-
2
-
-
34347381116
-
Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families
-
Wicker T, Keller B, (2007) Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Res 17: 1072-1081.
-
(2007)
Genome Res
, vol.17
, pp. 1072-1081
-
-
Wicker, T.1
Keller, B.2
-
3
-
-
73249153383
-
Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?
-
Tian Z, Rizzon C, Du J, Zhu L, Bennetzen JL, et al. (2009) Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons? Genome Res 19: 2221-2230.
-
(2009)
Genome Res
, vol.19
, pp. 2221-2230
-
-
Tian, Z.1
Rizzon, C.2
Du, J.3
Zhu, L.4
Bennetzen, J.L.5
-
4
-
-
77649149766
-
SoyTEdb: a comprehensive database of transposable elements in the soybean genome
-
Du J, Grant D, Tian Z, Nelson RT, Zhu L, et al. (2010) SoyTEdb: a comprehensive database of transposable elements in the soybean genome. BMC Genomics 11: 113.
-
(2010)
BMC Genomics
, vol.11
, pp. 113
-
-
Du, J.1
Grant, D.2
Tian, Z.3
Nelson, R.T.4
Zhu, L.5
-
5
-
-
58449137410
-
The Sorghum bicolor genome and the diversification of grasses
-
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, et al. (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556.
-
(2009)
Nature
, vol.457
, pp. 551-556
-
-
Paterson, A.H.1
Bowers, J.E.2
Bruggmann, R.3
Dubchak, I.4
Grimwood, J.5
-
6
-
-
70450202132
-
The B73 maize genome: complexity, diversity, and dynamics
-
Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, et al. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112-1115.
-
(2009)
Science
, vol.326
, pp. 1112-1115
-
-
Schnable, P.S.1
Ware, D.2
Fulton, R.S.3
Stein, J.C.4
Wei, F.5
-
7
-
-
0031707062
-
The paleontology of intergene retrotransposons of maize
-
SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL, (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20: 43-45.
-
(1998)
Nat Genet
, vol.20
, pp. 43-45
-
-
SanMiguel, P.1
Gaut, B.S.2
Tikhonov, A.3
Nakajima, Y.4
Bennetzen, J.L.5
-
8
-
-
77955689247
-
Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison
-
Du J, Tian Z, Hans CS, Laten HM, Cannon SB, et al. (2010) Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison. Plant J 63: 584-598.
-
(2010)
Plant J
, vol.63
, pp. 584-598
-
-
Du, J.1
Tian, Z.2
Hans, C.S.3
Laten, H.M.4
Cannon, S.B.5
-
9
-
-
0025006614
-
Origin and evolution of retroelements based upon their reverse transcriptase sequences
-
Xiong Y, Eickbush TH, (1990) Origin and evolution of retroelements based upon their reverse transcriptase sequences. The EMBO J 9: 3353.
-
(1990)
The EMBO J
, vol.9
, pp. 3353
-
-
Xiong, Y.1
Eickbush, T.H.2
-
10
-
-
84871856746
-
Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean
-
Tian Z, Zhao M, She M, Du J, Cannon SB, et al. (2012) Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean. Plant Cell 24: 4422-4436.
-
(2012)
Plant Cell
, vol.24
, pp. 4422-4436
-
-
Tian, Z.1
Zhao, M.2
She, M.3
Du, J.4
Cannon, S.B.5
-
11
-
-
28644441122
-
Visualization of diffuse centromeres with centromere-specific histone H3 in the holocentric plant Luzula nivea
-
Nagaki K, Kashihara K, Murata M, (2005) Visualization of diffuse centromeres with centromere-specific histone H3 in the holocentric plant Luzula nivea. Plant Cell 17: 1886-1893.
-
(2005)
Plant Cell
, vol.17
, pp. 1886-1893
-
-
Nagaki, K.1
Kashihara, K.2
Murata, M.3
-
12
-
-
38349001431
-
Centromeric retrotransposon lineages predate the maize/rice divergence and differ in abundance and activity
-
Sharma A, Presting GG, (2008) Centromeric retrotransposon lineages predate the maize/rice divergence and differ in abundance and activity. Mol Genet Genomics 279: 133-147.
-
(2008)
Mol Genet Genomics
, vol.279
, pp. 133-147
-
-
Sharma, A.1
Presting, G.G.2
-
13
-
-
84855188031
-
Plant centromeric retrotransposons: a structural and cytogenetic perspective
-
Neumann P, Navratilova A, Koblizkova A, Kejnovsky E, Hribova E, et al. (2011) Plant centromeric retrotransposons: a structural and cytogenetic perspective. Mob DNA 2: 4.
