-
1
-
-
0031707062
-
The paleontology of intergene retrotransposons of maize
-
San Miguel P, Gaut B, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nature Genetics 20: 43-45.
-
(1998)
Nature Genetics
, vol.20
, pp. 43-45
-
-
San Miguel, P.1
Gaut, B.2
Tikhonov, A.3
Nakajima, Y.4
Bennetzen, J.L.5
-
2
-
-
70450202132
-
The B73 maize genome: Complexity, diversity and dynamics
-
doi:1126/science.1178534
-
Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, et al. (2009) The B73 maize genome: complexity, diversity and dynamics. Science 326: doi:1126/science.1178534.
-
(2009)
Science
, vol.326
-
-
Schnable, P.S.1
Ware, D.2
Fulton, R.S.3
Stein, J.C.4
Wei, F.5
-
3
-
-
0030959648
-
DNA sequence evidence for the segmental allotetraploid origin of maize
-
Gaut BS, Doebley JF (1997) DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci U S A 94: 6809-6814.
-
(1997)
Proc Natl Acad Sci U S A
, vol.94
, pp. 6809-6814
-
-
Gaut, B.S.1
Doebley, J.F.2
-
4
-
-
5144234363
-
Close Split of Sorghum and Maize Genome Progenitors
-
Swigonova Z, Lai J, Ma J, Ramakrishna W, Llaca V, et al. (2004) Close Split of Sorghum and Maize Genome Progenitors. Genome Res 14: 1916-1923.
-
(2004)
Genome Res
, vol.14
, pp. 1916-1923
-
-
Swigonova, Z.1
Lai, J.2
Ma, J.3
Ramakrishna, W.4
Llaca, V.5
-
5
-
-
0031732044
-
Retrotransposon-related DNA sequences in the centromeres of grass chromosomes
-
Miller JT, Dong F, Jackson SA, Song J, Jiang J (1998) Retrotransposon-related DNA sequences in the centromeres of grass chromosomes. Genetics 150: 1615-1623.
-
(1998)
Genetics
, vol.150
, pp. 1615-1623
-
-
Miller, J.T.1
Dong, F.2
Jackson, S.A.3
Song, J.4
Jiang, J.5
-
6
-
-
0032419941
-
A Ty3/GYPSY retrotransposon-like sequence localizes to the centromeric region of cereal chromosomes
-
Presting G, Malysheva L, Fuchs J, Schubert I (1998) A Ty3/GYPSY retrotransposon-like sequence localizes to the centromeric region of cereal chromosomes. Plant Journal 16: 721-728.
-
(1998)
Plant Journal
, vol.16
, pp. 721-728
-
-
Presting, G.1
Malysheva, L.2
Fuchs, J.3
Schubert, I.4
-
7
-
-
0037295602
-
Molecular and Cytological Analyses of Large Tracks of Centromeric DNA Reveal the Structure and Evolutionary Dynamics of Maize Centromeres
-
Nagaki K, Song J, Stupar RM, Parokonny AS, Yuan Q, et al. (2003) Molecular and Cytological Analyses of Large Tracks of Centromeric DNA Reveal the Structure and Evolutionary Dynamics of Maize Centromeres. Genetics 163: 759-770.
-
(2003)
Genetics
, vol.163
, pp. 759-770
-
-
Nagaki, K.1
Song, J.2
Stupar, R.M.3
Parokonny, A.S.4
Yuan, Q.5
-
8
-
-
16344393155
-
Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice
-
Nagaki K, Neumann P, Zhang D, Ouyang S, Buell CR, et al. (2005) Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice. Mol Biol Evol 22: 845-855.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 845-855
-
-
Nagaki, K.1
Neumann, P.2
Zhang, D.3
Ouyang, S.4
Buell, C.R.5
-
9
-
-
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 Gen Genomics 279: 133-147.
-
(2008)
Mol Gen Genomics
, vol.279
, pp. 133-147
-
-
Sharma, A.1
Presting, G.G.2
-
10
-
-
55749095036
-
Sustained retrotransposition is mediated by nucleotide deletions and inter-element recombinations
-
Sharma A, Schneider KL, Presting GG (2008) Sustained retrotransposition is mediated by nucleotide deletions and inter-element recombinations. Proc Natl Acad Sci U S A 105: 15470-15474.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 15470-15474
-
-
Sharma, A.1
Schneider, K.L.2
Presting, G.G.3
-
11
-
-
0032573174
-
Chromosome-specific molecular organization of maize (Zea mays L.) centromeric regions
-
Ananiev EV, Phillips RL, Rines HW (1998) Chromosome-specific molecular organization of maize (Zea mays L.) centromeric regions. Proc Natl Acad Sci U S A 95: 13073-13078.
