-
1
-
-
14744277777
-
Polyploidy and genome evolution in plants
-
Adams, K.L., and Wendel, J.F. (2005). Polyploidy and genome evolution in plants. Curr. Opin. Plant Biol. 8: 135–141.
-
(2005)
Curr. Opin. Plant Biol
, vol.8
, pp. 135-141
-
-
Adams, K.L.1
Wendel, J.F.2
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389–3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
3
-
-
77950949952
-
The gene balance hypothesis: Implications for gene regulation, quantitative traits and evolution
-
Birchler, J.A., and Veitia, R.A. (2010). The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution. New Phytol. 186: 54–62.
-
(2010)
New Phytol
, vol.186
, pp. 54-62
-
-
Birchler, J.A.1
Veitia, R.A.2
-
4
-
-
84866294456
-
Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines
-
Birchler, J.A., and Veitia, R.A. (2012). Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines. Proc. Natl. Acad. Sci. USA 109: 14746–14753.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 14746-14753
-
-
Birchler, J.A.1
Veitia, R.A.2
-
5
-
-
3142700743
-
Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes
-
Blanc, G., and Wolfe, K.H. (2004). Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16: 1667–1678.
-
(2004)
Plant Cell
, vol.16
, pp. 1667-1678
-
-
Blanc, G.1
Wolfe, K.H.2
-
6
-
-
84956878515
-
A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response
-
Bousios, A., Diez, C.M., Takuno, S., Bystry, V., Darzentas, N., and Gaut, B.S. (2016). A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response. Genome Res. 26: 226–237.
-
(2016)
Genome Res
, vol.26
, pp. 226-237
-
-
Bousios, A.1
Diez, C.M.2
Takuno, S.3
Bystry, V.4
Darzentas, N.5
Gaut, B.S.6
-
7
-
-
84860424914
-
Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa
-
Cheng, F., Wu, J., Fang, L., Sun, S., Liu, B., Lin, K., Bonnema, G., and Wang, X. (2012). Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa. PLoS One 7: e36442.
-
(2012)
Plos One
, vol.7
-
-
Cheng, F.1
Wu, J.2
Fang, L.3
Sun, S.4
Liu, B.5
Lin, K.6
Bonnema, G.7
Wang, X.8
-
8
-
-
0036061848
-
Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis
-
Devos, K.M., Brown, J.K., and Bennetzen, J.L. (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
-
9
-
-
0041508533
-
Chloroplast-expressed gutamine synthetase in Glycine and related Leguminosae: Phylogeny, gene duplication, and ancient polyploidy
-
Doyle, J.J., Doyle, J.L., and Harbison, C. (2003). Chloroplast-expressed gutamine synthetase in Glycine and related Leguminosae: Phylogeny, gene duplication, and ancient polyploidy. Syst. Bot. 28: 567–577.
-
(2003)
Syst. Bot
, vol.28
, pp. 567-577
-
-
Doyle, J.J.1
Doyle, J.L.2
Harbison, C.3
-
10
-
-
77950931395
-
Dating the origins of polyploidy events
-
Doyle, J.J., and Egan, A.N. (2010). Dating the origins of polyploidy events. New Phytol. 186: 73–85.
-
(2010)
New Phytol
, vol.186
, pp. 73-85
-
-
Doyle, J.J.1
Egan, A.N.2
-
11
-
-
77649149766
-
SoyTEdb: A comprehensive database of transposable elements in the soybean genome
-
Du, J., Grant, D., Tian, Z., Nelson, R.T., Zhu, L., Shoemaker, R.C., and Ma, J. (2010a). 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
Shoemaker, R.C.6
Ma, J.7
-
12
-
-
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., Cannon, S.B., Cregan, P., and Ma, J. (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
Cannon, S.B.6
Cregan, P.7
Ma, J.8
-
13
-
-
77954299992
-
AgriGO: A GO analysis toolkit for the agricultural community
-
Du, Z., Zhou, X., Ling, Y., Zhang, Z., and Su, Z. (2010b). agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 38: W64–W70.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. W64-W70
-
-
Du, Z.1
Zhou, X.2
Ling, Y.3
Zhang, Z.4
Su, Z.5
-
14
-
-
13244255415
-
MUSCLE: A multiple sequence alignment method with reduced time and space complexity
-
Edgar, R.C. (2004). MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
15
-
-
85033359896
-
Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140-year-old naturally established neo-allopolyploid monkeyflower
-
Edger, P.P., et al. (2017). Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140-year-old naturally established neo-allopolyploid monkeyflower. Plant Cell 29: 2150–2167.
-
(2017)
Plant Cell
, vol.29
, pp. 2150-2167
-
-
Edger, P.P.1
-
16
-
-
84884697475
-
Epigenetic and genetic influences on DNA methylation variation in maize populations
-
Eichten, S.R., et al. (2013). Epigenetic and genetic influences on DNA methylation variation in maize populations. Plant Cell 25: 2783–2797.
-
(2013)
Plant Cell
, vol.25
, pp. 2783-2797
-
-
Eichten, S.R.1
-
17
-
-
84895528690
-
Regulatory modules controlling maize inflorescence architecture
-
Eveland, A.L., et al. (2014). Regulatory modules controlling maize inflorescence architecture. Genome Res. 24: 431–443.
-
(2014)
Genome Res
, vol.24
, pp. 431-443
-
-
Eveland, A.L.1
-
18
-
-
77950931393
-
Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation
-
Flagel, L.E., and Wendel, J.F. (2010). Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation. New Phytol. 186: 184–193.
-
(2010)
New Phytol
, vol.186
, pp. 184-193
-
-
Flagel, L.E.1
Wendel, J.F.2
-
19
-
-
67651039811
-
Bias in plant gene content following different sorts of duplication: Tandem, whole-genome, segmental, or by transposition
-
Freeling, M. (2009). Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu. Rev. Plant Biol. 60: 433–453.
