-
1
-
-
84885030225
-
Comparative genomics reveals insight into virulence strategies of plant pathogenic oomycetes
-
Adhikari, B. N., and Hamilton., J. P., Zerillo, M. M., Tisserat, N., Lévesque, C. A., and Buell, C. R. 2013. Comparative genomics reveals insight into virulence strategies of plant pathogenic oomycetes. PLoS One 8:e75072.
-
(2013)
PLoS One
, vol.8
-
-
Adhikari, B.N.1
Hamilton, J.P.2
Zerillo, M.M.3
Tisserat, N.4
Lévesque, C.A.5
Buell, C.R.6
-
2
-
-
0014243809
-
Cell wall chemistry, morphogenesis, and taxonomy of fungi
-
Bartnicki-Garcia, S. 1968. Cell wall chemistry, morphogenesis, and taxonomy of fungi. Annu. Rev. Microbiol. 22:87-108.
-
(1968)
Annu. Rev. Microbiol.
, vol.22
, pp. 87-108
-
-
Bartnicki-Garcia, S.1
-
3
-
-
59949097135
-
Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome
-
Baucom, R. S., and Estill., J. C., Leebens-Mack, J., and Bennetzen, J. L. 2009. Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Res. 19:243-254.
-
(2009)
Genome Res.
, vol.19
, pp. 243-254
-
-
Baucom, R.S.1
Estill, J.C.2
Leebens-Mack, J.3
Bennetzen, J.L.4
-
4
-
-
78650126298
-
Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome
-
Baxter, L., Tripathy, S., Ishaque, N., Boot, N., Cabral, A., Kemen, E., Thines, M., Ah-Fong, A., Anderson, R., Badejoko, W., Bittner-Eddy, P., Boore, J. L., and Chibucos., M. C., Coates, M., Dehal, P., Delehaunty, K., Dong, S., Downton, P., Dumas, B., Fabro, G., Fronick, C., Fuerstenberg, S. I., Fulton, L., Gaulin, E., Govers, F., Hughes, L., Humphray, S., Jiang, R. H. Y., Judelson, H., Kamoun, S., Kyung, K., Meijer, H., Minx, P., Morris, P., Nelson, J., Phuntumart, V., Qutob, D., Rehmany, A., Rougon-Cardoso, A., Ryden, P., Torto-Alalibo, T., Studholme, D., Wang, Y., Win, J., Wood, J., Clifton, S. W., Rogers, J., Van den Ackerveken, G., Jones, J. D. G., McDowell, J. M., Beynon, J., and Tyler, B. M. 2010. Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome. Science 330:1549-1551.
-
(2010)
Science
, vol.330
, pp. 1549-1551
-
-
Baxter, L.1
Tripathy, S.2
Ishaque, N.3
Boot, N.4
Cabral, A.5
Kemen, E.6
Thines, M.7
Ah-Fong, A.8
Anderson, R.9
Badejoko, W.10
Bittner-Eddy, P.11
Boore, J.L.12
Chibucos, M.C.13
Coates, M.14
Dehal, P.15
Delehaunty, K.16
Dong, S.17
Downton, P.18
Dumas, B.19
Fabro, G.20
Fronick, C.21
Fuerstenberg, S.I.22
Fulton, L.23
Gaulin, E.24
Govers, F.25
Hughes, L.26
Humphray, S.27
Jiang, R.H.Y.28
Judelson, H.29
Kamoun, S.30
Kyung, K.31
Meijer, H.32
Minx, P.33
Morris, P.34
Nelson, J.35
Phuntumart, V.36
Qutob, D.37
Rehmany, A.38
Rougon-Cardoso, A.39
Ryden, P.40
Torto-Alalibo, T.41
Studholme, D.42
Wang, Y.43
Win, J.44
Wood, J.45
Clifton, S.W.46
Rogers, J.47
Van Den Ackerveken, G.48
Jones, J.D.G.49
McDowell, J.M.50
Beynon, J.51
Tyler, B.M.52
more..
-
5
-
-
0033555906
-
Tandem repeats finder: A program to analyze DNA sequences
-
Benson, G. 1999. Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res. 27:573-580.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 573-580
-
-
Benson, G.1
-
6
-
-
79951530130
-
Scaffolding pre-assembled contigs using SSPACE
-
Boetzer, M., and Henkel., C. V., Jansen, H. J., Butler, D., and Pirovano, W. 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27: 578-579.
-
(2011)
Bioinformatics
, vol.27
, pp. 578-579
-
-
Boetzer, M.1
Henkel, C.V.2
Jansen, H.J.3
Butler, D.4
Pirovano, W.5
-
7
-
-
80052281811
-
Structures of Phytophthora RXLR effector proteins: A conserved but adaptable fold underpins functional diversity
-
Boutemy, L. S., King, S. R. F., Win, J., Hughes, R. K., and Clarke., T. A., Blumenschein, T. M., Kamoun, S., and Banfield, M. J. 2011. Structures of Phytophthora RXLR effector proteins: A conserved but adaptable fold underpins functional diversity. J. Biol. Chem. 286:35834-35842.
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 35834-35842
-
-
Boutemy, L.S.1
King, S.R.F.2
Win, J.3
Hughes, R.K.4
Clarke, T.A.5
Blumenschein, T.M.6
Kamoun, S.7
Banfield, M.J.8
-
8
-
-
0002441610
-
Evidence for resistance to metalaxyl in isolates of Peronospora tabacina
-
Bruck, R. I., and Gooding., G. V., and Main, C. E. 1982. Evidence for resistance to metalaxyl in isolates of Peronospora tabacina. Plant Dis. 66:44-45.
-
(1982)
Plant Dis.
, vol.66
, pp. 44-45
-
-
Bruck, R.I.1
Gooding, G.V.2
Main, C.E.3
-
9
-
-
0034520657
-
The life-cycle of Plasmopara viticola, cause of downy mildew of vine
-
Burruano, S. 2000. The life-cycle of Plasmopara viticola, cause of downy mildew of vine. Mycologist 14:179-182.
-
(2000)
Mycologist
, vol.14
, pp. 179-182
-
-
Burruano, S.1
-
10
-
-
43149086380
-
ALLPATHS: De novo assembly of whole-genome shotgun microreads
-
Butler, J., Maccallum, I., Kleber, M., Shlyakhter, I. A., and Belmonte., M. K., Lander, E. S., Nusbaum, C., and Jaffe, D. B. 2008. ALLPATHS: De novo assembly of whole-genome shotgun microreads. Genome Res. 18:810-820.
-
(2008)
Genome Res.
, vol.18
, pp. 810-820
-
-
Butler, J.1
Maccallum, I.2
Kleber, M.3
Shlyakhter, I.A.4
Belmonte, M.K.5
Lander, E.S.6
Nusbaum, C.7
Jaffe, D.B.8
-
11
-
-
38049057159
-
MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
-
Cantarel, B. L., Korf, I., Robb, S. M. C., Parra, G., Ross, E., Moore, B., Holt, C., Sánchez Alvarado, A., and Yandell, M. 2008. MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 18:188-196.
-
(2008)
Genome Res.
, vol.18
, pp. 188-196
-
-
Cantarel, B.L.1
Korf, I.2
Robb, S.M.C.3
Parra, G.4
Ross, E.5
Moore, B.6
Holt, C.7
Sánchez Alvarado, A.8
Yandell, M.9
-
12
-
-
0001630217
-
Systemic fungicides and the control of oomycetes
-
Cohen, Y., and Coffey, M. 1986. Systemic fungicides and the control of oomycetes. Annu. Rev. Phytopathol. 24:311-338.
-
(1986)
Annu. Rev. Phytopathol.
