinery of Nod-like receptors: refning the paths to immunity and cell death. Immunological Reviews 243, 235-246, doi: 10.1111/j.1600-065X.2011.01045.x (2011).
    • (2011) Immunological Reviews , vol.243 , pp. 235-246
    • Saleh, M.1
  • 17
    • 84907507219 scopus 로고    scopus 로고
    • Toll-like receptor recognition of bacteria in fsh: Ligand specifcity and signal pathways
    • Zhang, J. et al. Toll-like receptor recognition of bacteria in fsh: ligand specifcity and signal pathways. Fish Shellfsh Immunol 41, 380-388, doi: 10.1016/j.fsi.2014.09.022 (2014).
    • (2014) Fish Shellfsh Immunol , vol.41 , pp. 380-388
    • Zhang, J.1
  • 18
    • 78650680945 scopus 로고    scopus 로고
    • Molecular cloning and characterization of Toll-like receptor 14 in Japanese founder
    • Hwang, S. D., Kondo, H., Hirono, I. & Aoki, T. Molecular cloning and characterization of Toll-like receptor 14 in Japanese founder, Paralichthys olivaceus. Fish Shellfsh Immunol 30, 425-429, doi: 10.1016/j.fsi.2010.08.005 (2011).
    • (2011) Paralichthys Olivaceus. Fish Shellfsh Immunol , vol.30 , pp. 425-429
    • Hwang, S.D.1    Kondo, H.2    Hirono, I.3    Aoki, T.4
  • 19
    • 84882874320 scopus 로고    scopus 로고
    • Expression profiles of toll-like receptors in channel catfsh (Ictalurus punctatus) afer infection with Ichthyophthirius multifliis
    • Zhao, F. et al. Expression profiles of toll-like receptors in channel catfsh (Ictalurus punctatus) afer infection with Ichthyophthirius multifliis. Fish Shellfsh Immunol 35, 993-997, doi: 10.1016/j.fsi.2013.05.023 (2013).
    • (2013) Fish Shellfsh Immunol , vol.35 , pp. 993-997
    • Zhao, F.1
  • 20
    • 79959447465 scopus 로고    scopus 로고
    • Structural biology of the Toll-like receptor family
    • Kang, J. Y. & Lee, J. O. Structural biology of the Toll-like receptor family. Annual review of biochemistry 80, 917-941, doi: 10.1146/annurev-biochem-052909-141507 (2011).
    • (2011) Annual Review of Biochemistry , vol.80 , pp. 917-941
    • Kang, J.Y.1    Lee, J.O.2
  • 21
    • 83355166902 scopus 로고    scopus 로고
    • PAMPs, PRRs and the genomics of gram negative bacterial recognition in fsh
    • Boltana, S., Roher, N., Goetz, F. W. & Mackenzie, S. A. PAMPs, PRRs and the genomics of gram negative bacterial recognition in fsh. Dev Comp Immunol 35, 1195-1203, doi: 10.1016/j.dci.2011.02.010 (2011).
    • (2011) Dev Comp Immunol , vol.35 , pp. 1195-1203
    • Boltana, S.1    Roher, N.2    Goetz, F.W.3    Mackenzie, S.A.4
  • 22
    • 27744526784 scopus 로고    scopus 로고
    • TLR3 and TLR7 are targeted to the same intracellular compartments by distinct regulatory elements
    • Nishiya, T., Kajita, E., Miwa, S. & Defranco, A. L. TLR3 and TLR7 are targeted to the same intracellular compartments by distinct regulatory elements. The Journal of biological chemistry 280, 37107-37117, doi: 10.1074/jbc.M504951200 (2005).
    • (2005) The Journal of Biological Chemistry , vol.280 , pp. 37107-37117
    • Nishiya, T.1    Kajita, E.2    Miwa, S.3    Defranco, A.L.4
  • 23
    • 33845963384 scopus 로고    scopus 로고
    • Cytoplasmic targeting motifs control localization of toll-like receptor 9
    • Leifer, C. A. et al. Cytoplasmic targeting motifs control localization of toll-like receptor 9. The Journal of biological chemistry 281, 35585-35592, doi: 10.1074/jbc.M607511200 (2006).