-
(2009)
Annu. Rev. Plant Biol
, vol.60
, pp. 433-453
-
-
Freeling, M.1
-
20
-
-
57149120510
-
Many or most genes in Arabidopsis transposed after the origin of the order Brassicales
-
Freeling, M., Lyons, E., Pedersen, B., Alam, M., Ming, R., and Lisch, D. (2008). Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Res. 18: 1924–1937.
-
(2008)
Genome Res
, vol.18
, pp. 1924-1937
-
-
Freeling, M.1
Lyons, E.2
Pedersen, B.3
Alam, M.4
Ming, R.5
Lisch, D.6
-
21
-
-
33745610025
-
Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity
-
Freeling, M., and Thomas, B.C. (2006). Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res. 16: 805–814.
-
(2006)
Genome Res
, vol.16
, pp. 805-814
-
-
Freeling, M.1
Thomas, B.C.2
-
22
-
-
84859890589
-
Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants
-
Freeling, M., Woodhouse, M.R., Subramaniam, S., Turco, G., Lisch, D., and Schnable, J.C. (2012). Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants. Curr. Opin. Plant Biol. 15: 131–139.
-
(2012)
Curr. Opin. Plant Biol
, vol.15
, pp. 131-139
-
-
Freeling, M.1
Woodhouse, M.R.2
Subramaniam, S.3
Turco, G.4
Lisch, D.5
Schnable, J.C.6
-
23
-
-
84893062974
-
Two evolutionarily distinct classes of paleopolyploidy
-
Garsmeur, O., Schnable, J.C., Almeida, A., Jourda, C., D’Hont, A., and Freeling, M. (2014). Two evolutionarily distinct classes of paleopolyploidy. Mol. Biol. Evol. 31: 448–454.
-
(2014)
Mol. Biol. E
, vol.31
, pp. 448-454
-
-
Garsmeur, O.1
Schnable, J.C.2
Almeida, A.3
Jourda, C.4
D’Hont, A.5
Freeling, M.6
-
24
-
-
0030959648
-
DNA sequence evidence for the segmental allotetraploid origin of maize
-
Gaut, B.S., and Doebley, J.F. (1997). DNA sequence evidence for the segmental allotetraploid origin of maize. Proc. Natl. Acad. Sci. USA 94: 6809–6814.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 6809-6814
-
-
Gaut, B.S.1
Doebley, J.F.2
-
25
-
-
84875971371
-
CHH islands: De novo DNA methylation in near-gene chromatin regulation in maize
-
Gent, J.I., Ellis, N.A., Guo, L., Harkess, A.E., Yao, Y., Zhang, X., and Dawe, R.K. (2013). CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize. Genome Res. 23: 628–637.
-
(2013)
Genome Res
, vol.23
, pp. 628-637
-
-
Gent, J.I.1
Ellis, N.A.2
Guo, L.3
Harkess, A.E.4
Yao, Y.5
Zhang, X.6
Dawe, R.K.7
-
26
-
-
70350630311
-
Molecular and chromosomal evidence for allopolyploidy in soybean
-
Gill, N., Findley, S., Walling, J.G., Hans, C., Ma, J., Doyle, J., Stacey, G., and Jackson, S.A. (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
Doyle, J.6
Stacey, G.7
Jackson, S.A.8
-
27
-
-
14144255920
-
Rapid evolution of expression and regulatory divergences after yeast gene duplication
-
Gu, X., Zhang, Z., and Huang, W. (2005). Rapid evolution of expression and regulatory divergences after yeast gene duplication. Proc. Natl. Acad. Sci. USA 102: 707–712.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 707-712
-
-
Gu, X.1
Zhang, Z.2
Huang, W.3
-
28
-
-
68149144366
-
Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression
-
Hollister, J.D., and Gaut, B.S. (2009). Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res. 19: 1419–1428.
-
(2009)
Genome Res
, vol.19
, pp. 1419-1428
-
-
Hollister, J.D.1
Gaut, B.S.2
-
29
-
-
79952303685
-
Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata
-
Hollister, J.D., Smith, L.M., Guo, Y.L., Ott, F., Weigel, D., and Gaut, B.S. (2011). Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc. Natl. Acad. Sci. USA 108: 2322–2327.
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 2322-2327
-
-
Hollister, J.D.1
Smith, L.M.2
Guo, Y.L.3
Ott, F.4
Weigel, D.5
Gaut, B.S.6
-
30
-
-
0344287498
-
Non-random association of transposable elements with duplicated genomic blocks in Arabidopsis thaliana
-
Hughes, A.L., Friedman, R., Ekollu, V., and Rose, J.R. (2003). Non-random association of transposable elements with duplicated genomic blocks in Arabidopsis thaliana. Mol. Phylogenet. Evol. 29: 410–416.
-
(2003)
Mol. Phylogenet. Evol
, vol.29
, pp. 410-416
-
-
Hughes, A.L.1
Friedman, R.2
Ekollu, V.3
Rose, J.R.4
-
31
-
-
0142059819
-
A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes
-
Ilic, K., SanMiguel, P.J., and Bennetzen, J.L. (2003). A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes. Proc. Natl. Acad. Sci. USA 100: 12265–12270.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 12265-12270
-
-
Ilic, K.1
Sanmiguel, P.J.2
Bennetzen, J.L.3
-
32
-
-
75549087305
-
The evolution of gene duplications: Classifying and distinguishing between models
-
Innan, H., and Kondrashov, F. (2010). The evolution of gene duplications: classifying and distinguishing between models. Nat. Rev. Genet. 11: 97–108.