, vol.24
, pp. 311-338
-
-
Cohen, Y.1
Coffey, M.2
-
13
-
-
0000980748
-
The Role of pectic enzymes in plant pathogenesis
-
Collmer, A., and Keen, N. T. 1986. The Role of pectic enzymes in plant pathogenesis. Annu. Rev. Phytopathol. 24:383-409.
-
(1986)
Annu. Rev. Phytopathol.
, vol.24
, pp. 383-409
-
-
Collmer, A.1
Keen, N.T.2
-
14
-
-
24644503098
-
Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research
-
Conesa, A., Götz, S., Garía-Gómez, J. M., Terol, J., Talón, M., and Robles, M. 2005. Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674-3676.
-
(2005)
Bioinformatics
, vol.21
, pp. 3674-3676
-
-
Conesa, A.1
Götz, S.2
Garía-Gómez, J.M.3
Terol, J.4
Talón, M.5
Robles, M.6
-
15
-
-
0021022247
-
Specific interference of metalaxyl with endogenous RNA polymerase activity in isolated nuclei from Phytophthora megasperma f. Sp. Medicaginis
-
Davidse, L. C., and Hofman., A. E., and Velthius, G. C. M. 1983. Specific interference of metalaxyl with endogenous RNA polymerase activity in isolated nuclei from Phytophthora megasperma f. sp. medicaginis. Exp. Mycol. 7:344-361
-
(1983)
Exp. Mycol.
, vol.7
, pp. 344-361
-
-
Davidse, L.C.1
Hofman, A.E.2
Velthius, G.C.M.3
-
16
-
-
0031743421
-
Profile hidden Markov models
-
Eddy, S. R. 1998. Profile hidden Markov models. Bioinformatics 14: 755-763.
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
17
-
-
80055082271
-
Accelerated profile HMM searches
-
Eddy, S. R. 2011. Accelerated profile HMM searches. PLOS Comput. Biol. 7:e1002195.
-
(2011)
PLOS Comput. Biol.
, vol.7
-
-
Eddy, S.R.1
-
18
-
-
39749179047
-
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
-
Ellinghaus, D., Kurtz, S., and Willhoeft, U. 2008. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics 9:18.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 18
-
-
Ellinghaus, D.1
Kurtz, S.2
Willhoeft, U.3
-
19
-
-
84891782659
-
Pfam: The protein families database
-
Finn, R. D., Bateman, A., Clements, J., Coggill, P., and Eberhardt., R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L., Mistry, J., Sonnhammer, E. L. L., Tate, J., and Punta, M. 2014. Pfam: The protein families database. Nucleic Acids Res. 42:D222-D230.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D222-D230
-
-
Finn, R.D.1
Bateman, A.2
Clements, J.3
Coggill, P.4
Eberhardt, R.Y.5
Eddy, S.R.6
Heger, A.7
Hetherington, K.8
Holm, L.9
Mistry, J.10
Sonnhammer, E.L.L.11
Tate, J.12
Punta, M.13
-
20
-
-
84857570169
-
Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups
-
John Wiley & Sons, Inc., New York
-
Fischer, S., and Brunk., B. P., Chen, F., Gao, X., Harb, O. S., and Iodice., J. B., Shanmugam, D., Roos, D. S., and Stoeckert, C. J. 2011. Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Pages 6.12.1-6.12.19 in: Current Protocols in Bioinformatics, John Wiley & Sons, Inc., New York.
-
(2011)
Current Protocols in Bioinformatics
, pp. 6121-61219
-
-
Fischer, S.1
Brunk, B.P.2
Chen, F.3
Gao, X.4
Harb, O.S.5
Iodice, J.B.6
Shanmugam, D.7
Roos, D.S.8
Stoeckert, C.J.9
-
21
-
-
33747595647
-
Nep1-like proteins from plant pathogens: Recruitment and diversification of the NPP1 domain across taxa
-
Gijzen, M., and Nürnberger, T. 2006. Nep1-like proteins from plant pathogens: Recruitment and diversification of the NPP1 domain across taxa. Phytochemistry 67:1800-1807.
-
(2006)
Phytochemistry
, vol.67
, pp. 1800-1807
-
-
Gijzen, M.1
Nürnberger, T.2
-
22
-
-
6044235515
-
The mitochondrial genome of Saprolegnia ferax: Organization, gene content and nucleotide sequence
-
Grayburn, W. S., Hudspeth, D. S. S., Gane, M. K., and Hudspeth, M. E. S. 2004. The mitochondrial genome of Saprolegnia ferax: Organization, gene content and nucleotide sequence. Mycologia 96:981-989.
-
(2004)
Mycologia
, vol.96
, pp. 981-989
-
-
Grayburn, W.S.1
Hudspeth, D.S.S.2
Gane, M.K.3
Hudspeth, M.E.S.4
-
23
-
-
70349281388
-
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans
-
Haas, B. J., Kamoun, S., Zody, M. C., Jiang, R. H. Y., Handsaker, R. E., and Cano., L. M., Grabherr, M., Kodira, C. D., Raffaele, S., Torto-Alalibo, T., Bozkurt, T. O., Ah-Fong, A. M. V., Alvarado, L., Anderson, V. L., Armstrong, M. R., Avrova, A., Baxter, L., Beynon, J., Boevink, P. C., Bollmann, S. R., Bos, J. I. B., Bulone, V., Cai, G., Cakir, C., Carrington, J. C., Chawner, M., Conti, L., Costanzo, S., Ewan, R., Fahlgren, N., Fischbach, M. A., Fugelstad, J., Gilroy, E. M., Gnerre, S., Green, P. J., Grenville-Briggs, L. J., Griffith, J., Grünwald, N. J., Horn, K., Horner, N. R., Hu, C. H., Huitema, E., Jeong, D. H., Jones, A. M., Jones, J. D., Jones, R. W., Karlsson, E. K., Kunjeti, S. G., Lamour, K., Liu, Z., Ma, L., Maclean, D., Chibucos, M. C., McDonald, H., McWalters, J., Meijer, H. J., Morgan, W., Morris, P. F., Munro, C. A., O'Neill, K., Ospina-Giraldo, M., Pinzón, A., Pritchard, L., Ramsahoye, B., Ren, Q., Restrepo, S., Roy, S., Sadanandom, A., Savidor, A., Schornack, S., Schwartz, D. C., Schumann, U. D., Schwessinger, B., Seyer, L., Sharpe, T., Silvar, C., Song, J., Studholme, D. J., Sykes, S., Thines, M., van de Vondervoort, P. J., Phuntumart, V., Wawra, S., Weide, R., Win, J., Young, C., Zhou, S., Fry, W., Meyers, B. C., van West, P., Ristaino, J., Govers, F., Birch, P. R., Whisson, S. C., Judelson, H. S., and Nusbaum, C. 2009. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461:393-398.