-
(1998)
Proc Natl Acad Sci U S A
, vol.95
, pp. 13073-13078
-
-
Ananiev, E.V.1
Phillips, R.L.2
Rines, H.W.3
-
12
-
-
33745341997
-
Retroelement Genome Painting: Cytological Visualization of Retroelement Expansions in the Genera Zea and Tripsacum
-
Lamb JC, Birchler JA (2006) Retroelement Genome Painting: Cytological Visualization of Retroelement Expansions in the Genera Zea and Tripsacum. Genetics 173: 1007-1021.
-
(2006)
Genetics
, vol.173
, pp. 1007-1021
-
-
Lamb, J.C.1
Birchler, J.A.2
-
14
-
-
0036671661
-
Functional Rice Centromeres Are Marked by a Satellite Repeat and a Centromere-Specific Retrotransposon
-
Cheng Z, Dong F, Langdon T, Ouyang S, Buell CR, et al. (2002) Functional Rice Centromeres Are Marked by a Satellite Repeat and a Centromere-Specific Retrotransposon. Plant Cell 14: 1691-1704.
-
(2002)
Plant Cell
, vol.14
, pp. 1691-1704
-
-
Cheng, Z.1
Dong, F.2
Langdon, T.3
Ouyang, S.4
Buell, C.R.5
-
15
-
-
0036847093
-
Centromeric retroelements and satellites interact with maize kinetochore protein CENH3
-
Zhong CX, Marshall JB, Topp C, Mroczek R, Kato A, et al. (2002) Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. Plant Cell 14: 2825-2836.
-
(2002)
Plant Cell
, vol.14
, pp. 2825-2836
-
-
Zhong, C.X.1
Marshall, J.B.2
Topp, C.3
Mroczek, R.4
Kato, A.5
-
16
-
-
0037355216
-
Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres
-
Nagaki K, Talbert PB, Zhong CX, Dawe RK, Henikoff S, et al. (2003) Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres. Genetics 163: 1221-1225.
-
(2003)
Genetics
, vol.163
, pp. 1221-1225
-
-
Nagaki, K.1
Talbert, P.B.2
Zhong, C.X.3
Dawe, R.K.4
Henikoff, S.5
-
17
-
-
1542647343
-
Maize centromeres: Organization and functional adaptation in the genetic background of oat
-
Jin W, Melo JR, Nagaki K, Talbert PB, Henikoff S, et al. (2004) Maize centromeres: organization and functional adaptation in the genetic background of oat. Plant Cell 16: 571-581.
-
(2004)
Plant Cell
, vol.16
, pp. 571-581
-
-
Jin, W.1
Melo, J.R.2
Nagaki, K.3
Talbert, P.B.4
Henikoff, S.5
-
18
-
-
0029812835
-
Substitution rate comparisons between grasses and palms: Synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL
-
Gaut BS, Morton BR, McCaig BC, Clegg MT (1996) Substitution rate comparisons between grasses and palms: Synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci U S A 93: 10274-10279.
-
(1996)
Proc Natl Acad Sci U S A
, vol.93
, pp. 10274-10279
-
-
Gaut, B.S.1
Morton, B.R.2
McCaig, B.C.3
Clegg, M.T.4
-
19
-
-
0036344092
-
Godwanan evolution of the grass alliance of families (Poales)
-
Bremer K (2002) Godwanan evolution of the grass alliance of families (Poales). Evolution 56: 1374-1387.
-
(2002)
Evolution
, vol.56
, pp. 1374-1387
-
-
Bremer, K.1
-
20
-
-
23844434604
-
Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species
-
Lee H-R, Zhang W, Langdon T, Jin W, Yan H, et al. (2005) Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species. Proc Natl Acad Sci U S A 102: 11793-11798.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 11793-11798
-
-
Lee, H.-R.1
Zhang, W.2
Langdon, T.3
Jin, W.4
Yan, H.5
-
21
-
-
0035839066
-
The Centromere Paradox: Stable inheritance with rapidly evolving DNA
-
Henikoff S, Ahmad K, Malik HS (2001) The Centromere Paradox: Stable inheritance with rapidly evolving DNA. Science 293: 1098-1102.
-
(2001)
Science
, vol.293
, pp. 1098-1102
-
-
Henikoff, S.1
Ahmad, K.2
Malik, H.S.3
-
22
-
-
56849120549
-
Intergenic locations of rice centromeric chromatin
-
doi:10.1371/journal. pbio.0060286
-
Yan H, Talbert PB, Lee H-R, Jett J, Henikoff S, et al. (2008) Intergenic locations of rice centromeric chromatin. PLoS Biol 6: e286. doi:10.1371/journal. pbio.0060286.