-
(2010)
Nat. Rev. Genet
, vol.11
, pp. 97-108
-
-
Innan, H.1
Kondrashov, F.2
-
33
-
-
57749105200
-
Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean
-
Innes, R.W., et al. (2008). Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean. Plant Physiol. 148: 1740–1759.
-
(2008)
Plant Physiol
, vol.148
, pp. 1740-1759
-
-
Innes, R.W.1
-
34
-
-
79955630390
-
Ancestral polyploidy in seed plants and angiosperms
-
Jiao, Y., et al. (2011). Ancestral polyploidy in seed plants and angiosperms. Nature 473: 97–100.
-
(2011)
Nature
, vol.473
, pp. 97-100
-
-
Jiao, Y.1
-
35
-
-
84891810676
-
PlantTFDB 3.0: A portal for the functional and evolutionary study of plant transcription factors
-
Jin, J., Zhang, H., Kong, L., Gao, G., and Luo, J. (2014). PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res. 42: D1182–D1187.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D1182-D1187
-
-
Jin, J.1
Zhang, H.2
Kong, L.3
Gao, G.4
Luo, J.5
-
36
-
-
84939139239
-
A comparative epigenomic analysis of polyploidy-derived genes in soybean and common bean
-
Kim, K.D., El Baidouri, M., Abernathy, B., Iwata-Otsubo, A., Chavarro, C., Gonzales, M., Libault, M., Grimwood, J., and Jackson, S.A. (2015). A comparative epigenomic analysis of polyploidy-derived genes in soybean and common bean. Plant Physiol. 168: 1433–1447.
-
(2015)
Plant Physiol
, vol.168
, pp. 1433-1447
-
-
Kim, K.D.1
El Baidouri, M.2
Abernathy, B.3
Iwata-Otsubo, A.4
Chavarro, C.5
Gonzales, M.6
Libault, M.7
Grimwood, J.8
Jackson, S.A.9
-
37
-
-
0033804889
-
Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Bras-sicaceae)
-
Koch, M.A., Haubold, B., and Mitchell-Olds, T. (2000). Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Bras-sicaceae). Mol. Biol. Evol. 17: 1483–1498.
-
(2000)
Mol. Biol. Evol
, vol.17
, pp. 1483-1498
-
-
Koch, M.A.1
Haubold, B.2
Mitchell-Olds, T.3
-
38
-
-
79957868920
-
Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications
-
Krueger, F., and Andrews, S.R. (2011). Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27: 1571–1572.
-
(2011)
Bioinformatics
, vol.27
, pp. 1571-1572
-
-
Krueger, F.1
Andrews, S.R.2
-
39
-
-
5144230950
-
Gene loss and movement in the maize genome
-
Lai, J., Ma, J., Swigonová, Z., Ramakrishna, W., Linton, E., Llaca, V., Tanyolac, B., Park, Y.J., Jeong, O.Y., Bennetzen, J.L., and Messing, J. (2004). Gene loss and movement in the maize genome. Genome Res. 14 (10A): 1924–1931.
-
(2004)
Genome Res
, vol.14
, Issue.10
, pp. 1924-1931
-
-
Lai, J.1
Ma, J.2
Swigonová, Z.3
Ramakrishna, W.4
Linton, E.5
Llaca, V.6
Tanyolac, B.7
Park, Y.J.8
Jeong, O.Y.9
Bennetzen, J.L.10
Messing, J.11
-
40
-
-
1542338594
-
Genomic duplication, fractionation and the origin of regulatory novelty
-
Langham, R.J., Walsh, J., Dunn, M., Ko, C., Goff, S.A., and Freeling, M. (2004). Genomic duplication, fractionation and the origin of regulatory novelty. Genetics 166: 935–945.
-
(2004)
Genetics
, vol.166
, pp. 935-945
-
-
Langham, R.J.1
Walsh, J.2
Dunn, M.3
Ko, C.4
Goff, S.A.5
Freeling, M.6
-
41
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10: R25.
-
(2009)
Genome Biol
, vol.10
, pp. 25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
42
-
-
25144446148
-
Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary
-
Lavin, M., Herendeen, P.S., and Wojciechowski, M.F. (2005). Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary. Syst. Biol. 54: 575–594.
-
(2005)
Syst. Biol
, vol.54
, pp. 575-594
-
-
Lavin, M.1
Herendeen, P.S.2
Wojciechowski, M.F.3
-
43
-
-
84947967022
-
RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome
-
Li, Q., et al. (2015). RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome. Proc. Natl. Acad. Sci. USA 112: 14728–14733.
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, pp. 14728-14733
-
-
Li, Q.1
-
44
-
-
84923019049
-
De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits
-
Li, Y.H., et al. (2014). De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat. Biotechnol. 32: 1045–1052.
-
(2014)
Nat. Biotechnol
, vol.32
, pp. 1045-1052
-
-
Li, Y.H.1
-
45
-
-
84904618108
-
Genome duplication and gene loss affect the evolution of heat shock transcription factor genes in legumes
-
Lin, Y., Cheng, Y., Jin, J., Jin, X., Jiang, H., Yan, H., and Cheng, B. (2014). Genome duplication and gene loss affect the evolution of heat shock transcription factor genes in legumes. PLoS One 9: e102825.
-
(2014)
Plos One
, vol.9
-
-
Lin, Y.1
Cheng, Y.2
Jin, J.3
Jin, X.4
Jiang, H.5
Yan, H.6
Cheng, B.7
-
46
-
-
13144251179
-
Plant conserved non-coding sequences and paralogue evolution
-
Lockton, S., and Gaut, B.S. (2005). Plant conserved non-coding sequences and paralogue evolution. Trends Genet. 21: 60–65.