-
(2009)
Nature
, vol.461
, pp. 393-398
-
-
Haas, B.J.1
Kamoun, S.2
Zody, M.C.3
Jiang, R.H.Y.4
Handsaker, R.E.5
Cano, L.M.6
Grabherr, M.7
Kodira, C.D.8
Raffaele, S.9
Torto-Alalibo, T.10
Bozkurt, T.O.11
Ah-Fong, A.M.V.12
Alvarado, L.13
Anderson, V.L.14
Armstrong, M.R.15
Avrova, A.16
Baxter, L.17
Beynon, J.18
Boevink, P.C.19
Bollmann, S.R.20
Bos, J.I.B.21
Bulone, V.22
Cai, G.23
Cakir, C.24
Carrington, J.C.25
Chawner, M.26
Conti, L.27
Costanzo, S.28
Ewan, R.29
Fahlgren, N.30
Fischbach, M.A.31
Fugelstad, J.32
Gilroy, E.M.33
Gnerre, S.34
Green, P.J.35
Grenville-Briggs, L.J.36
Griffith, J.37
Grünwald, N.J.38
Horn, K.39
Horner, N.R.40
Hu, C.H.41
Huitema, E.42
Jeong, D.H.43
Jones, A.M.44
Jones, J.D.45
Jones, R.W.46
Karlsson, E.K.47
Kunjeti, S.G.48
Lamour, K.49
Liu, Z.50
Ma, L.51
Maclean, D.52
Chibucos, M.C.53
McDonald, H.54
McWalters, J.55
Meijer, H.J.56
Morgan, W.57
Morris, P.F.58
Munro, C.A.59
O'Neill, K.60
Ospina-Giraldo, M.61
Pinzón, A.62
Pritchard, L.63
Ramsahoye, B.64
Ren, Q.65
Restrepo, S.66
Roy, S.67
Sadanandom, A.68
Savidor, A.69
Schornack, S.70
Schwartz, D.C.71
Schumann, U.D.72
Schwessinger, B.73
Seyer, L.74
Sharpe, T.75
Silvar, C.76
Song, J.77
Studholme, D.J.78
Sykes, S.79
Thines, M.80
Van De Vondervoort, P.J.81
Phuntumart, V.82
Wawra, S.83
Weide, R.84
Win, J.85
Young, C.86
Zhou, S.87
Fry, W.88
Meyers, B.C.89
Van West, P.90
Ristaino, J.91
Govers, F.92
Birch, P.R.93
Whisson, S.C.94
Judelson, H.S.95
Nusbaum, C.96
more..
-
24
-
-
0036217802
-
Interactions of Peronospora tabacina with roots of Nicotiana spp. in gnotobiotic associations
-
Heist, E., Nesmith, W., and Schardl, C. 2002. Interactions of Peronospora tabacina with roots of Nicotiana spp. in gnotobiotic associations. Phytopathology 92:400-405.
-
(2002)
Phytopathology
, vol.92
, pp. 400-405
-
-
Heist, E.1
Nesmith, W.2
Schardl, C.3
-
25
-
-
0020687716
-
Organization of Achlya mtDNA: A population with two orientations and a large inverted repeat containing the rRNA genes
-
Hudspeth, M. E. S., and Shumard., D. S., Bradford, C. J. R., and Grossman, L. I. 1983. Organization of Achlya mtDNA: A population with two orientations and a large inverted repeat containing the rRNA genes. Proc. Natl. Acad. Sci. U.S.A. 80:142-146
-
(1983)
Proc. Natl. Acad. Sci. U.S.A.
, vol.80
, pp. 142-146
-
-
Hudspeth, M.E.S.1
Shumard, D.S.2
Bradford, C.J.R.3
Grossman, L.I.4
-
26
-
-
69949096587
-
Polygalacturonase, pectate lyase and pectin methylesterase activity in pathogenic strains of Phytophthora capsici incubated under different conditions
-
Jia, Y. J., and Feng., B. Z., Sun, W. X., and Zhang, X. G. 2009. Polygalacturonase, pectate lyase and pectin methylesterase activity in pathogenic strains of Phytophthora capsici incubated under different conditions. J. Phytopathol. 157:585-591.
-
(2009)
J. Phytopathol.
, vol.157
, pp. 585-591
-
-
Jia, Y.J.1
Feng, B.Z.2
Sun, W.X.3
Zhang, X.G.4
-
27
-
-
42449116668
-
RXLR effector reservoir in two Phytophthora species is dominated by a single rapidly evolving superfamily with more than 700 members
-
Jiang, R. H. Y., Tripathy, S., Govers, F., and Tyler, B. M. 2008. RXLR effector reservoir in two Phytophthora species is dominated by a single rapidly evolving superfamily with more than 700 members. Proc. Natl. Acad. Sci. U.S.A. 105:4874-4879.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 4874-4879
-
-
Jiang, R.H.Y.1
Tripathy, S.2
Govers, F.3
Tyler, B.M.4
-
28
-
-
84871783446
-
Mechanisms and evolution of virulence in oomycetes
-
Jiang, R. H. Y., and Tyler, B. M. 2012. Mechanisms and evolution of virulence in oomycetes. Annu. Rev. Phytopathol. 50:295-318.
-
(2012)
Annu. Rev. Phytopathol.
, vol.50
, pp. 295-318
-
-
Jiang, R.H.Y.1
Tyler, B.M.2
-
29
-
-
84899518211
-
InterProScan 5: Genome-scale protein function classification
-
Jones, P., Binns, D., Chang, H.-Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., Pesseat, S., Quinn, A. F., Sangrador-Vegas, A., Scheremetjew, M., Yong, S.-Y., Lopez, R., and Hunter, S. 2014. InterProScan 5: Genome-scale protein function classification. Bioinformatics 30:1236-1240.
-
(2014)
Bioinformatics
, vol.30
, pp. 1236-1240
-
-
Jones, P.1
Binns, D.2
Chang, H.-Y.3
Fraser, M.4
Li, W.5
McAnulla, C.6
McWilliam, H.7
Maslen, J.8
Mitchell, A.9
Nuka, G.10
Pesseat, S.11
Quinn, A.F.12
Sangrador-Vegas, A.13
Scheremetjew, M.14
Yong, S.-Y.15
Lopez, R.16
Hunter, S.17
-
30
-
-
77955041178
-
External lipid PI3P mediates entry of eukaryotic pathogen effectors into plant and animal host cells
-
Kale, S. D., Gu, B., Capelluto, D. G. S. S., Dou, D., Feldman, E., Rumore, A., Arredondo, F. D., Hanlon, R., Fudal, I., Rouxel, T., Lawrence, C. B., Shan, W., and Tyler, B. M. 2010. External lipid PI3P mediates entry of eukaryotic pathogen effectors into plant and animal host cells. Cell 142: 284-295.
-
(2010)
Cell
, vol.142
, pp. 284-295
-
-
Kale, S.D.1
Gu, B.2
Capelluto, D.G.S.S.3
Dou, D.4
Feldman, E.5
Rumore, A.6
Arredondo, F.D.7
Hanlon, R.8
Fudal, I.9
Rouxel, T.10
Lawrence, C.B.11
Shan, W.12
Tyler, B.M.13
-
31
-
-
33748334490
-
A catalogue of the effector secretome of plant pathogenic oomycetes
-
Kamoun, S. 2006. A catalogue of the effector secretome of plant pathogenic oomycetes. Annu. Rev. Phytopathol. 44:41-60.
-
(2006)
Annu. Rev. Phytopathol.
, vol.44
, pp. 41-60
-
-
Kamoun, S.1
-
32
-
-
79960927037
-
Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana
-
Kemen, E., Gardiner, A., Schultz-Larsen, T., Kemen, A. C., and Balmuth., A. L., Robert-Seilaniantz, A., Bailey, K., Holub, E., Studholme, D. J., Maclean, D., and Jones, J. D. G. 2011. Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana. PLoS Biol. 9:e1001094.
-
(2011)
PLoS Biol.
, vol.9
-
-
Kemen, E.1
Gardiner, A.2
Schultz-Larsen, T.3
Kemen, A.C.4
Balmuth, A.L.5
Robert-Seilaniantz, A.6
Bailey, K.7
Holub, E.8
Studholme, D.J.9
Maclean, D.10
Jones, J.D.G.11
-
33
-
-
2942544417
-
Gene finding in novel genomes
-
Korf, I. 2004. Gene finding in novel genomes. BMC Bioinformatics 5:59.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 59
-
-
Korf, I.1
-
34
-
-
69649109364
-
Circos: An information aesthetic for comparative genomics
-
Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S. J., and Marra, M. A. 2009. Circos: An information aesthetic for comparative genomics. Genome Res. 19:1639-1645.