    • (2006) The Journal of Biological Chemistry , vol.281 , pp. 35585-35592
    • Leifer, C.A.1
  • 24
    • 84866558003 scopus 로고    scopus 로고
    • Proteolytic processing regulates Toll-like receptor 3 stability and endosomal localization
    • Qi, R., Singh, D. & Kao, C. C. Proteolytic processing regulates Toll-like receptor 3 stability and endosomal localization. The Journal of biological chemistry 287, 32617-32629, doi: 10.1074/jbc.M112.387803 (2012).
    • (2012) The Journal of Biological Chemistry , vol.287 , pp. 32617-32629
    • Qi, R.1    Singh, D.2    Kao, C.C.3
  • 25
    • 57349191215 scopus 로고    scopus 로고
    • The ectodomain of Toll-like receptor 9 is cleaved to generate a functional receptor
    • Ewald, S. E. et al. The ectodomain of Toll-like receptor 9 is cleaved to generate a functional receptor. Nature 456, 658-662, doi: 10.1038/nature07405 (2008).
    • (2008) Nature , vol.456 , pp. 658-662
    • Ewald, S.E.1
  • 26
    • 68749108013 scopus 로고    scopus 로고
    • Chicken TLR21 acts as a functional homologue to mammalian TLR9 in the recognition of CpG oligodeoxynucleotides
    • Brownlie, R. et al. Chicken TLR21 acts as a functional homologue to mammalian TLR9 in the recognition of CpG oligodeoxynucleotides. Mol Immunol 46, 3163-3170, doi: 10.1016/j.molimm.2009.06.002 (2009).
    • (2009) Mol Immunol , vol.46 , pp. 3163-3170
    • Brownlie, R.1
  • 27
    • 77956216374 scopus 로고    scopus 로고
    • Chicken TLR21 is an innate CpG DNA receptor distinct from mammalian TLR9
    • Keestra, A. M., de Zoete, M. R., Bouwman, L. I. & van Putten, J. P. Chicken TLR21 is an innate CpG DNA receptor distinct from mammalian TLR9. J Immunol 185, 460-467, doi: 10.4049/jimmunol.0901921 (2010).
    • (2010) J Immunol , vol.185 , pp. 460-467
    • Keestra, A.M.1    De Zoete, M.R.2    Bouwman, L.I.3    Van Putten, J.P.4
  • 28
    • 51549108374 scopus 로고    scopus 로고
    • Teleost TLR22 recognizes RNA duplex to induce IFN and protect cells from birnaviruses
    • Matsuo, A. et al. Teleost TLR22 recognizes RNA duplex to induce IFN and protect cells from birnaviruses. J Immunol 181, 3474-3485 (2008).
    • (2008) J Immunol , vol.181 , pp. 3474-3485
    • Matsuo, A.1
  • 29
    • 84865153588 scopus 로고    scopus 로고
    • Positive selection pressure within teleost Toll-like receptors tlr21 and tlr22 subfamilies and their response to temperature stress and microbial components in zebrafsh
    • Sundaram, A. Y., Consuegra, S., Kiron, V. & Fernandes, J. M. Positive selection pressure within teleost Toll-like receptors tlr21 and tlr22 subfamilies and their response to temperature stress and microbial components in zebrafsh. Molecular biology reports 39, 8965-8975, doi: 10.1007/s11033-012-1765-y (2012).
    • (2012) Molecular Biology Reports , vol.39 , pp. 8965-8975
    • Sundaram, A.Y.1    Consuegra, S.2    Kiron, V.3    Fernandes, J.M.4
  • 30
    • 84871537925 scopus 로고    scopus 로고
    • Diversifcation of the expanded teleost-specifc toll-like receptor family in Atlantic cod, Gadus morhua
    • Sundaram, A. Y., Kiron, V., Dopazo, J. & Fernandes, J. M. Diversifcation of the expanded teleost-specifc toll-like receptor family in Atlantic cod, Gadus morhua. BMC evolutionary biology 12, 256, doi: 10.1186/1471-2148-12-256 (2012).