-
(2005)
Trends Genet
, vol.21
, pp. 60-65
-
-
Lockton, S.1
Gaut, B.S.2
-
47
-
-
42749087226
-
Highly integrated single-base resolution maps of the epigenome in Arabidopsis
-
Lister, R., O’Malley, R.C., Tonti-Filippini, J., Gregory, B.D., Berry, C.C., Millar, A.H., and Ecker, J.R. (2008). Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523–536.
-
(2008)
Cell
, vol.133
, pp. 523-536
-
-
Lister, R.1
O’Malley, R.C.2
Tonti-Filippini, J.3
Gregory, B.D.4
Berry, C.C.5
Millar, A.H.6
Ecker, J.R.7
-
48
-
-
2342466982
-
Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice
-
Ma, J., Devos, K.M., and Bennetzen, J.L. (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
-
49
-
-
84876761942
-
Genomic distribution of maize facultative heterochromatin marked by trimethylation of H3K27
-
Makarevitch, I., Eichten, S.R., Briskine, R., Waters, A.J., Danilevskaya, O.N., Meeley, R.B., Myers, C.L., Vaughn, M.W., and Springer, N.M. (2013). Genomic distribution of maize facultative heterochromatin marked by trimethylation of H3K27. Plant Cell 25: 780–793.
-
(2013)
Plant Cell
, vol.25
, pp. 780-793
-
-
Makarevitch, I.1
Eichten, S.R.2
Briskine, R.3
Waters, A.J.4
Danilevskaya, O.N.5
Meeley, R.B.6
Myers, C.L.7
Vaughn, M.W.8
Springer, N.M.9
-
50
-
-
84924405848
-
Transposable elements contribute to activation of maize genes in response to abiotic stress
-
Makarevitch, I., Waters, A.J., West, P.T., Stitzer, M., Hirsch, C.N., Ross-Ibarra, J., and Springer, N.M. (2015). Transposable elements contribute to activation of maize genes in response to abiotic stress. PLoS Genet. 11: e1004915.
-
(2015)
Plos Genet
, vol.11
-
-
Makarevitch, I.1
Waters, A.J.2
West, P.T.3
Stitzer, M.4
Hirsch, C.N.5
Ross-Ibarra, J.6
Springer, N.M.7
-
51
-
-
84901041535
-
RNA-directed DNA methylation: An epigenetic pathway of increasing complexity
-
Matzke, M.A., and Mosher, R.A. (2014). RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat. Rev. Genet. 15: 394–408.
-
(2014)
Nat. Rev. Genet
, vol.15
, pp. 394-408
-
-
Matzke, M.A.1
Mosher, R.A.2
-
52
-
-
84926496186
-
RNA-directed DNA methylation: The evolution of a complex epigenetic pathway in flowering plants
-
Matzke, M.A., Kanno, T., and Matzke, A.J. (2015). RNA-directed DNA methylation: the evolution of a complex epigenetic pathway in flowering plants. Annu. Rev. Plant Biol. 66: 243–267.
-
(2015)
Annu. Rev. Plant Biol
, vol.66
, pp. 243-267
-
-
Matzke, M.A.1
Kanno, T.2
Matzke, A.J.3
-
53
-
-
0037390933
-
Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis
-
Meyers, B.C., Kozik, A., Griego, A., Kuang, H., and Michelmore, R.W. (2003). Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15: 809–834.
-
(2003)
Plant Cell
, vol.15
, pp. 809-834
-
-
Meyers, B.C.1
Kozik, A.2
Griego, A.3
Kuang, H.4
Michelmore, R.W.5
-
54
-
-
77951933487
-
Synteny mapping between common bean and soybean reveals extensive blocks of shared loci
-
McClean, P.E., Mamidi, S., McConnell, M., Chikara, S., and Lee, R. (2010). Synteny mapping between common bean and soybean reveals extensive blocks of shared loci. BMC Genomics 11: 184.
-
(2010)
BMC Genomics
, vol.11
, pp. 184
-
-
McClean, P.E.1
Mamidi, S.2
McConnell, M.3
Chikara, S.4
Lee, R.5
-
55
-
-
84903648903
-
Consequences of whole-genome triplication as revealed by comparative genomic analyses of the wild radish Raphanus raphanistrum and three other Brassicaceae species
-
Moghe, G.D., Hufnagel, D.E., Tang, H., Xiao, Y., Dworkin, I., Town, C.D., Conner, J.K., and Shiu, S.H. (2014). Consequences of whole-genome triplication as revealed by comparative genomic analyses of the wild radish Raphanus raphanistrum and three other Brassicaceae species. Plant Cell 26: 1925–1937.
-
(2014)
Plant Cell
, vol.26
, pp. 1925-1937
-
-
Moghe, G.D.1
Hufnagel, D.E.2
Tang, H.3
Xiao, Y.4
Dworkin, I.5
Town, C.D.6
Conner, J.K.7
Shiu, S.H.8
-
57
-
-
0034500239
-
Polyploid incidence and evolution
-
Otto, S.P., and Whitton, J. (2000). Polyploid incidence and evolution. Annu. Rev. Genet. 34: 401–437.
-
(2000)
Annu. Rev. Genet
, vol.34
, pp. 401-437
-
-
Otto, S.P.1
Whitton, J.2
-
58
-
-
84982899807
-
Evolution of gene duplication in plants
-
Panchy, N., Lehti-Shiu, M., and Shiu, S.H. (2016). Evolution of gene duplication in plants. Plant Physiol. 171: 2294–2316.
-
(2016)
Plant Physiol
, vol.171
, pp. 2294-2316
-
-
Panchy, N.1
Lehti-Shiu, M.2
Shiu, S.H.3
-
59
-
-
0038157152
-
Dosage sensitivity and the evolution of gene families in yeast
-
Papp, B., Pál, C., and Hurst, L.D. (2003). Dosage sensitivity and the evolution of gene families in yeast. Nature 424: 194–197.