-
(2009)
Genome Res.
, vol.19
, pp. 1639-1645
-
-
Krzywinski, M.1
Schein, J.2
Birol, I.3
Connors, J.4
Gascoyne, R.5
Horsman, D.6
Jones, S.J.7
Marra, M.A.8
-
35
-
-
34250665888
-
RNAmmer: Consistent and rapid annotation of ribosomal RNA genes
-
Lagesen, K., Hallin, P., Rødland, E. A., Staerfeldt, H.-H., Rognes, T., and Ussery, D. W. 2007. RNAmmer: Consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100-3108.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 3100-3108
-
-
Lagesen, K.1
Hallin, P.2
Rødland, E.A.3
Staerfeldt, H.-H.4
Rognes, T.5
Ussery, D.W.6
-
36
-
-
84865734218
-
Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici
-
Lamour, K. H., Mudge, J., Gobena, D., Hurtado-Gonzales, O. P., Schmutz, J., Kuo, A., Miller, N. A., Rice, B. J., Raffaele, S., Cano, L. M., Bharti, A. K., Donahoo, R. S., Finley, S., Huitema, E., Hulvey, J., Platt, D., Salamov, A., Savidor, A., Sharma, R., Stam, R., Storey, D., Thines, M., Win, J., Haas, B. J., Dinwiddie, D. L., Jenkins, J., Knight, J. R., Affourtit, J. P., Han, C. S., Chertkov, O., Lindquist, E. A., Detter, C., Grigoriev, I. V., Kamoun, S., and Kingsmore, S. F. 2012. Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici. Mol. Plant-Microbe Interact. 25:1350-1360.
-
(2012)
Mol. Plant-Microbe Interact.
, vol.25
, pp. 1350-1360
-
-
Lamour, K.H.1
Mudge, J.2
Gobena, D.3
Hurtado-Gonzales, O.P.4
Schmutz, J.5
Kuo, A.6
Miller, N.A.7
Rice, B.J.8
Raffaele, S.9
Cano, L.M.10
Bharti, A.K.11
Donahoo, R.S.12
Finley, S.13
Huitema, E.14
Hulvey, J.15
Platt, D.16
Salamov, A.17
Savidor, A.18
Sharma, R.19
Stam, R.20
Storey, D.21
Thines, M.22
Win, J.23
Haas, B.J.24
Dinwiddie, D.L.25
Jenkins, J.26
Knight, J.R.27
Affourtit, J.P.28
Han, C.S.29
Chertkov, O.30
Lindquist, E.A.31
Detter, C.32
Grigoriev, I.V.33
Kamoun, S.34
Kingsmore, S.F.35
more..
-
37
-
-
34547493232
-
Oomycete genomics: New insights and future directions
-
Lamour, K. H., Win, J., and Kamoun, S. 2007. Oomycete genomics: New insights and future directions. FEMS Microbiol. Lett. 274:1-8.
-
(2007)
FEMS Microbiol. Lett.
, vol.274
, pp. 1-8
-
-
Lamour, K.H.1
Win, J.2
Kamoun, S.3
-
38
-
-
77954417202
-
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire
-
Lévesque, C. A., Brouwer, H., Cano, L., and Hamilton., J. P., Holt, C., Huitema, E., Raffaele, S., and Robideau., G. P., Thines, M., Win, J., Zerillo, M. M., and Beakes., G. W., Boore, J. L., Busam, D., Dumas, B., Ferriera, S., Fuerstenberg, S. I., Gachon, C. M. M., Gaulin, E., Govers, F., Grenville-Briggs, L., Horner, N., Hostetler, J., Jiang, R. H. Y., Johnson, J., Krajaejun, T., Lin, H., Meijer, H. J. G., Moore, B., Morris, P., Phuntmart, V., Puiu, D., Shetty, J., Stajich, J. E., Tripathy, S., Wawra, S., van West, P., Whitty, B. R., Coutinho, P. M., Henrissat, B., Martin, F., Thomas, P. D., Tyler, B. M., De Vries, R. P., Kamoun, S., Yandell, M., Tisserat, N., and Buell, C. R. 2010. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol. 11:R73.
-
(2010)
Genome Biol.
, vol.11
, pp. R73
-
-
Lévesque, C.A.1
Brouwer, H.2
Cano, L.3
Hamilton, J.P.4
Holt, C.5
Huitema, E.6
Raffaele, S.7
Robideau, G.P.8
Thines, M.9
Win, J.10
Zerillo, M.M.11
Beakes, G.W.12
Boore, J.L.13
Busam, D.14
Dumas, B.15
Ferriera, S.16
Fuerstenberg, S.I.17
Gachon, C.M.M.18
Gaulin, E.19
Govers, F.20
Grenville-Briggs, L.21
Horner, N.22
Hostetler, J.23
Jiang, R.H.Y.24
Johnson, J.25
Krajaejun, T.26
Lin, H.27
Meijer, H.J.G.28
Moore, B.29
Morris, P.30
Phuntmart, V.31
Puiu, D.32
Shetty, J.33
Stajich, J.E.34
Tripathy, S.35
Wawra, S.36
Van West, P.37
Whitty, B.R.38
Coutinho, P.M.39
Henrissat, B.40
Martin, F.41
Thomas, P.D.42
Tyler, B.M.43
De Vries, R.P.44
Kamoun, S.45
Yandell, M.46
Tisserat, N.47
Buell, C.R.48
more..
-
39
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., and 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
40
-
-
0030854739
-
tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
-
Lowe, T. M., and Eddy, S. R. 1997. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
41
-
-
0033582628
-
A computational screen for methylation guide snoRNAs in yeast
-
Lowe, T. M., and Eddy, S. R. 1999. A computational screen for methylation guide snoRNAs in yeast. Science 283:1168-1171.
-
(1999)
Science
, vol.283
, pp. 1168-1171
-
-
Lowe, T.M.1
Eddy, S.R.2
-
42
-
-
38949151064
-
How to usefully compare homologous plant genes and chromosomes as DNA sequences
-
Lyons, E., and Freeling, M. 2008. How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J. 53:661-673.
-
(2008)
Plant J.
, vol.53
, pp. 661-673
-
-
Lyons, E.1
Freeling, M.2
-
43
-
-
84877936532
-
Analyses of the population structure in a global collection of Phytophthora nicotianae isolates inferred from mitochondrial and nuclear DNA sequences
-
Mammella, M. A., and Martin., F. N., Cacciola, S. O., Coffey, M. D., Faedda, R., and Schena, L., 2013. Analyses of the population structure in a global collection of Phytophthora nicotianae isolates inferred from mitochondrial and nuclear DNA sequences. Phytopathology 103:610-622.
-
(2013)
Phytopathology
, vol.103
, pp. 610-622
-
-
Mammella, M.A.1
Martin, F.N.2
Cacciola, S.O.3
Coffey, M.D.4
Faedda, R.5
Schena, L.6
-
44
-
-
78651285748
-
CDD: A conserved domain database for the functional annotation of proteins
-
Marchler-Bauer, A., Lu, S., and Anderson., J. B., Chitsaz, F., Derbyshire, M. K., DeWeese-Scott, C., Fong, J. H., and Geer., L. Y., Geer, R. C., Gonzales, N. R., Gwadz, M., and Hurwitz., D. I., Jackson, J. D., Ke, Z., Lanczycki, C. J., Lu, F., and Marchler., G. H., Mullokandov, M., Omelchenko, M. V., and Robertson., C. L., Song, J. S., Thanki, N., Yamashita, R. A., Zhang, D., Zhang, N., Zheng, C., and Bryant, S. H. 2011. CDD: A conserved domain database for the functional annotation of proteins. Nucleic Acids Res. 39:D225-D229.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D225-D229
-
-
Marchler-Bauer, A.1
Lu, S.2
Anderson, J.B.3
Chitsaz, F.4
Derbyshire, M.K.5
DeWeese-Scott, C.6
Fong, J.H.7
Geer, L.Y.8
Geer, R.C.9
Gonzales, N.R.10
Gwadz, M.11
Hurwitz, D.I.12
Jackson, J.D.13
Ke, Z.14
Lanczycki, C.J.15
Lu, F.16
Marchler, G.H.17
Mullokandov, M.18
Omelchenko, M.V.19
Robertson, C.L.20
Song, J.S.21
Thanki, N.22
Yamashita, R.A.23
Zhang, D.24
Zhang, N.25
Zheng, C.26
Bryant, S.H.27
more..