    • (2012) BMC Evolutionary Biology , vol.12 , pp. 256
    • Sundaram, A.Y.1    Kiron, V.2    Dopazo, J.3    Fernandes, J.M.4
  • 31
    • 84937896920 scopus 로고    scopus 로고
    • Molecular cloning and comparative responses of Toll-like receptor 22 following ligands stimulation and parasitic infection in yellowtail (Seriola lalandi)
    • Reyes-Becerril, M. et al. Molecular cloning and comparative responses of Toll-like receptor 22 following ligands stimulation and parasitic infection in yellowtail (Seriola lalandi). Fish Shellfsh Immunol 46, 323-333, doi: 10.1016/j.fsi.2015.06.020 (2015).
    • (2015) Fish Shellfsh Immunol , vol.46 , pp. 323-333
    • Reyes-Becerril, M.1
  • 32
    • 84954367628 scopus 로고    scopus 로고
    • Molecular cloning of Salmo salar Toll-like receptors (TLR1, TLR22, TLR5M and TLR5S) and expression analysis in SHK-1 cells during Piscirickettsia salmonis infection
    • Salazar, C., Haussmann, D., Kausel, G. & Figueroa, J. Molecular cloning of Salmo salar Toll-like receptors (TLR1, TLR22, TLR5M and TLR5S) and expression analysis in SHK-1 cells during Piscirickettsia salmonis infection. J Fish Dis, doi: 10.1111/jfd.12354 (2015).
    • (2015) J Fish Dis
    • Salazar, C.1    Haussmann, D.2    Kausel, G.3    Figueroa, J.4
  • 33
    • 79952789527 scopus 로고    scopus 로고
    • UNC93B1 is essential for TLR11 activation and IL-12-dependent host resistance to Toxoplasma gondii
    • Pifer, R., Benson, A., Sturge, C. R. & Yarovinsky, F. UNC93B1 is essential for TLR11 activation and IL-12-dependent host resistance to Toxoplasma gondii. The Journal of biological chemistry 286, 3307-3314, doi: 10.1074/jbc.M110.171025 (2011).
    • (2011) The Journal of Biological Chemistry , vol.286 , pp. 3307-3314
    • Pifer, R.1    Benson, A.2    Sturge, C.R.3    Yarovinsky, F.4
  • 34
    • 84872761427 scopus 로고    scopus 로고
    • Recognition of proflin by Toll-like receptor 12 is critical for host resistance to Toxoplasma gondii
    • Koblansky, A. A. et al. Recognition of proflin by Toll-like receptor 12 is critical for host resistance to Toxoplasma gondii. Immunity 38, 119-130, doi: 10.1016/j.immuni.2012.09.016 (2013).
    • (2013) Immunity , vol.38 , pp. 119-130
    • Koblansky, A.A.1
  • 35
    • 84925537059 scopus 로고    scopus 로고
    • Understanding the distinguishable structural and functional features in zebrafsh TLR3 and TLR22, and their binding modes with fsh dsRNA viruses: An exploratory structural model analysis
    • Sahoo, B. R. et al. Understanding the distinguishable structural and functional features in zebrafsh TLR3 and TLR22, and their binding modes with fsh dsRNA viruses: an exploratory structural model analysis. Amino acids 47, 381-400, doi: 10.1007/s00726-014-1872-2 (2015).
    • (2015) Amino Acids , vol.47 , pp. 381-400
    • Sahoo, B.R.1
  • 36
    • 79953890803 scopus 로고    scopus 로고
    • The structural biology of Toll-like receptors
    • Botos, I., Segal, D. M. & Davies, D. R. The structural biology of Toll-like receptors. Structure (London, England: 1993) 19, 447-459, doi: 10.1016/j.str.2011.02.004 (2011).
    • (2011) Structure (London England: 1993) , vol.19 , pp. 447-459
    • Botos, I.1    Segal, D.M.2    Davies, D.R.3
  • 37
    • 43349087755 scopus 로고    scopus 로고
    • Heterodimerization of TLR2 with TLR1 or TLR6 expands the ligand spectrum but does not lead to diferential signaling
    • Farhat, K. et al. Heterodimerization of TLR2 with TLR1 or TLR6 expands the ligand spectrum but does not lead to diferential signaling. Journal of leukocyte biology 83, 692-701, doi: 10.1189/jlb.0807586 (2008).