-
(2011)
Mob DNA
, vol.2
, pp. 4
-
-
Neumann, P.1
Navratilova, A.2
Koblizkova, A.3
Kejnovsky, E.4
Hribova, E.5
-
14
-
-
0036061848
-
Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis
-
Devos KM, Brown JK, Bennetzen JL, (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12: 1075-1079.
-
(2002)
Genome Res
, vol.12
, pp. 1075-1079
-
-
Devos, K.M.1
Brown, J.K.2
Bennetzen, J.L.3
-
15
-
-
4344616881
-
Rapid recent growth and divergence of rice nuclear genomes
-
Ma J, Bennetzen JL, (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A 101: 12404-12410.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 12404-12410
-
-
Ma, J.1
Bennetzen, J.L.2
-
16
-
-
84863693752
-
The tomato genome sequence provides insights into fleshy fruit evolution
-
The Tomato Genome Consortium
-
The Tomato Genome Consortium, (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635-641.
-
(2012)
Nature
, vol.485
, pp. 635-641
-
-
-
17
-
-
33646170036
-
Euchromatin and pericentromeric heterochromatin: comparative composition in the tomato genome
-
Wang Y, Tang X, Cheng Z, Mueller L, Giovannoni J, et al. (2006) Euchromatin and pericentromeric heterochromatin: comparative composition in the tomato genome. Genetics 172: 2529-2540.
-
(2006)
Genetics
, vol.172
, pp. 2529-2540
-
-
Wang, Y.1
Tang, X.2
Cheng, Z.3
Mueller, L.4
Giovannoni, J.5
-
18
-
-
40849085290
-
A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit
-
Xiao H, Jiang N, Schaffner E, Stockinger EJ, van der Knaap E, (2008) A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319: 1527-1530.
-
(2008)
Science
, vol.319
, pp. 1527-1530
-
-
Xiao, H.1
Jiang, N.2
Schaffner, E.3
Stockinger, E.J.4
van der Knaap, E.5
-
19
-
-
70349515979
-
Genome organization of the tomato sun locus and characterization of the unusual retrotransposon Rider
-
Jiang N, Gao D, Xiao H, van der Knaap E, (2009) Genome organization of the tomato sun locus and characterization of the unusual retrotransposon Rider. Plant J 60: 181-193.
-
(2009)
Plant J
, vol.60
, pp. 181-193
-
-
Jiang, N.1
Gao, D.2
Xiao, H.3
van der Knaap, E.4
-
20
-
-
67650321229
-
A new family of Ty1-copia-like retrotransposons originated in the tomato genome by a recent horizontal transfer event
-
Cheng X, Zhang D, Cheng Z, Keller B, Ling H-Q, (2009) A new family of Ty1-copia-like retrotransposons originated in the tomato genome by a recent horizontal transfer event. Genetics 181: 1183-1193.
-
(2009)
Genetics
, vol.181
, pp. 1183-1193
-
-
Cheng, X.1
Zhang, D.2
Cheng, Z.3
Keller, B.4
Ling, H.-Q.5
-
21
-
-
0037433054
-
LTR_STRUC: a novel search and identification program for LTR retrotransposons
-
McCarthy EM, McDonald JF, (2003) LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 19: 362-367.
-
(2003)
Bioinformatics
, vol.19
, pp. 362-367
-
-
McCarthy, E.M.1
McDonald, J.F.2
-
22
-
-
0032419941
-
A Ty3/gypsy retrotransposon-like sequence localizes to the centromeric regions of cereal chromosomes
-
Presting GG, Malysheva L, Fuchs J, Schubert I, (1998) A Ty3/gypsy retrotransposon-like sequence localizes to the centromeric regions of cereal chromosomes. Plant J 16: 721-728.
-
(1998)
Plant J
, vol.16
, pp. 721-728
-
-
Presting, G.G.1
Malysheva, L.2
Fuchs, J.3
Schubert, I.4
-
23
-
-
0346668134
-
Dasheng and RIRE2. A nonautonomous long terminal repeat element and its putative autonomous partner in the rice genome
-
Jiang N, Jordan IK, Wessler SR, (2002) Dasheng and RIRE2. A nonautonomous long terminal repeat element and its putative autonomous partner in the rice genome. Plant Physiol 130: 1697-1705.