-
45
-
-
47249144256
-
Mitochondrial haplotype determination in the oomycete plant pathogen Phytophthora ramorum
-
Martin, F. N. 2008. Mitochondrial haplotype determination in the oomycete plant pathogen Phytophthora ramorum. Curr. Genet. 54:23-34.
-
(2008)
Curr. Genet.
, vol.54
, pp. 23-34
-
-
Martin, F.N.1
-
46
-
-
34247223751
-
Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. Sojae
-
Martin, F. N., Bensasson, D., Tyler, B. M., and Boore, J. L. 2007. Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojae. Curr. Genet. 51:285-296.
-
(2007)
Curr. Genet.
, vol.51
, pp. 285-296
-
-
Martin, F.N.1
Bensasson, D.2
Tyler, B.M.3
Boore, J.L.4
-
47
-
-
84856681195
-
Mitochondrial haplotype analysis for differentiation of isolates of Phytophthora cinnamomi
-
Martin, F. N., and Coffey, M. D. 2012. Mitochondrial haplotype analysis for differentiation of isolates of Phytophthora cinnamomi. Phytopathology 102:229-239.
-
(2012)
Phytopathology
, vol.102
, pp. 229-239
-
-
Martin, F.N.1
Coffey, M.D.2
-
48
-
-
0344886603
-
-
First Edition. W. E. McKeen, ed. American Phytopathological Society, St. Paul, MN, U.S.A.
-
McKeen, W. E. 1989. Blue Mold of Tobacco. First Edition. W. E. McKeen, ed. American Phytopathological Society, St. Paul, MN, U.S.A.
-
(1989)
Blue Mold of Tobacco
-
-
McKeen, W.E.1
-
49
-
-
0001144765
-
An inverted repeat comprises more than three-quarters of the mitochondrial genome in two species of Pythium
-
Mcnabb, S. A., and Boyd., D. A., Belkhiri, A., Dick, M. W., and Klassen, G. R. 1987. An inverted repeat comprises more than three-quarters of the mitochondrial genome in two species of Pythium. Curr. Genet. 12:205-208.
-
(1987)
Curr. Genet.
, vol.12
, pp. 205-208
-
-
Mcnabb, S.A.1
Boyd, D.A.2
Belkhiri, A.3
Dick, M.W.4
Klassen, G.R.5
-
50
-
-
84900166524
-
Classical and molecular genetics of Bremia lactucae, cause of lettuce downy mildew
-
Michelmore, R., and Wong, J. 2008. Classical and molecular genetics of Bremia lactucae, cause of lettuce downy mildew. Eur. J. Plant Pathol. 122:19-30.
-
(2008)
Eur. J. Plant Pathol.
, vol.122
, pp. 19-30
-
-
Michelmore, R.1
Wong, J.2
-
51
-
-
0022507362
-
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
-
Nei, M., and Gojobori, T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. EVol. 3:418-426.
-
(1986)
Mol. Biol. Evol.
, vol.3
, pp. 418-426
-
-
Nei, M.1
Gojobori, T.2
-
52
-
-
84896321263
-
Mitochondrial genome sequences and comparative genomics of Achlya hypogyna and Thraustotheca clavata
-
O'Brien, M. A., Misner, I., and Lane, C. E. 2014. Mitochondrial genome sequences and comparative genomics of Achlya hypogyna and Thraustotheca clavata. J. Eukaryot. Microbiol. 61:146-154.
-
(2014)
J. Eukaryot. Microbiol.
, vol.61
, pp. 146-154
-
-
O'Brien, M.A.1
Misner, I.2
Lane, C.E.3
-
53
-
-
84912535345
-
Nep1-like proteins from three kingdoms of life act as a microbe-associated molecular pattern in Arabidopsis
-
Oome, S., and Raaymakers., T. M., Cabral, A., Samwel, S., Böhm, H., Albert, I., Nürnberger, T., and Van den Ackerveken, G. 2014. Nep1-like proteins from three kingdoms of life act as a microbe-associated molecular pattern in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 111:16955-16960.
-
(2014)
Proc. Natl. Acad. Sci. U.S.A.
, vol.111
, pp. 16955-16960
-
-
Oome, S.1
Raaymakers, T.M.2
Cabral, A.3
Samwel, S.4
Böhm, H.5
Albert, I.6
Nürnberger, T.7
Van Den Ackerveken, G.8
-
54
-
-
84907225537
-
Comparative and functional analysis of the widely occurring family of Nep1-like proteins
-
Oome, S., and Van den Ackerveken, G. 2014. Comparative and functional analysis of the widely occurring family of Nep1-like proteins. Mol. Plant-Microbe Interact. 27:1081-1094.
-
(2014)
Mol. Plant-Microbe Interact.
, vol.27
, pp. 1081-1094
-
-
Oome, S.1
Van Den Ackerveken, G.2
-
55
-
-
34249848751
-
CEGMA: A pipeline to accurately annotate core genes in eukaryotic genomes
-
Parra, G., Bradnam, K., and Korf, I. 2007. CEGMA: A pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:1061-1067.
-
(2007)
Bioinformatics
, vol.23
, pp. 1061-1067
-
-
Parra, G.1
Bradnam, K.2
Korf, I.3
-
56
-
-
58149337101
-
Simple sequence repeat markers useful for sorghum downy mildew (Peronosclerospora sorghi) and related species
-
Perumal, R., Nimmakayala, P., Erattaimuthu, S. R., No, E.-G., and Reddy., U. K., Prom, L. K., Odvody, G. N., and Luster., D. G., and Magill, C. W. 2008. Simple sequence repeat markers useful for sorghum downy mildew (Peronosclerospora sorghi) and related species. BMC Genet. 9:77.
-
(2008)
BMC Genet.
, vol.9
, pp. 77
-
-
Perumal, R.1
Nimmakayala, P.2
Erattaimuthu, S.R.3
No, E.-G.4
Reddy, U.K.5
Prom, L.K.6
Odvody, G.N.7
Luster, D.G.8
Magill, C.W.9
-
57
-
-
80053345905
-
SignalP 4.0: Discriminating signal peptides from transmembrane regions
-
Petersen, T. N., Brunak, S., von Heijne, G., and Nielsen, H. 2011. SignalP 4.0: Discriminating signal peptides from transmembrane regions. Nat. Methods 8:785-786.
-
(2011)
Nat. Methods
, vol.8
, pp. 785-786
-
-
Petersen, T.N.1
Brunak, S.2
Von Heijne, G.3
Nielsen, H.4
-
58
-
-
84864503262
-
Challenges and progress towards understanding the role of effectors in plant-fungal interactions
-
Rafiqi, M., and Ellis., J. G., Ludowici, V. A., Hardham, A. R., and Dodds, P. N. 2012. Challenges and progress towards understanding the role of effectors in plant-fungal interactions. Curr. Opin. Plant Biol. 15:477-482.
-
(2012)
Curr. Opin. Plant Biol.