    • (2008) Journal of Leukocyte Biology , vol.83 , pp. 692-701
    • Farhat, K.1
  • 38
    • 84886041693 scopus 로고    scopus 로고
    • Cooperation of TLR12 and TLR11 in the IRF8-dependent IL-12 response to Toxoplasma gondii proflin
    • Raetz, M. et al. Cooperation of TLR12 and TLR11 in the IRF8-dependent IL-12 response to Toxoplasma gondii proflin. J Immunol 191, 4818-4827, doi: 10.4049/jimmunol.1301301 (2013).
    • (2013) J Immunol , vol.191 , pp. 4818-4827
    • Raetz, M.1
  • 39
    • 84872596639 scopus 로고    scopus 로고
    • Combined action of nucleic acid-sensing Toll-like receptors and TLR11/TLR12 heterodimers imparts resistance to Toxoplasma gondii in mice
    • Andrade, W. A. et al. Combined action of nucleic acid-sensing Toll-like receptors and TLR11/TLR12 heterodimers imparts resistance to Toxoplasma gondii in mice. Cell host & microbe 13, 42-53, doi: 10.1016/j.chom.2012.12.003 (2013).
    • (2013) Cell Host & Microbe , vol.13 , pp. 42-53
    • Andrade, W.A.1
  • 40
    • 75649087741 scopus 로고    scopus 로고
    • CD36 ligands promote sterile infammation through assembly of a Toll-like receptor 4 and 6 heterodimer
    • Stewart, C. R. et al. CD36 ligands promote sterile infammation through assembly of a Toll-like receptor 4 and 6 heterodimer. Nat Immunol 11, 155-161, doi: 10.1038/ni.1836 (2010).
    • (2010) Nat Immunol , vol.11 , pp. 155-161
    • Stewart, C.R.1
  • 41
    • 34548608447 scopus 로고    scopus 로고
    • Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide
    • Jin, M. S. et al. Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide. Cell 130, 1071-1082, doi: 10.1016/j.cell.2007.09.008 (2007).
    • (2007) Cell , vol.130 , pp. 1071-1082
    • Jin, M.S.1
  • 42
    • 84911977204 scopus 로고    scopus 로고
    • Diferential Toll-like receptor (TLR) mRNA expression patterns during chicken embryological development
    • Kannaki, T. R., Reddy, M. R., Verma, P. C. & Shanmugam, M. Diferential Toll-like receptor (TLR) mRNA expression patterns during chicken embryological development. Animal biotechnology 26, 130-135, doi: 10.1080/10495398.2014.939658 (2015).
    • (2015) Animal Biotechnology , vol.26 , pp. 130-135
    • Kannaki, T.R.1    Reddy, M.R.2    Verma, P.C.3    Shanmugam, M.4
  • 43
    • 70349325524 scopus 로고    scopus 로고
    • The evolutionary signifcance of ancient genome duplications
    • Van de Peer, Y., Maere, S. & Meyer, A. The evolutionary signifcance of ancient genome duplications. Nat Rev Genet 10, 725-732, doi: 10.1038/nrg2600 (2009).
    • (2009) Nat Rev Genet , vol.10 , pp. 725-732
    • Van De Peer, Y.1    Maere, S.2    Meyer, A.3
  • 44
    • 84925861941 scopus 로고    scopus 로고
    • The birth-and-death evolution of multigene families revisited
    • Eirin-Lopez, J. M., Rebordinos, L., Rooney, A. P. & Rozas, J. The birth-and-death evolution of multigene families revisited. Genome dynamics 7, 170-196, doi: 10.1159/000337119 (2012).
    • (2012) Genome Dynamics , vol.7 , pp. 170-196
    • Eirin-Lopez, J.M.1    Rebordinos, L.2    Rooney, A.P.3    Rozas, J.4
  • 45
    • 27944477670 scopus 로고    scopus 로고
    • Concerted and birth-and-death evolution of multigene families
    • Nei, M. & Rooney, A. P. Concerted and birth-and-death evolution of multigene families. Annual review of genetics 39, 121-152, doi: 10.1146/annurev.genet.39.073003.112240 (2005).