-
(2008)
PLoS Biol
, vol.6
-
-
Yan, H.1
Talbert, P.B.2
Lee, H.-R.3
Jett, J.4
Henikoff, S.5
-
24
-
-
33750452293
-
Precise centromere mapping using a combination of repeat junction markers and chromatin immunoprecipitation-PCR
-
Luce A, Sharma A, Mollere O, Wolfgruber TK, Nagaki K, et al. (2006) Precise centromere mapping using a combination of repeat junction markers and chromatin immunoprecipitation-PCR. Genetics 174: 1057-61.
-
(2006)
Genetics
, vol.174
, pp. 1057-1061
-
-
Luce, A.1
Sharma, A.2
Mollere, O.3
Wolfgruber, T.K.4
Nagaki, K.5
-
25
-
-
0031886532
-
Transposon Display identifies individual transposable elements in high copy number lines
-
Van den Broeck D, Maes T, Sauer M, Zethof J, De Keukeleire P, et al. (1998) Transposon Display identifies individual transposable elements in high copy number lines. Plant J 13: 121-129.
-
(1998)
Plant J
, vol.13
, pp. 121-129
-
-
Van den Broeck, D.1
Maes, T.2
Sauer, M.3
Zethof, J.4
De Keukeleire, P.5
-
26
-
-
0034730039
-
The MITE family Heartbreaker (Hbr): Molecular markers in maize
-
Casas AM, Brouwer C, Nagel A, Wang L, Zhang Q, et al. (2000) The MITE family Heartbreaker (Hbr): Molecular markers in maize. Proc Natl Acad Sci U S A 97: 10083-10089.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 10083-10089
-
-
Casas, A.M.1
Brouwer, C.2
Nagel, A.3
Wang, L.4
Zhang, Q.5
-
27
-
-
0036010768
-
Expanding the genetic map of maize with the intermated B73 x Mo17 (IBM) population
-
Lee M, Sharopova N, Beavis WD, Grant D, Katt M, et al. (2002) Expanding the genetic map of maize with the intermated B73 x Mo17 (IBM) population. Plant Mol Biol 48: 453-461.
-
(2002)
Plant Mol Biol
, vol.48
, pp. 453-461
-
-
Lee, M.1
Sharopova, N.2
Beavis, W.D.3
Grant, D.4
Katt, M.5
-
28
-
-
85047683551
-
Access to the maize genome: An integrated physical and genetic map
-
Coe E, Cone K, McMullen M, Chen S, Davis G, et al. (2002) Access to the maize genome: an integrated physical and genetic map. Plant Physiology 128: 9-12.
-
(2002)
Plant Physiology
, vol.128
, pp. 9-12
-
-
Coe, E.1
Cone, K.2
McMullen, M.3
Chen, S.4
Davis, G.5
-
29
-
-
4544245758
-
Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize
-
Kato A, Lamb JC, Birchler JA (2004) Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Natl Acad Sci U S A 101: 13554-13559.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 13554-13559
-
-
Kato, A.1
Lamb, J.C.2
Birchler, J.A.3
-
30
-
-
73649136247
-
JunctionViewer: Customizable annotation software for repeat-rich genomic regions
-
in press
-
Wolfgruber TK, Presting GG (2009) JunctionViewer: Customizable annotation software for repeat-rich genomic regions. BMC Bioinformatics, in press.
-
(2009)
BMC Bioinformatics
-
-
Wolfgruber, T.K.1
Presting, G.G.2
-
31
-
-
34547634071
-
Physical and genetic structure of the maize genome reflects its complex evolutionary history
-
doi:10.1371/journal.pgen.0030123
-
Wei F, Coe E, Nelson W, Bharti AK, Engler F, et al. (2007) Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet 3: e123. doi:10.1371/journal.pgen.0030123.
-
(2007)
PLoS Genet
, vol.3
-
-
Wei, F.1
Coe, E.2
Nelson, W.3
Bharti, A.K.4
Engler, F.5
-
32
-
-
18944382213
-
Happy together: The life and times of Ty retrotransposons and their hosts
-
Lesage P, Todeschini AL (2005) Happy together: the life and times of Ty retrotransposons and their hosts. Cytogenet Genome Res 110: 70-90.
-
(2005)
Cytogenet Genome Res
, vol.110
, pp. 70-90
-
-
Lesage, P.1
Todeschini, A.L.2
-
33
-
-
33847155507
-
Distinct chromosomal distributions of highly repetitive sequences in maize
-
Lamb JC, Meyer JM, Corcoran B, Kato A, Han F, et al. (2007) Distinct chromosomal distributions of highly repetitive sequences in maize. Chromosome Res 15: 33-49.