-
(2003)
Nature
, vol.424
, pp. 194-197
-
-
Papp, B.1
Pál, C.2
Hurst, L.D.3
-
60
-
-
84871428041
-
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres
-
Paterson, A.H., et al. (2012). Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492: 423–427.
-
(2012)
Nature
, vol.492
, pp. 423-427
-
-
Paterson, A.H.1
-
61
-
-
84959444610
-
Population level purifying selection and gene expression shape subgenome evolution in maize
-
Pophaly, S.D., and Tellier, A. (2015). Population level purifying selection and gene expression shape subgenome evolution in maize. Mol. Biol. Evol. 32: 3226–3235.
-
(2015)
Mol. Biol. Evol
, vol.32
, pp. 3226-3235
-
-
Pophaly, S.D.1
Tellier, A.2
-
62
-
-
84926662881
-
Persistence of subgenomes in paleopolyploid cotton after 60 my of evolution
-
Renny-Byfield, S., Gong, L., Gallagher, J.P., and Wendel, J.F. (2015). Persistence of subgenomes in paleopolyploid cotton after 60 my of evolution. Mol. Biol. Evol. 32: 1063–1071.
-
(2015)
Mol. Biol. Evol
, vol.32
, pp. 1063-1071
-
-
Renny-Byfield, S.1
Gong, L.2
Gallagher, J.P.3
Wendel, J.F.4
-
63
-
-
85028373494
-
Gene fractionation and function in the ancient subgenomes of maize
-
Renny-Byfield, S., Rodgers-Melnick, E., and Ross-Ibarra, J. (2017). Gene fractionation and function in the ancient subgenomes of maize. Mol. Biol. Evol. 34: 1825–1832.
-
(2017)
Mol. Biol. Evol
, vol.34
, pp. 1825-1832
-
-
Renny-Byfield, S.1
Rodgers-Melnick, E.2
Ross-Ibarra, J.3
-
64
-
-
33749357831
-
Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice
-
Rizzon, C., Ponger, L., and Gaut, B.S. (2006). Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLOS Comput. Biol. 2: e115.
-
(2006)
PLOS Comput. Biol
, vol.2
-
-
Rizzon, C.1
Ponger, L.2
Gaut, B.S.3
-
65
-
-
84925428433
-
Recombination in diverse maize is stable, predictable, and associated with genetic load
-
Rodgers-Melnick, E., Bradbury, P.J., Elshire, R.J., Glaubitz, J.C., Acharya, C.B., Mitchell, S.E., Li, C., Li, Y., and Buckler, E.S. (2015). Recombination in diverse maize is stable, predictable, and associated with genetic load. Proc. Natl. Acad. Sci. USA 112: 3823– 3828.
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, pp. 3823-3828
-
-
Rodgers-Melnick, E.1
Bradbury, P.J.2
Elshire, R.J.3
Glaubitz, J.C.4
Acharya, C.B.5
Mitchell, S.E.6
Li, C.7
Li, Y.8
Buckler, E.S.9
-
66
-
-
84871965646
-
The fate of duplicated genes in a polyploid plant genome
-
Roulin, A., Auer, P.L., Libault, M., Schlueter, J., Farmer, A., May, G., Stacey, G., Doerge, R.W., and Jackson, S.A. (2013). The fate of duplicated genes in a polyploid plant genome. Plant J. 73: 143– 153.
-
(2013)
Plant J
, vol.73
, pp. 143-153
-
-
Roulin, A.1
Auer, P.L.2
Libault, M.3
Schlueter, J.4
Farmer, A.5
May, G.6
Stacey, G.7
Doerge, R.W.8
Jackson, S.A.9
-
67
-
-
0031707062
-
The paleontology of intergene retrotransposons of maize
-
SanMiguel, P., Gaut, B.S., Tikhonov, A., Nakajima, Y., and Bennetzen, J.L. (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
-
68
-
-
2442712340
-
Mining EST databases to resolve evolutionary events in major crop species
-
Schlueter, J.A., Dixon, P., Granger, C., Grant, D., Clark, L., Doyle, J.J., and Shoemaker, R.C. (2004). Mining EST databases to resolve evolutionary events in major crop species. Genome 47: 868–876.
-
(2004)
Genome
, vol.47
, pp. 868-876
-
-
Schlueter, J.A.1
Dixon, P.2
Granger, C.3
Grant, D.4
Clark, L.5
Doyle, J.J.6
Shoemaker, R.C.7
-
69
-
-
74549221016
-
Genome sequence of the palaeopolyploid soybean
-
Schmutz, J., et al. (2010). Genome sequence of the palaeopolyploid soybean. Nature 463: 178–183.
-
(2010)
Nature
, vol.463
, pp. 178-183
-
-
Schmutz, J.1
-
70
-
-
84903517143
-
A reference genome for common bean and genome-wide analysis of dual domestications
-
Schmutz, J., et al. (2014). A reference genome for common bean and genome-wide analysis of dual domestications. Nat. Genet. 46: 707–713.
-
(2014)
Nat. Genet
, vol.46
, pp. 707-713
-
-
Schmutz, J.1
-
71
-
-
79952744855
-
Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss
-
Schnable, J.C., Springer, N.M., and Freeling, M. (2011). Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc. Natl. Acad. Sci. USA 108: 4069–4074.
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 4069-4074
-
-
Schnable, J.C.1
Springer, N.M.2
Freeling, M.3
-
72
-
-
70450202132
-
The B73 maize genome: Complexity, diversity, and dynamics
-
Schnable, P.S., 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
-
73
-
-
32044442759
-
Promoter features related to tissue specificity as measured by Shannon entropy
-
Schug, J., Schuller, W.P., Kappen, C., Salbaum, J.M., Bucan, M., and Stoeckert, C.J., Jr. (2005). Promoter features related to tissue specificity as measured by Shannon entropy. Genome Biol. 6: R33.