    • (2005) Annual Review of Genetics , vol.39 , pp. 121-152
    • Nei, M.1    Rooney, A.P.2
  • 46
    • 83655181433 scopus 로고    scopus 로고
    • Signatures of positive selection in Toll-like receptor (TLR) genes in mammals
    • Areal, H., Abrantes, J. & Esteves, P. J. Signatures of positive selection in Toll-like receptor (TLR) genes in mammals. BMC evolutionary biology 11, 368, doi: 10.1186/1471-2148-11-368 (2011).
    • (2011) BMC Evolutionary Biology , vol.11 , pp. 368
    • Areal, H.1    Abrantes, J.2    Esteves, P.J.3
  • 47
    • 68249118173 scopus 로고    scopus 로고
    • Evolutionary dynamics of human Toll-like receptors and their diferent contributions to host defense
    • Barreiro, L. B. et al. Evolutionary dynamics of human Toll-like receptors and their diferent contributions to host defense. PLoS genetics 5, e1000562, doi: 10.1371/journal.pgen.1000562 (2009).
    • (2009) PLoS Genetics , vol.5 , pp. e1000562
    • Barreiro, L.B.1
  • 48
    • 84861816807 scopus 로고    scopus 로고
    • Molecular evolution of vertebrate Toll-like receptors: Evolutionary rate difference between their leucine-rich repeats and their TIR domains
    • Mikami, T., Miyashita, H., Takatsuka, S., Kuroki, Y. & Matsushima, N. Molecular evolution of vertebrate Toll-like receptors: Evolutionary rate difference between their leucine-rich repeats and their TIR domains. Gene 503, 235-243, doi: 10.1016/j. gene.2012.04.007 (2012).
    • (2012) Gene , vol.503 , pp. 235-243
    • Mikami, T.1    Miyashita, H.2    Takatsuka, S.3    Kuroki, Y.4    Matsushima, N.5
  • 49
    • 80054913451 scopus 로고    scopus 로고
    • FLASH: Fast length adjustment of short reads to improve genome assemblies
    • Magoc, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics (Oxford, England) 27, 2957-2963, doi: 10.1093/bioinformatics/btr507 (2011).
    • (2011) Bioinformatics (Oxford England) , vol.27 , pp. 2957-2963
    • Magoc, T.1    Salzberg, S.L.2
  • 50
    • 57249105124 scopus 로고    scopus 로고
    • Aggressive assembly of pyrosequencing reads with mates
    • Miller, J. R. et al. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics (Oxford, England) 24, 2818-2824, doi: 10.1093/bioinformatics/btn548 (2008).
    • (2008) Bioinformatics (Oxford, England) , vol.24 , pp. 2818-2824
    • Miller, J.R.1
  • 51
    • 84869814079 scopus 로고    scopus 로고
    • Mind the gap: Upgrading genomes with Pacific Biosciences RS long-read sequencing technology
    • English, A. C. et al. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One 7, e47768, doi: 10.1371/journal.pone.0047768 (2012).
    • (2012) PLoS One , vol.7 , pp. e47768
    • English, A.C.1
  • 52
    • 84914689868 scopus 로고    scopus 로고
    • Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement
    • Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9, e112963, doi: 10.1371/journal.pone.0112963 (2014).
    • (2014) PLoS One , vol.9 , pp. e112963
    • Walker, B.J.1
  • 53
    • 84946037477 scopus 로고    scopus 로고
    • Ensembl 2015
    • Cunningham, F. et al. Ensembl 2015. Nucleic Acids Res 43, D662-669, doi: 10.1093/nar/gku1010 (2015).
    • (2015) Nucleic Acids Res , vol.43 , pp. D662-669
    • Cunningham, F.1
  • 54
    • 84946069451 scopus 로고    scopus 로고
    • UniProt. UniProt: A hub for protein information
    • UniProt. UniProt: a hub for protein information. Nucleic Acids Res 43, D204-212, doi: 10.1093/nar/gku989 (2015).
    • (2015) Nucleic Acids Res , vol.43 , pp. D204-212
  • 55
    • 74049108922 scopus 로고    scopus 로고
    • BLAST+: Architecture and applications
    • Camacho, C. et al. BLAST+: architecture and applications. BMC bioinformatics 10, 421, doi: 10.1186/1471-2105-10-421 (2009).