-
(2002)
Plant Physiol
, vol.130
, pp. 1697-1705
-
-
Jiang, N.1
Jordan, I.K.2
Wessler, S.R.3
-
24
-
-
84857757793
-
Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the paleopolyploid soybean
-
Du J, Tian Z, Sui Y, Zhao M, Song Q, et al. (2012) Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the paleopolyploid soybean. Plant Cell 24: 21-32.
-
(2012)
Plant Cell
, vol.24
, pp. 21-32
-
-
Du, J.1
Tian, Z.2
Sui, Y.3
Zhao, M.4
Song, Q.5
-
25
-
-
84863183645
-
A highly conserved, small LTR retrotransposon that preferentially targets genes in grass genomes
-
Gao D, Chen J, Chen M, Meyers BC, Jackson S, (2012) A highly conserved, small LTR retrotransposon that preferentially targets genes in grass genomes. PLoS One 7: e32010.
-
(2012)
PLoS One
, vol.7
-
-
Gao, D.1
Chen, J.2
Chen, M.3
Meyers, B.C.4
Jackson, S.5
-
26
-
-
77950536369
-
Genomic analysis of wild tomato introgressions determining metabolism-and yield-associated traits
-
Kamenetzky L, Asís R, Bassi S, de Godoy F, Bermúdez L, et al. (2010) Genomic analysis of wild tomato introgressions determining metabolism-and yield-associated traits. Plant Physiol 152: 1772-1786.
-
(2010)
Plant Physiol
, vol.152
, pp. 1772-1786
-
-
Kamenetzky, L.1
Asís, R.2
Bassi, S.3
de Godoy, F.4
Bermúdez, L.5
-
27
-
-
0002557518
-
Molecular clocks and nucleotide substitution rates in higher plants
-
Gaut BS, (1998) Molecular clocks and nucleotide substitution rates in higher plants. Evol Biol 30: 93-120.
-
(1998)
Evol Biol
, vol.30
, pp. 93-120
-
-
Gaut, B.S.1
-
28
-
-
0036743506
-
Comparative sequencing in the genus Lycopersicon: implications for the evolution of fruit size in the domestication of cultivated tomatoes
-
Nesbitt TC, Tanksley SD, (2002) Comparative sequencing in the genus Lycopersicon: implications for the evolution of fruit size in the domestication of cultivated tomatoes. Genetics 162: 365-379.
-
(2002)
Genetics
, vol.162
, pp. 365-379
-
-
Nesbitt, T.C.1
Tanksley, S.D.2
-
29
-
-
79957761306
-
Molecular evidence for a single evolutionary origin of domesticated rice
-
Molina J, Sikora M, Garud N, Flowers JM, Rubinstein S, et al. (2011) Molecular evidence for a single evolutionary origin of domesticated rice. Proc Natl Acad Sci U S A 108: 8351-8356.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 8351-8356
-
-
Molina, J.1
Sikora, M.2
Garud, N.3
Flowers, J.M.4
Rubinstein, S.5
-
30
-
-
13244264889
-
Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.)
-
Vitte C, Ishii T, Lamy F, Brar D, Panaud O, (2004) Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.). Mol Genet Genomics 272: 504-511.
-
(2004)
Mol Genet Genomics
, vol.272
, pp. 504-511
-
-
Vitte, C.1
Ishii, T.2
Lamy, F.3
Brar, D.4
Panaud, O.5
-
31
-
-
0033580401
-
The limits of selection during maize domestication
-
Wang RL, Stec A, Hey J, Lukens L, Doebley J, (1999) The limits of selection during maize domestication. Nature 398: 236-239.
-
(1999)
Nature
, vol.398
, pp. 236-239
-
-
Wang, R.L.1
Stec, A.2
Hey, J.3
Lukens, L.4
Doebley, J.5
-
32
-
-
70350630311
-
Molecular and chromosomal evidence for allopolyploidy in soybean
-
Gill N, Findley S, Walling JG, Hans C, Ma J, et al. (2009) Molecular and chromosomal evidence for allopolyploidy in soybean. Plant Physiol 151: 1167-1174.
-
(2009)
Plant Physiol
, vol.151
, pp. 1167-1174
-
-
Gill, N.1
Findley, S.2
Walling, J.G.3
Hans, C.4
Ma, J.5
-
33
-
-
34547592867
-
LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons
-
Xu Z, Wang H, (2007) LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res 35: W265-268.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Xu, Z.1
Wang, H.2
-
34
-
-
39749179047
-
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
-
Ellinghaus D, Kurtz S, 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
-
35
-
-
84860998859
-
A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons
-
Steinbauerova V, Neumann P, Novak P, Macas J, (2011) A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons. Genetica 139: 1543-1555.