-
(2005)
Genome Biol
, vol.6
, pp. 33
-
-
Schug, J.1
Schuller, W.P.2
Kappen, C.3
Salbaum, J.M.4
Bucan, M.5
Stoeckert, C.J.6
-
74
-
-
84869092574
-
‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes
-
Schultz, M.D., Schmitz, R.J., and Ecker, J.R. (2012). ‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes. Trends Genet. 28: 583–585.
-
(2012)
Trends Genet
, vol.28
, pp. 583-585
-
-
Schultz, M.D.1
Schmitz, R.J.2
Ecker, J.R.3
-
75
-
-
84876533257
-
Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays
-
Sekhon, R.S., Briskine, R., Hirsch, C.N., Myers, C.L., Springer, N.M., Buell, C.R., de Leon, N., and Kaeppler, S.M. (2013). Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays. PLoS One 8: e61005.
-
(2013)
Plos One
, vol.8
-
-
Sekhon, R.S.1
Briskine, R.2
Hirsch, C.N.3
Myers, C.L.4
Springer, N.M.5
Buell, C.R.6
De Leon, N.7
Kaeppler, S.M.8
-
76
-
-
36549038087
-
Consequences of genome duplication
-
Sémon, M., and Wolfe, K.H. (2007). Consequences of genome duplication. Curr. Opin. Genet. Dev. 17: 505–512.
-
(2007)
Curr. Opin. Genet. Dev
, vol.17
, pp. 505-512
-
-
Sémon, M.1
Wolfe, K.H.2
-
77
-
-
84899134141
-
Global dissection of alternative splicing in paleopolyploid soybean
-
Shen, Y., Zhou, Z., Wang, Z., Li, W., Fang, C., Wu, M., Ma, Y., Liu, T., Kong, L.A., Peng, D.L., and Tian, Z. (2014). Global dissection of alternative splicing in paleopolyploid soybean. Plant Cell 26: 996–1008.
-
(2014)
Plant Cell
, vol.26
, pp. 996-1008
-
-
Shen, Y.1
Zhou, Z.2
Wang, Z.3
Li, W.4
Fang, C.5
Wu, M.6
Ma, Y.7
Liu, T.8
Kong, L.A.9
Peng, D.L.10
Tian, Z.11
-
78
-
-
84907203918
-
The wild side of a major crop: Soybean’s perennial cousins from Down Under
-
Sherman-Broyles, S., Bombarely, A., Powell, A.F., Doyle, J.L., Egan, A.N., Coate, J.E., and Doyle, J.J. (2014). The wild side of a major crop: soybean’s perennial cousins from Down Under. Am. J. Bot. 101: 1651–1665.
-
(2014)
Am. J. Bot
, vol.101
, pp. 1651-1665
-
-
Sherman-Broyles, S.1
Bombarely, A.2
Powell, A.F.3
Doyle, J.L.4
Egan, A.N.5
Coate, J.E.6
Doyle, J.J.7
-
79
-
-
33947303168
-
Transposable elements and the epigenetic regulation of the genome
-
Slotkin, R.K., and Martienssen, R. (2007). Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 8: 272–285.
-
(2007)
Nat. Rev. Genet
, vol.8
, pp. 272-285
-
-
Slotkin, R.K.1
Martienssen, R.2
-
80
-
-
67651052323
-
The role of hybridization in plant speciation
-
Soltis, P.S., and Soltis, D.E. (2009). The role of hybridization in plant speciation. Annu. Rev. Plant Biol. 60: 561–588.
-
(2009)
Annu. Rev. Plant Biol
, vol.60
, pp. 561-588
-
-
Soltis, P.S.1
Soltis, D.E.2
-
81
-
-
84962437293
-
Ancient WGD events as drivers of key innovations in angiosperms
-
Soltis, P.S., and Soltis, D.E. (2016). Ancient WGD events as drivers of key innovations in angiosperms. Curr. Opin. Plant Biol. 30: 159–165.
-
(2016)
Curr. Opin. Plant Biol
, vol.30
, pp. 159-165
-
-
Soltis, P.S.1
Soltis, D.E.2
-
82
-
-
84949228107
-
Polyploidy and genome evolution in plants
-
Soltis, P.S., Marchant, D.B., Van de Peer, Y., and Soltis, D.E. (2015). Polyploidy and genome evolution in plants. Curr. Opin. Genet. Dev. 35: 119–125.
-
(2015)
Curr. Opin. Genet. Dev
, vol.35
, pp. 119-125
-
-
Soltis, P.S.1
Marchant, D.B.2
Van De Peer, Y.3
Soltis, D.E.4
-
83
-
-
84861062626
-
Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly
-
Takuno, S., and Gaut, B.S. (2012). Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly. Mol. Biol. Evol. 29: 219–227.
-
(2012)
Mol. Biol. Evol
, vol.29
, pp. 219-227
-
-
Takuno, S.1
Gaut, B.S.2
-
84
-
-
84873156452
-
Gene body methylation is conserved between plant orthologs and is of evolutionary consequence
-
Takuno, S., and Gaut, B.S. (2013). Gene body methylation is conserved between plant orthologs and is of evolutionary consequence. Proc. Natl. Acad. Sci. USA 110: 1797–1802.
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 1797-1802
-
-
Takuno, S.1
Gaut, B.S.2
-
85
-
-
34547781750
-
MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0
-
Tamura, K., Dudley, J., Nei, M., and Kumar, S. (2007). MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596–1599.