    • (2009) BMC Bioinformatics , vol.10 , pp. 421
    • Camacho, C.1
  • 56
    • 80053651587 scopus 로고    scopus 로고
    • GenBank
    • Benson, D. A. et al. GenBank. Nucleic Acids Res 41, D36-42, doi: 10.1093/nar/gks1195 (2013).
    • (2013) Nucleic Acids Res , vol.41 , pp. D36-42
    • Benson, D.A.1
  • 57
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura, K. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular biology and evolution 28, 2731-2739, doi: 10.1093/molbev/msr121 (2011).
    • (2011) Molecular Biology and Evolution , vol.28 , pp. 2731-2739
    • Tamura, K.1
  • 58
    • 79960264362 scopus 로고    scopus 로고
    • Full-length transcriptome assembly from RNA-Seq data without a reference genome
    • Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature biotechnology 29, 644-652, doi: 10.1038/nbt.1883 (2011).
    • (2011) Nature Biotechnology , vol.29 , pp. 644-652
    • Grabherr, M.G.1
  • 59
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: A Bioconductor package for diferential expression analysis of digital gene expression data
    • Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for diferential expression analysis of digital gene expression data. Bioinformatics (Oxford, England) 26, 139-140, doi: 10.1093/bioinformatics/btp616 (2010).
    • (2010) Bioinformatics (Oxford, England) , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 60
    • 84964901589 scopus 로고    scopus 로고
    • Sickle-a windowed adaptive trimming tool for FASTQ fles using quality
    • Sickle-a windowed adaptive trimming tool for FASTQ fles using quality.
  • 61
    • 80255127234 scopus 로고    scopus 로고
    • Cutadapt removes adapter sequences from high-throughput sequencing reads
    • doi: citeulike-article-id:11851772
    • Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. Bioinformatics in Action 17, 10-12, doi: citeulike-article-id:11851772 (2012).
    • (2012) Bioinformatics in Action , vol.17 , pp. 10-12
    • Martin, M.1
  • 62
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28, 27-30 (2000).
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 63
    • 84930074657 scopus 로고    scopus 로고
    • The Phyre2 web portal for protein modeling, prediction and analysis
    • Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N. & Sternberg, M. J. The Phyre2 web portal for protein modeling, prediction and analysis. Nature protocols 10, 845-858, doi: 10.1038/nprot.2015.053 (2015).
    • (2015) Nature Protocols , vol.10 , pp. 845-858
    • Kelley, L.A.1    Mezulis, S.2    Yates, C.M.3    Wass, M.N.4    Sternberg, M.J.5
  • 64
    • 84964872767 scopus 로고    scopus 로고
    • Jmol: an open-source Java viewer for chemical structures in 3D
    • Jmol: an open-source Java viewer for chemical structures in 3D, http://www.jmol.org/.
  • 65
    • 77957233168 scopus 로고    scopus 로고
    • Datamonkey 2010: A suite of phylogenetic analysis tools for evolutionary biology
    • Delport, W., Poon, A. F., Frost, S. D. & Kosakovsky Pond, S. L. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics (Oxford, England) 26, 2455-2457, doi: 10.1093/bioinformatics/btq429 (2010).
    • (2010) Bioinformatics (Oxford, England) , vol.26 , pp. 2455-2457
    • Delport, W.1    Poon, A.F.2    Frost, S.D.3    Kosakovsky Pond, S.L.4
  • 66
    • 18744382506 scopus 로고    scopus 로고
    • ProtTest: Selection of best-ft models of protein evolution
    • Abascal, F., Zardoya, R. & Posada, D. ProtTest: selection of best-ft models of protein evolution. Bioinformatics (Oxford, England) 21, 2104-2105, doi: 10.1093/bioinformatics/bti263 (2005).
    • (2005) Bioinformatics (Oxford, England) , vol.21 , pp. 2104-2105
    • Abascal, F.1    Zardoya, R.2    Posada, D.3
  • 67
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (Oxford, England) 22, 2688-2690, doi: 10.1093/bioinformatics/btl446 (2006).
    • (2006) Bioinformatics (Oxford, England) , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 68
    • 84964815049 scopus 로고    scopus 로고
    • FigTree
    • FigTree http://tree.bio.ed.ac.uk/sofware/fgtree/(2015).
    • (2015)


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.