, vol.15
, pp. 477-482
-
-
Rafiqi, M.1
Ellis, J.G.2
Ludowici, V.A.3
Hardham, A.R.4
Dodds, P.N.5
-
59
-
-
84906082430
-
Sequence diversity in the large subunit of RNA polymerase I contributes to mefenoxam insensitivity in Phytophthora infestans
-
Randall, E., Young, V., Sierotzki, H., Scalliet, G., Birch, P. R. J., Cooke, D. E. L., Csukai, M., and Whisson, S. C. 2014. Sequence diversity in the large subunit of RNA polymerase I contributes to mefenoxam insensitivity in Phytophthora infestans. Mol. Plant Pathol. 15:664-676.
-
(2014)
Mol. Plant Pathol.
, vol.15
, pp. 664-676
-
-
Randall, E.1
Young, V.2
Sierotzki, H.3
Scalliet, G.4
Birch, P.R.J.5
Cooke, D.E.L.6
Csukai, M.7
Whisson, S.C.8
-
60
-
-
75549091468
-
MEROPS: The peptidase database
-
Rawlings, N. D., and Barrett., A. J., and Bateman, A. 2010. MEROPS: The peptidase database. Nucleic Acids Res. 38:D227-D233.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. D227-D233
-
-
Rawlings, N.D.1
Barrett, A.J.2
Bateman, A.3
-
61
-
-
84864444502
-
A web-based multi-genome synteny viewer for customized data
-
Revanna, K. V., Munro, D., Gao, A., Chiu, C. C., Pathak, A., and Dong, Q. 2012. A web-based multi-genome synteny viewer for customized data. BMC Bioinformatics 13:190.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 190
-
-
Revanna, K.V.1
Munro, D.2
Gao, A.3
Chiu, C.C.4
Pathak, A.5
Dong, Q.6
-
62
-
-
0035822055
-
PCR amplification of the Irish potato famine pathogen from historic specimens
-
Ristaino, J. B., and Groves., C. T., and Parra, G. R. 2001. PCR amplification of the Irish potato famine pathogen from historic specimens. Nature 411: 695-697.
-
(2001)
Nature
, vol.411
, pp. 695-697
-
-
Ristaino, J.B.1
Groves, C.T.2
Parra, G.R.3
-
63
-
-
34249085921
-
Identification of the tobacco blue mold pathogen, Peronospora tabacina, by polymerase chain reaction
-
Ristaino, J. B., Johnson, A., Blancomeneses, M., Liu, B., Pathology, P., and Carolina, N. 2007. Identification of the tobacco blue mold pathogen, Peronospora tabacina, by polymerase chain reaction. Plant Dis. 91:685-691.
-
(2007)
Plant Dis.
, vol.91
, pp. 685-691
-
-
Ristaino, J.B.1
Johnson, A.2
Blancomeneses, M.3
Liu, B.4
Pathology, P.5
Carolina, N.6
-
64
-
-
0034895922
-
Leaf disc inoculation, a fast and precise test for the screening of metalaxyl tolerance in sunflower downy mildew
-
Rozynek, R., and Spring, O. 2001. Leaf disc inoculation, a fast and precise test for the screening of metalaxyl tolerance in sunflower downy mildew. Phytopathology 149:309-312.
-
(2001)
Phytopathology
, vol.149
, pp. 309-312
-
-
Rozynek, R.1
Spring, O.2
-
65
-
-
0031434731
-
Characterization of the genome of Sclerospora graminicola, the causal fungus of downy mildew of pearl millet
-
Sastry, J. G., Sivaramakrishnan, S., Thakur, R. P., and Gupta., V. S., and Ranjekar, P. K. 1997. Characterization of the genome of Sclerospora graminicola, the causal fungus of downy mildew of pearl millet. World J. Microb. Biot. 13:693-697.
-
(1997)
World J. Microb. Biot.
, vol.13
, pp. 693-697
-
-
Sastry, J.G.1
Sivaramakrishnan, S.2
Thakur, R.P.3
Gupta, V.S.4
Ranjekar, P.K.5
-
66
-
-
84901625138
-
Two-dimensional data binning for the analysis of genome architecture in filamentous plant pathogens and other eukaryotes
-
P. Birch, J. T. Jones, and J. I. B. Bos, eds. Humana Press, New York
-
Saunders, D. G. O., Win, J., Kamoun, S., and Raffaele, S. 2014. Two-dimensional data binning for the analysis of genome architecture in filamentous plant pathogens and other eukaryotes. Pages 29-51 In: Methods in Molecular Biology, Vol 1127. P. Birch, J. T. Jones, and J. I. B. Bos, eds. Humana Press, New York.
-
(2014)
Methods in Molecular Biology
, vol.1127
, pp. 29-51
-
-
Saunders, D.G.O.1
Win, J.2
Kamoun, S.3
Raffaele, S.4
-
67
-
-
79952390994
-
Fast identification and removal of sequence contamination from genomic and metagenomic datasets
-
Schmieder, R., and Edwards, R. 2011. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One 6:e17288.
-
(2011)
PLoS One
, vol.6
-
-
Schmieder, R.1
Edwards, R.2
-
68
-
-
84923132280
-
The genome of the saprophytic fungus Verticillium tricorpus reveals a complex effector repertoire resembling that of its pathogenic relatives
-
Seidl, M. F., Faino, L., Shikunne, X., van den Berg, G. C. M., Bolton, M. D., and Thomma, B. P. H. J. 2015. The genome of the saprophytic fungus Verticillium tricorpus reveals a complex effector repertoire resembling that of its pathogenic relatives. Mol. Plant-Microbe Interact. 28:362-373.
-
(2015)
Mol. Plant-Microbe Interact.
, vol.28
, pp. 362-373
-
-
Seidl, M.F.1
Faino, L.2
Shikunne, X.3
Van Den Berg, G.C.M.4
Bolton, M.D.5
Thomma, B.P.H.J.6
-
69
-
-
80054078476
-
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
-
Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., Thompson, J. D., and Higgins, D. G. 2011. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7:539.
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 539
-
-
Sievers, F.1
Wilm, A.2
Dineen, D.3
Gibson, T.J.4
Karplus, K.5
Li, W.6
Lopez, R.7
McWilliam, H.8
Remmert, M.9
Söding, J.10
Thompson, J.D.11
Higgins, D.G.12
-
71
-
-
84947764707
-
-
Institute for Systems Biology, Seattle, WA, U.S.A.
-
Smit, A. F. A., Hubley, R. and Green, P. 2013. RepeatMasker Open-4.0. http://www.repeatmasker.org. Institute for Systems Biology, Seattle, WA, U.S.A.
-
(2013)
-
-
Smit, A.F.A.1
Hubley, R.2
Green, P.3
-
72
-
-
84947705820
-
Oomycota
-
W. Frey, ed. Gebrüder Borntraeger verlagsbuchhandlung, Stuttgart, Germany
-
Spring, O. 2012. Oomycota. Pages 98-105 In: Syllabus of Plant Families. W. Frey, ed. Gebrüder Borntraeger verlagsbuchhandlung, Stuttgart, Germany.
-
(2012)
Syllabus of Plant Families
, pp. 98-105
-
-
Spring, O.1
-
73
-
-
84871399195
-
Population dynamics in tobacco blue mold incidences as a consequence of pathogen control and virulence performance of Peronospora tabacina phenotypes
-
Spring, O., and Hammer., T. R., Zipper, R., and Billenkamp, N. 2013. Population dynamics in tobacco blue mold incidences as a consequence of pathogen control and virulence performance of Peronospora tabacina phenotypes. Crop Prot. 45:76-82.
-
(2013)
Crop Prot.