-
(2007)
Mol. Biol. Evol
, vol.24
, pp. 1596-1599
-
-
Tamura, K.1
Dudley, J.2
Nei, M.3
Kumar, S.4
-
86
-
-
84859564587
-
Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy
-
Tang, H., Woodhouse, M.R., Cheng, F., Schnable, J.C., Pedersen, B.S., Conant, G., Wang, X., Freeling, M., and Pires, J.C. (2012). Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics 190: 1563–1574.
-
(2012)
Genetics
, vol.190
, pp. 1563-1574
-
-
Tang, H.1
Woodhouse, M.R.2
Cheng, F.3
Schnable, J.C.4
Pedersen, B.S.5
Conant, G.6
Wang, X.7
Freeling, M.8
Pires, J.C.9
-
87
-
-
0034084963
-
The complete sequence of 340 kb of DNA around the rice Adh1-adh2 region reveals interrupted colinearity with maize chromosome 4
-
Tarchini, R., Biddle, P., Wineland, R., Tingey, S., and Rafalski, A. (2000). The complete sequence of 340 kb of DNA around the rice Adh1-adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell 12: 381–391.
-
(2000)
Plant Cell
, vol.12
, pp. 381-391
-
-
Tarchini, R.1
Biddle, P.2
Wineland, R.3
Tingey, S.4
Rafalski, A.5
-
88
-
-
79960095966
-
Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea lux-urians
-
Tenaillon, M.I., Hufford, M.B., Gaut, B.S., and Ross-Ibarra, J. (2011). Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea lux-urians. Genome Biol. Evol. 3: 219–229.
-
(2011)
Genome Biol. E
, vol.3
, pp. 219-229
-
-
Tenaillon, M.I.1
Hufford, M.B.2
Gaut, B.S.3
Ross-Ibarra, J.4
-
89
-
-
33745617700
-
Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes
-
Thomas, B.C., Pedersen, B., and Freeling, M. (2006). Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res. 16: 934–946.
-
(2006)
Genome Res
, vol.16
, pp. 934-946
-
-
Thomas, B.C.1
Pedersen, B.2
Freeling, M.3
-
90
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson, J.D., Higgins, D.G., and Gibson, T.J. (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
-
91
-
-
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, J.L., Jackson, S.A., Gaut, B.S., and Ma, J. (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
Jackson, S.A.6
Gaut, B.S.7
Ma, J.8
-
92
-
-
84871856746
-
Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean
-
Tian, Z., Zhao, M., She, M., Du, J., Cannon, S.B., Liu, X., Xu, X., Qi, X., Li, M.W., Lam, H.M., and Ma, J. (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
Liu, X.6
Xu, X.7
Qi, X.8
Li, M.W.9
Lam, H.M.10
Ma, J.11
-
93
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-Seq
-
Trapnell, C., Pachter, L., and Salzberg, S.L. (2009). TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105– 1111.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
94
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell, C., Williams, B.A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M.J., Salzberg, S.L., Wold, B.J., and Pachter, L. (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28: 511–515.
-
(2010)
Nat. Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
Van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
95
-
-
84862956715
-
Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers
-
Varshney, R.K., et al. (2011). Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat. Biotechnol. 30: 83–89.
-
(2011)
Nat. Biotechnol
, vol.30
, pp. 83-89
-
-
Varshney, R.K.1
-
96
-
-
85018972698
-
Hierarchically aligning 10 legume genomes establishes a family-level genomics platform
-
Wang, J., et al. (2017). Hierarchically aligning 10 legume genomes establishes a family-level genomics platform. Plant Physiol. 174: 284–300.
-
(2017)
Plant Physiol
, vol.174
, pp. 284-300
-
-
Wang, J.1
-
97
-
-
80053386792
-
Brassica rapa Genome Sequencing Project Consortium (2011). The genome of the mesopolyploid crop species Brassica rapa. Nat
-
Wang, X., et al.; Brassica rapa Genome Sequencing Project Consortium (2011). The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 43: 1035–1039.
-
Genet
, vol.43
, pp. 1035-1039
-
-
Wang, X.1
-
98
-
-
84860137835
-
MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity
-
Wang, Y., Tang, H., Debarry, J.D., Tan, X., Li, J., Wang, X., Lee, T.H., Jin, H., Marler, B., Guo, H., Kissinger, J.C., and Paterson, A.H. (2012). MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40: e49.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Wang, Y.1
Tang, H.2
Debarry, J.D.3
Tan, X.4
Li, J.5
Wang, X.6
Lee, T.H.7
Jin, H.8
Marler, B.9
Guo, H.10
Kissinger, J.C.11
Paterson, A.H.12
-
99
-
-
0033974956
-
Genome evolution in polyploids
-
Wendel, J.F. (2000). Genome evolution in polyploids. Plant Mol. Biol. 42: 225–249.
-
(2000)
Plant Mol. Biol
, vol.42
, pp. 225-249
-
-
Wendel, J.F.1
-
100
-
-
84947093244
-
The wondrous cycles of polyploidy in plants
-
Wendel, J.F. (2015). The wondrous cycles of polyploidy in plants. Am. J. Bot. 102: 1753–1756.
-
(2015)
Am. J. Bot
, vol.102
, pp. 1753-1756
-
-
Wendel, J.F.1
-
101
-
-
36148975768
-
Polyploidy and the evolutionary history of cotton
-
Wendel, J.F., and Cronn, R.C. (2003). Polyploidy and the evolutionary history of cotton. Adv. Agron. 78: 139–186.
-
(2003)
Adv. Agron
, vol.78
, pp. 139-186
-
-
Wendel, J.F.1
Cronn, R.C.2
-
102
-
-
79959839889
-
Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives
-
Wicker, T., et al. (2011). Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell 23: 1706–1718.