-
(2007)
Chromosome Res
, vol.15
, pp. 33-49
-
-
Lamb, J.C.1
Meyer, J.M.2
Corcoran, B.3
Kato, A.4
Han, F.5
-
34
-
-
40449136688
-
Chromodomains direct integration of retrotransposons to heterochromatin
-
Gao X, Hou Y, Ebina H, Levin HL, Voytas (2008) Chromodomains direct integration of retrotransposons to heterochromatin. Genome Res 18: 359-369.
-
(2008)
Genome Res
, vol.18
, pp. 359-369
-
-
Gao, X.1
Hou, Y.2
Ebina, H.3
Levin, H.L.4
Voytas5
-
35
-
-
33746450910
-
Partitioning of the maize epigenome by the number of methyl groups on histone H3 lysines 9 and 27
-
Shi J, Dawe RK (2006) Partitioning of the maize epigenome by the number of methyl groups on histone H3 lysines 9 and 27. Genetics 173: 1571-1583.
-
(2006)
Genetics
, vol.173
, pp. 1571-1583
-
-
Shi, J.1
Dawe, R.K.2
-
36
-
-
58149166748
-
Histone modifications associated with both A and B chromosomes of maize
-
Jin W, Lamb JC, Zhang W, Kolano B, Birchler JA, et al. (2008) Histone modifications associated with both A and B chromosomes of maize. Chromosome Research 16: 1203-1214.
-
(2008)
Chromosome Research
, vol.16
, pp. 1203-1214
-
-
Jin, W.1
Lamb, J.C.2
Zhang, W.3
Kolano, B.4
Birchler, J.A.5
-
37
-
-
2342466982
-
Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice
-
Ma J, Devos KM, Bennetzen JL (2004) Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res 14: 860-869.
-
(2004)
Genome Res
, vol.14
, pp. 860-869
-
-
Ma, J.1
Devos, K.M.2
Bennetzen, J.L.3
-
38
-
-
33750970858
-
Loading of Arabidopsis centromeric histone CENH3 occurs mainly during G2 and requires the presence of the histone fold domain
-
Lermontova I, Schubert V, Fuchs J, Klatte S, Macas J, et al. (2006) Loading of Arabidopsis centromeric histone CENH3 occurs mainly during G2 and requires the presence of the histone fold domain. Plant Cell 18: 2443-2451.
-
(2006)
Plant Cell
, vol.18
, pp. 2443-2451
-
-
Lermontova, I.1
Schubert, V.2
Fuchs, J.3
Klatte, S.4
Macas, J.5
-
39
-
-
0036200147
-
Conserved organization of centromeric chromatin in flies and humans
-
Blower M, Sullivan B, Karpen G (2002) Conserved organization of centromeric chromatin in flies and humans. Dev Cell 2: 319-330.
-
(2002)
Dev Cell
, vol.2
, pp. 319-330
-
-
Blower, M.1
Sullivan, B.2
Karpen, G.3
-
40
-
-
7544227521
-
Centromeric chromatin exhibits a histone modification pattern that is distinct from both euchromatin and heterochromatin
-
Sullivan BA, Karpen GH (2004) Centromeric chromatin exhibits a histone modification pattern that is distinct from both euchromatin and heterochromatin. Nat Struct Mol Biol 11: 1076-1083.
-
(2004)
Nat Struct Mol Biol
, vol.11
, pp. 1076-1083
-
-
Sullivan, B.A.1
Karpen, G.H.2
-
41
-
-
0842289255
-
Sequencing of a rice centromere uncovers active genes
-
Nagaki K, Cheng Z, Ouyang S, Talbert PB, Kim M, et al. (2004) Sequencing of a rice centromere uncovers active genes. Nature Genetics 36: 138-145.
-
(2004)
Nature Genetics
, vol.36
, pp. 138-145
-
-
Nagaki, K.1
Cheng, Z.2
Ouyang, S.3
Talbert, P.B.4
Kim, M.5
-
42
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
43
-
-
34547781750
-
-
Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599
-
Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
-
-
-
-
44
-
-
15444355385
-
Application of Fiber-FISH in physical mapping of Arabidopsis thaliana
-
Jackson SA, Wang ML, Goodman HM, Jiang J (1998) Application of Fiber-FISH in physical mapping of Arabidopsis thaliana. Genome 41: 566-572.
-
(1998)
Genome
, vol.41
, pp. 566-572
-
-
Jackson, S.A.1
Wang, M.L.2
Goodman, H.M.3
Jiang, J.4
-
45
-
-
0036039916
-
Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers
-
Cheng Z, Buell CR, Wing RA, Jiang J (2002) Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers. Chrom Res 10: 379-387.
-
(2002)
Chrom Res
, vol.10
, pp. 379-387
-
-
Cheng, Z.1
Buell, C.R.2
Wing, R.A.3
Jiang, J.4
|