, vol.45
, pp. 76-82
-
-
Spring, O.1
Hammer, T.R.2
Zipper, R.3
Billenkamp, N.4
-
74
-
-
84947706962
-
Oospores in blue mold diseased North Carolina burley and flue-cured tobacco
-
Spurr, H. W., and Todd, F. A. 1919. Oospores in blue mold diseased North Carolina burley and flue-cured tobacco. Tobacco Sci. 184:27-29.
-
(1919)
Tobacco Sci.
, vol.184
, pp. 27-29
-
-
Spurr, H.W.1
Todd, F.A.2
-
75
-
-
3242889577
-
AUGUSTUS: A web server for gene finding in eukaryotes
-
Stanke, M., Steinkamp, R., Waack, S., and Morgenstern, B. 2004. AUGUSTUS: A web server for gene finding in eukaryotes. Nucleic Acids Res. 32:W309-W312.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. W309-W312
-
-
Stanke, M.1
Steinkamp, R.2
Waack, S.3
Morgenstern, B.4
-
76
-
-
84864244548
-
Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing
-
Stassen, J. H. M., and Seidl., M. F., Vergeer, P. W. J., Nijman, I. J., Snel, B., Cuppen, E., and van den Ackerveken, G. 2012. Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing. Mol. Plant Pathol. 13:719-731.
-
(2012)
Mol. Plant Pathol.
, vol.13
, pp. 719-731
-
-
Stassen, J.H.M.1
Seidl, M.F.2
Vergeer, P.W.J.3
Nijman, I.J.4
Snel, B.5
Cuppen, E.6
Van Den Ackerveken, G.7
-
77
-
-
75349090212
-
Fine-grained annotation and classification of de novo predicted LTR retrotransposons
-
Steinbiss, S., Willhoeft, U., Gremme, G., and Kurtz, S. 2009. Fine-grained annotation and classification of de novo predicted LTR retrotransposons. Nucleic Acids Res. 37:7002-7013.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 7002-7013
-
-
Steinbiss, S.1
Willhoeft, U.2
Gremme, G.3
Kurtz, S.4
-
78
-
-
47749146161
-
Molecular demographic history of the annual sunflowers Helianthus annuus and H. Petiolaris - Large effective population sizes and rates of long-term gene flow
-
Strasburg, J. L., and Rieseberg, L. H. 2008. Molecular demographic history of the annual sunflowers Helianthus annuus and H. petiolaris - Large effective population sizes and rates of long-term gene flow. Evolution 62:1936-1950.
-
(2008)
Evolution
, vol.62
, pp. 1936-1950
-
-
Strasburg, J.L.1
Rieseberg, L.H.2
-
79
-
-
0036827607
-
Genetic uniformity among isolates of Peronospora tabacina, the tobacco blue mold pathogen
-
Sukno, S. A., and Taylor., A. M., and Farman, M. L. 2002. Genetic uniformity among isolates of Peronospora tabacina, the tobacco blue mold pathogen. Phytopathology 92:1236-1244.
-
(2002)
Phytopathology
, vol.92
, pp. 1236-1244
-
-
Sukno, S.A.1
Taylor, A.M.2
Farman, M.L.3
-
80
-
-
33747847779
-
PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments
-
Suyama, M., Torrents, D., and Bork, P. 2006. PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34:W609-W612.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. W609-W612
-
-
Suyama, M.1
Torrents, D.2
Bork, P.3
-
81
-
-
84894284376
-
Phylogeny and evolution of plant pathogenic oomycetes - A global overview
-
Thines, M. 2014. Phylogeny and evolution of plant pathogenic oomycetes - A global overview. Eur. J. Plant Pathol. 138:431-447.
-
(2014)
Eur. J. Plant Pathol.
, vol.138
, pp. 431-447
-
-
Thines, M.1
-
82
-
-
24044523879
-
Exceptional length of ITS in Plasmopara halstedii is due to multiple repetitions in the ITS-2 region
-
Thines, M., Komjáti, H., and Spring, O. 2005. Exceptional length of ITS in Plasmopara halstedii is due to multiple repetitions in the ITS-2 region. Eur. J. Plant Pathol. 112:395-398.
-
(2005)
Eur. J. Plant Pathol.
, vol.112
, pp. 395-398
-
-
Thines, M.1
Komjáti, H.2
Spring, O.3
-
83
-
-
79953744721
-
454 Genome sequencing of Pseudoperonospora cubensis reveals effector proteins with a QXLR translocation motif
-
Tian, M., Win, J., Savory, E., Burkhardt, A., Held, M., Brandizzi, F., and Day, B. 2011. 454 Genome sequencing of Pseudoperonospora cubensis reveals effector proteins with a QXLR translocation motif. Mol. Plant-Microbe Interact. 24:543-553.
-
(2011)
Mol. Plant-Microbe Interact.
, vol.24
, pp. 543-553
-
-
Tian, M.1
Win, J.2
Savory, E.3
Burkhardt, A.4
Held, M.5
Brandizzi, F.6
Day, B.7
-
84
-
-
0037963480
-
EST mining and functional expression assays identify extracellular effector proteins from the plant pathogen Phytophthora
-
Torto, T. A., Li, S., Styer, A., Huitema, E., Testa, A., Gow, N. A., van West, P., and Kamoun, S. 2003. EST mining and functional expression assays identify extracellular effector proteins from the plant pathogen Phytophthora. Genome Res. 13:1675-1685.
-
(2003)
Genome Res.
, vol.13
, pp. 1675-1685
-
-
Torto, T.A.1
Li, S.2
Styer, A.3
Huitema, E.4
Testa, A.5
Gow, N.A.6
Van West, P.7
Kamoun, S.8
-
85
-
-
84863503656
-
Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina
-
Trigiano, R. N., and Wadl., P. A., Dean, D., Hadziabdic, D., Scheffler, B. E., Runge, F., Telle, S., Thines, M., Ristaino, J., and Spring, O. 2012. Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina. Mycologia 104:633-640.
-
(2012)
Mycologia
, vol.104
, pp. 633-640
-
-
Trigiano, R.N.1
Wadl, P.A.2
Dean, D.3
Hadziabdic, D.4
Scheffler, B.E.5
Runge, F.6
Telle, S.7
Thines, M.8
Ristaino, J.9
Spring, O.10
-
86
-
-
33748329373
-
Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis
-
Tyler, B. M., Tripathy, S., Zhang, X., Dehal, P., Jiang, R. H. Y., Aerts, A., Arredondo, F. D., Baxter, L., Bensasson, D., Beynon, J. L., Chapman, J., Damasceno, C. M. B., Dorrance, A. E., Dou, D., and Dickerman., A. W., Dubchak, I. L., Garbelotto, M., Gijzen, M., and Gordon., S. G., Govers, F., Grunwald, N. J., Huang, W., and Ivors., K. L., Jones, R. W., Kamoun, S., Krampis, K., Lamour, K. H., Lee, M.-K., McDonald, W. H., Medina, M., Meijer, H. J. G., Nordberg, E. K., Maclean, D. J., Ospina-Giraldo, M. D., Morris, P. F., Phuntumart, V., Putnam, N. H., Rash, S., Rose, J. K. C., Sakihama, Y., Salamov, A. A., Savidor, A., Scheuring, C. F., Smith, B. M., Sobral, B. W., Terry, A., Torto-Alalibo, T. A., Win, J., Xu, Z., Zhang, H., Grigoriev, I. V., Rokhsar, D. S., and Boore, J. L. 2006. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313:1261-1266.