-
(2011)
Plant Cell
, vol.23
, pp. 1706-1718
-
-
Wicker, T.1
-
103
-
-
77954741256
-
Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs
-
Woodhouse, M.R., Schnable, J.C., Pedersen, B.S., Lyons, E., Lisch, D., Subramaniam, S., and Freeling, M. (2010a). Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. PLoS Biol. 8: e1000409.
-
(2010)
Plos Biol
, vol.8
-
-
Woodhouse, M.R.1
Schnable, J.C.2
Pedersen, B.S.3
Lyons, E.4
Lisch, D.5
Subramaniam, S.6
Freeling, M.7
-
104
-
-
77953179573
-
Transposed genes in Arabidopsis are often associated with flanking repeats
-
Woodhouse, M.R., Pedersen, B., and Freeling, M. (2010b). Transposed genes in Arabidopsis are often associated with flanking repeats. PLoS Genet. 6: e1000949.
-
(2010)
Plos Genet
, vol.6
-
-
Woodhouse, M.R.1
Pedersen, B.2
Freeling, M.3
-
105
-
-
84898052115
-
Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids
-
Woodhouse, M.R., Cheng, F., Pires, J.C., Lisch, D., Freeling, M., and Wang, X. (2014). Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids. Proc. Natl. Acad. Sci. USA 111: 5283–5288.
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. 5283-5288
-
-
Woodhouse, M.R.1
Cheng, F.2
Pires, J.C.3
Lisch, D.4
Freeling, M.5
Wang, X.6
-
106
-
-
33745487720
-
Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa
-
Yang, T.J., et al. (2006). Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa. Plant Cell 18: 1339–1347.
-
(2006)
Plant Cell
, vol.18
, pp. 1339-1347
-
-
Yang, T.J.1
-
107
-
-
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
-
108
-
-
84944809725
-
DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis
-
Yelina, N.E., Lambing, C., Hardcastle, T.J., Zhao, X., Santos, B., and Henderson, I.R. (2015). DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis. Genes Dev. 29: 2183–2202.
-
(2015)
Genes Dev
, vol.29
, pp. 2183-2202
-
-
Yelina, N.E.1
Lambing, C.2
Hardcastle, T.J.3
Zhao, X.4
Santos, B.5
Henderson, I.R.6
-
109
-
-
34249068213
-
Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis
-
Zhang, X., Clarenz, O., Cokus, S., Bernatavichute, Y.V., Pellegrini, M., Goodrich, J., and Jacobsen, S.E. (2007). Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol. 5: e129.
-
(2007)
Plos Biol
, vol.5
-
-
Zhang, X.1
Clarenz, O.2
Cokus, S.3
Bernatavichute, Y.V.4
Pellegrini, M.5
Goodrich, J.6
Jacobsen, S.E.7
-
110
-
-
84927709627
-
Evolutionary patterns and coevolutionary consequences of MIRNA genes and microRNA targets triggered by multiple mechanisms of genomic duplications in soybean
-
Zhao, M., Meyers, B.C., Cai, C., Xu, W., and Ma, J. (2015). Evolutionary patterns and coevolutionary consequences of MIRNA genes and microRNA targets triggered by multiple mechanisms of genomic duplications in soybean. Plant Cell 27: 546–562.
-
(2015)
Plant Cell
, vol.27
, pp. 546-562
-
-
Zhao, M.1
Meyers, B.C.2
Cai, C.3
Xu, W.4
Ma, J.5
-
111
-
-
85025667109
-
Phylogenomic synteny network analysis of MADS-Box transcription factor genes reveals lineage-specific transpositions, ancient tandem duplications, and deep positional conservation
-
Zhao, T., Holmer, R., de Bruijn, S., Angenent, G.C., van den Burg, H.A., and Schranz, M.E. (2017). Phylogenomic synteny network analysis of MADS-Box transcription factor genes reveals lineage-specific transpositions, ancient tandem duplications, and deep positional conservation. Plant Cell 29: 1278–1292.
-
(2017)
Plant Cell
, vol.29
, pp. 1278-1292
-
-
Zhao, T.1
Holmer, R.2
De Bruijn, S.3
Angenent, G.C.4
Van Den Burg, H.A.5
Schranz, M.E.6
-
112
-
-
84885292642
-
Comprehensive analyses of microRNA gene evolution in paleopolyploid soybean genome
-
Zhou, Z., Wang, Z., Li, W., Fang, C., Shen, Y., Li, C., Wu, Y., and Tian, Z. (2013). Comprehensive analyses of microRNA gene evolution in paleopolyploid soybean genome. Plant J. 76: 332–344.
-
(2013)
Plant J
, vol.76
, pp. 332-344
-
-
Zhou, Z.1
Wang, Z.2
Li, W.3
Fang, C.4
Shen, Y.5
Li, C.6
Wu, Y.7
Tian, Z.8
-
113
-
-
0028089904
-
Hypo-methylated sequences: Characterization of the duplicate soybean genome
-
Zhu, T., Schupp, J.M., Oliphant, A., and Keim, P. (1994). Hypo-methylated sequences: characterization of the duplicate soybean genome. Mol. Gen. Genet. 244: 638–645.
-
(1994)
Mol. Gen. Genet
, vol.244
, pp. 638-645
-
-
Zhu, T.1
Schupp, J.M.2
Oliphant, A.3
Keim, P.4
-
114
-
-
33845880624
-
Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
-
Zilberman, D., Gehring, M., Tran, R.K., Ballinger, T., and Henikoff, S. (2007). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 39: 61–69.
-
(2007)
Nat. Genet
, vol.39
, pp. 61-69
-
-
Zilberman, D.1
Gehring, M.2
Tran, R.K.3
Ballinger, T.4
Henikoff, S.5
|