-
(2011)
Genetica
, vol.139
, pp. 1543-1555
-
-
Steinbauerova, V.1
Neumann, P.2
Novak, P.3
Macas, J.4
-
36
-
-
0029824259
-
Retrotransposons of rice involved in mutations induced by tissue culture
-
Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M, (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci U S A 93: 7783-7788.
-
(1996)
Proc Natl Acad Sci U S A
, vol.93
, pp. 7783-7788
-
-
Hirochika, H.1
Sugimoto, K.2
Otsuki, Y.3
Tsugawa, H.4
Kanda, M.5
-
37
-
-
0035115215
-
Contribution of the Tos17 retrotransposon to rice functional genomics
-
Hirochika H, (2001) Contribution of the Tos17 retrotransposon to rice functional genomics. Curr Opin Plant Biol 4: 118-122.
-
(2001)
Curr Opin Plant Biol
, vol.4
, pp. 118-122
-
-
Hirochika, H.1
-
38
-
-
55549123888
-
Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice
-
Huang X, Lu G, Zhao Q, Liu X, Han B, (2008) Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice. Plant Physiol 148: 25-40.
-
(2008)
Plant Physiol
, vol.148
, pp. 25-40
-
-
Huang, X.1
Lu, G.2
Zhao, Q.3
Liu, X.4
Han, B.5
-
39
-
-
78649479141
-
Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection
-
Lam HM, Xu X, Liu X, Chen W, Yang G, et al. (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42: 1053-1059.
-
(2010)
Nat Genet
, vol.42
, pp. 1053-1059
-
-
Lam, H.M.1
Xu, X.2
Liu, X.3
Chen, W.4
Yang, G.5
-
40
-
-
78650668282
-
Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome
-
Kim MY, Lee S, Van K, Kim TH, Jeong SC, et al. (2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc Natl Acad Sci U S A 107: 22032-22037.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 22032-22037
-
-
Kim, M.Y.1
Lee, S.2
Van, K.3
Kim, T.H.4
Jeong, S.C.5
-
41
-
-
77950346033
-
Bifurcation and enhancement of autonomous-nonautonomous retrotransposon partnership through LTR Swapping in soybean
-
Du J, Tian Z, Bowen NJ, Schmutz J, Shoemaker RC, et al. (2010) Bifurcation and enhancement of autonomous-nonautonomous retrotransposon partnership through LTR Swapping in soybean. Plant Cell 22: 48-61.
-
(2010)
Plant Cell
, vol.22
, pp. 48-61
-
-
Du, J.1
Tian, Z.2
Bowen, N.J.3
Schmutz, J.4
Shoemaker, R.C.5
-
42
-
-
31044442399
-
Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice
-
Ma J, Bennetzen JL, (2006) Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice. Proc Natl Acad Sci U S A 103: 383-388.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 383-388
-
-
Ma, J.1
Bennetzen, J.L.2
-
43
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
44
-
-
0015488244
-
On the stochastic model for estimation of mutational distance between homologous proteins
-
Kimura M, Ota T, (1972) On the stochastic model for estimation of mutational distance between homologous proteins. J Mol Evol 2: 87-90.
-
(1972)
J Mol Evol
, vol.2
, pp. 87-90
-
-
Kimura, M.1
Ota, T.2
-
45
-
-
32044442068
-
Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice
-
Ma J, Jackson SA, (2006) Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice. Genome Res 16: 251-259.
-
(2006)
Genome Res
, vol.16
, pp. 251-259
-
-
Ma, J.1
Jackson, S.A.2
-
46
-
-
0030045979
-
The age of Alu subfamilies
-
Kapitonov V, Jurka J, (1996) The age of Alu subfamilies. J Mol Evol 42: 59-65.
-
(1996)
J Mol Evol
, vol.42
, pp. 59-65
-
-
Kapitonov, V.1
Jurka, J.2
-
47
-
-
0033973992
-
Evolutionary history of the human endogenous retrovirus family ERV9
-
Costas J, Naveira H, (2000) Evolutionary history of the human endogenous retrovirus family ERV9. Mol Biol Evol 17: 320-330.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 320-330
-
-
Costas, J.1
Naveira, H.2
-
48
-
-
0023375195
-
The neighbor-joining method: a new method for reconstructing phylogenetic trees
-
Saitou N, Nei M, (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
-
(1987)
Mol Biol Evol
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
49
-
-
79957613599
-
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
-
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 2731-2739
-
-
Tamura, K.1
Peterson, D.2
Peterson, N.3
Stecher, G.4
Nei, M.5
|