-
(2006)
Science
, vol.313
, pp. 1261-1266
-
-
Tyler, B.M.1
Tripathy, S.2
Zhang, X.3
Dehal, P.4
Jiang, R.H.Y.5
Aerts, A.6
Arredondo, F.D.7
Baxter, L.8
Bensasson, D.9
Beynon, J.L.10
Chapman, J.11
Damasceno, C.M.B.12
Dorrance, A.E.13
Dou, D.14
Dickerman, A.W.15
Dubchak, I.L.16
Garbelotto, M.17
Gijzen, M.18
Gordon, S.G.19
Govers, F.20
Grunwald, N.J.21
Huang, W.22
Ivors, K.L.23
Jones, R.W.24
Kamoun, S.25
Krampis, K.26
Lamour, K.H.27
Lee, M.-K.28
McDonald, W.H.29
Medina, M.30
Meijer, H.J.G.31
Nordberg, E.K.32
Maclean, D.J.33
Ospina-Giraldo, M.D.34
Morris, P.F.35
Phuntumart, V.36
Putnam, N.H.37
Rash, S.38
Rose, J.K.C.39
Sakihama, Y.40
Salamov, A.A.41
Savidor, A.42
Scheuring, C.F.43
Smith, B.M.44
Sobral, B.W.45
Terry, A.46
Torto-Alalibo, T.A.47
Win, J.48
Xu, Z.49
Zhang, H.50
Grigoriev, I.V.51
Rokhsar, D.S.52
Boore, J.L.53
more..
-
87
-
-
34547740136
-
LTR retrotransposons in rice (Oryza sativa, L.): Recent burst amplifications followed by rapid DNA loss
-
Vitte, C., Panaud, O., and Quesneville, H. 2007. LTR retrotransposons in rice (Oryza sativa, L.): Recent burst amplifications followed by rapid DNA loss. BMC Genomics 8:218.
-
(2007)
BMC Genomics
, vol.8
, pp. 218
-
-
Vitte, C.1
Panaud, O.2
Quesneville, H.3
-
88
-
-
0242495270
-
Phylogenetic relationships of Peronospora and related genera based on nuclear ribosomal ITS sequences
-
Voglmayr, H. 2003. Phylogenetic relationships of Peronospora and related genera based on nuclear ribosomal ITS sequences. Mycol. Res. 107: 1132-1142.
-
(2003)
Mycol. Res.
, vol.107
, pp. 1132-1142
-
-
Voglmayr, H.1
-
89
-
-
0032459042
-
Genome size determination in peronosporales (Oomycota) by Feulgen image analysis
-
Voglmayr, H., and Greilhuber, J. 1998. Genome size determination in peronosporales (Oomycota) by Feulgen image analysis. Fungal Genet. Biol. 25:181-195.
-
(1998)
Fungal Genet. Biol.
, vol.25
, pp. 181-195
-
-
Voglmayr, H.1
Greilhuber, J.2
-
90
-
-
35948991117
-
A translocation signal for delivery of oomycete effector proteins into host plant cells
-
Whisson, S. C., and Boevink., P. C., Moleleki, L., Avrova, A. O., and Morales., J. G., Gilroy, E. M., Armstrong, M. R., Grouffaud, S., van West, P., Chapman, S., Hein, I., and Toth., I. K., Pritchard, L., and Birch, P. R. J. 2007. A translocation signal for delivery of oomycete effector proteins into host plant cells. Nature 450:115-118.
-
(2007)
Nature
, vol.450
, pp. 115-118
-
-
Whisson, S.C.1
Boevink, P.C.2
Moleleki, L.3
Avrova, A.O.4
Morales, J.G.5
Gilroy, E.M.6
Armstrong, M.R.7
Grouffaud, S.8
Van West, P.9
Chapman, S.10
Hein, I.11
Toth, I.K.12
Pritchard, L.13
Birch, P.R.J.14
-
91
-
-
0037700013
-
TREP: A database for Triticeae repetitive elements
-
Wicker, T., and Matthews., D. E., and Keller, B. 2002. TREP: A database for Triticeae repetitive elements. Trends Plant Sci. 7:561-562.
-
(2002)
Trends Plant Sci.
, vol.7
, pp. 561-562
-
-
Wicker, T.1
Matthews, D.E.2
Keller, B.3
-
92
-
-
36249023071
-
A unified classification system for eukaryotic transposable elements
-
Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J. L., Capy, P., Chalhoub, B., Flavell, A., Leroy, P., Morgante, M., Panaud, O., Paux, E., SanMiguel, P., and Schulman, A. H. 2007. A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 8:973-982.
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 973-982
-
-
Wicker, T.1
Sabot, F.2
Hua-Van, A.3
Bennetzen, J.L.4
Capy, P.5
Chalhoub, B.6
Flavell, A.7
Leroy, P.8
Morgante, M.9
Panaud, O.10
Paux, E.11
SanMiguel, P.12
Schulman, A.H.13
-
93
-
-
0001655419
-
Resistance of Peronospora tabacina to metalaxyl in Texas and Mexico
-
Wiglesworth, M. D., Reuveni, M., Nesmith, W.C., Siegel, M. R., Kuc, J., Juarez, J., and Tabamex, 1988. Resistance of Peronospora tabacina to metalaxyl in Texas and Mexico. Plant Dis. 72:964-967.
-
(1988)
Plant Dis.
, vol.72
, pp. 964-967
-
-
Wiglesworth, M.D.1
Reuveni, M.2
Nesmith, W.C.3
Siegel, M.R.4
Kuc, J.5
Juarez, J.6
Tabamex7
-
94
-
-
42549146892
-
Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes
-
Win, J., and Kamoun, S. 2008. Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes. Plant Signal Behav. 3:251-253.
-
(2008)
Plant Signal Behav.
, vol.3
, pp. 251-253
-
-
Win, J.1
Kamoun, S.2
-
95
-
-
84857479035
-
Sequence divergent RXLR effectors share a structural fold conserved across plant pathogenic oomycete species
-
Win, J., and Krasileva., K. V., Kamoun, S., Shirasu, K., Staskawicz, B. J., and Banfield, M. J. 2012. Sequence divergent RXLR effectors share a structural fold conserved across plant pathogenic oomycete species. PLoS Pathog. 8:e1002400.
-
(2012)
PLoS Pathog.
, vol.8
-
-
Win, J.1
Krasileva, K.V.2
Kamoun, S.3
Shirasu, K.4
Staskawicz, B.J.5
Banfield, M.J.6
-
96
-
-
35348915452
-
Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes
-
Win, J., Morgan, W., Bos, J., Krasileva, K. V., and Cano., L. M., Chaparro-Garcia, A., Ammar, R., and Staskawicz., B. J., and Kamoun, S. 2007. Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes. Plant Cell 19:2349-2369.
-
(2007)
Plant Cell
, vol.19
, pp. 2349-2369
-
-
Win, J.1
Morgan, W.2
Bos, J.3
Krasileva, K.V.4
Cano, L.M.5
Chaparro-Garcia, A.6
Ammar, R.7
Staskawicz, B.J.8
Kamoun, S.9
-
98
-
-
84859898660
-
A beginner's guide to eukaryotic genome annotation
-
Yandell, M., and Ence, D. 2012. A beginner's guide to eukaryotic genome annotation. Nat. Rev. Genet. 13:329-342.
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 329-342
-
-
Yandell, M.1
Ence, D.2
-
99
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Yang, Z. 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol. EVol. 24:1586-1591.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
100
-
-
59449106805
-
PCR-based monitoring of recent isolates of tobacco blue mold from Europe reveals the presence of two genetically distinct phenotypes differing in fungicide sensitivity
-
Zipper, R., and Hammer., T. R., and Spring, O. 2009. PCR-based monitoring of recent isolates of tobacco blue mold from Europe reveals the presence of two genetically distinct phenotypes differing in fungicide sensitivity. Eur. J. Plant Pathol. 123:367-375.
-
(2009)
Eur. J. Plant Pathol.
, vol.123
, pp. 367-375
-
-
Zipper, R.1
Hammer, T.R.2
Spring, O.3
|