References
Brassica at PubMed
Brassica oleracea at PubMed
Brassica at Google Scholar
Brassica oleracea at Google Scholar
Review and Important Papers:
1) Jiao, Y., N. J. WICKETT, S. AYYAMPALAYAM, A. S. CHANDERBALI, L. LANDHERR et al., 2011 Ancestral polyploidy in seed plants and angiosperms. Nature 473: 97-100.
2) Schnable, J. C., and M. FREELING, 2011 Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize. PLoS One 6: e17855.
3) Schnable, J. C., N. M. SPRINGER and M. FREELING, 2011b Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Natl Acad Sci U S A 108: 4069-4074.
4) Wang, X., et al., 2011 The genome of the mesopolyploid crop species Brassica rapa. Nat Genet.
5) Xiong, Z., R. T. Gaeta and J. C. Pires, 2011 Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus. Proc Natl Acad Sci U S A 108: 7908-7913.
6) Buggs, R. J., et al., 2010b Tissue-specific silencing of homoeologs in natural populations of the recent allopolyploid Tragopogon mirus. New Phytol 186: 175-183.
7) Buggs, R. J., et al., 2010a Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping. Mol Ecol 19 Suppl 1: 132-146.
8) Chang, P. L., et al., 2010 Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners. Genome Biol 11: R125.
9) Flagel, L. E., and J. F. Wendel, 2010 Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation. New Phytol 186: 184-193.
10) Sankoff, D., C. Zheng and Q. Zhu, 2010 The collapse of gene complement following whole genome duplication. BMC Genomics 11: 313.
11) Tang, H., J. E. Bowers, X. Wang and A. H. Paterson, 2010 Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc Natl Acad Sci U S A 107: 472-477.
12) Woodhouse, M. R., et al., 2010 Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. PLoS Biol 8: e1000409.
13) Wu, X., and X. QI, 2010 Genes encoding hub and bottleneck enzymes of the Arabidopsis metabolic network preferentially retain homeologs through whole genome duplication. BMC Evol Biol 10: 145.
14) Schrider, D. R., J. C. Costello and M. W. Hahn, 2009 All human-specific gene losses are present in the genome as pseudogenes. J Comput Biol 16: 1419-1427.
15) Van De Peer, Y., et al.,  2009 The flowering world: a tale of duplications. Trends Plant Sci 14: 680-688.
16) Leitch, A. R., and I. J. Leitch, 2008 Genomic plasticity and the diversity of polyploid plants. Science 320: 481-483.
17) LYONS, E., and M. FREELING, 2008 How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J 53: 661-673.
18) Tang, H., et al., 2008 Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res 18: 1944-1954.
19) Gaeta, R. T., et al. 2007 Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell 19: 3403-3417.
20) Al-Shehbaz, I.A. et al. 2006 Systematics and phylogeny of the Brassicaceae (Cruciferae): an overview. Plant Syst. Evol. 259, 89–120
21) Aury, J. M., et al., 2006 Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444: 171-178.
22) Bailey, C.D. et al. 2006 Toward a global phylogeny of the Brassicaceae. Mol. Biol. Evol. DOI: 10.1093/molbev/msl087
23) Beilstein, M.A. et al. 2006 Brassicaceae phylogeny and trichome evolution. Am. J. Bot. 93, 607–619
24) Cronk, Q. et al. 2006 Legume comparative genomics: progress in phylogenetics and phylogenomics. Curr. Opin. Plant Biol. 9, 99–103
25) Hansson, B. et al. 2006 Comparative gene mapping in Arabidopsis lyrata chromosomes 1 and 2 and the corresponding A. thaliana chromosome 1: recombination rates, rearrangements and centromere location. Genet. Res. 87, 75–85
26) Henry, Y. et al. 2006 History, protohistory and prehistory of the Arabidopsis thaliana chromosome complement. Trends Plant Sci.11, 267–273
27) Kawabe, A. et al. 2006 Centromere locations and associated chromosome rearrangements in Arabidopsis lyrata and A. thaliana. Genetics 173, 1613–1619
28) Lysak, M. and Lexer, C. 2006 Towards the era of comparative evolutionary genomics in Brassicaceae. Plant Syst. Evol. 259, 175–198
29) Lysak, M. et al. 2006 Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. Proc. Natl.Acad. Sci. U. S. A. 103, 5224–5229
30) Ma, X. F., and J. P. GUSTAFSON, 2006 Timing and rate of genome variation in triticale following allopolyploidization. Genome 49: 950-958.
31) Marhold, K. and Lihova, J. 2006 Polyploidy, hybridization and reticulate evolution: lessons from the Brassicaceae. Plant Systemat.Evol. 259, 143–174
32) Schranz, M.E. and Mitchell-Olds, T. 2006 Independent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae. Plant Cell 18, 1152–1165
33) THOMAS, B. C., B. PEDERSEN and M. FREELING, 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.
34) Town, C.D. et al. 2006 Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 18, 1348–1359
35) Wang, J., et al., 2006 Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172: 507-517.
36) Warwick, S.I. and Al-Shehbaz, I.A. 2006 Brassicaceae: chromosome number index and database on CD-Rom. Plant Systemat. Evol. 259, 237–248
37) 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.
38) 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
39) Ziolkowski, P.A. et al. 2006 Genome evolution in Arabidopsis/ Brassica: conservation and divergence of ancient rearranged segments and their breakpoints. Plant J. 47, 63–74
40) Bennett, M. D., and I. J. Leitch, 2005 Nuclear DNA amounts in angiosperms: progress, problems and prospects. Ann Bot 95: 45-90.
41) De Bodt, S. et al. 2005 Genome duplication and the origin of angiosperms. Trends Ecol. Evol. 20, 591–597
42) Johnston, J.S. et al. 2005 Evolution of genome size in Brassicaceae. Ann. Bot. (Lond.) 95, 229–235
43) Koch, M.A. and Kiefer, M. 2005 Genome evolution among cruciferous plants: a lecture from the comparison of the genetic maps of three diploid species – Capsella rubella, Arabidopsis lyrata subsp Petraea, and A. thaliana. Am. J. Bot. 92, 761–767
44) Lysak, M.A. et al. 2005 Chromosome triplication found across the tribe Brassiceae. Genome Res. 15, 516–525
45) Mitchell-Olds, T. et al. 2005 Crucifer evolution in the post-genomic era. In Plant Diversity and Evolution: Genotypic and Phenotypic Variation in Higher Plants (Henry, R.J., ed.), pp. 119–137, CAB International
46) Mueller, L.A. et al. 2005 The SOL Genomics Network. A comparative resource for Solanaceae biology and beyond. Plant Physiol. 138, 1310–1317
47) Parkin, I.A.P. et al. 2005 Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics 171, 765–781
48) Yogeeswaran, K. et al. 2005 Comparative genome analyses of Arabidopsis spp: inferring chromosomal rearrangement events in the evolutionary history of A. thaliana. Genome Res. 15, 505–515
49) Zhu, H. et al. 2005 Bridging model and crop legumes through comparative genomics. Plant Physiol. 137, 1189–1196
50) Boivin, K. et al. 2004 The Arabidopsis genome sequence as a tool for genome analysis in Brassicaceae. A comparison of the Arabidopsis and Capsella rubella genomes. Plant Physiol. 135, 735–744
51) Dirlewanger, E. et al. 2004 Comparative mapping and markerassisted selection in Rosaceae fruit crops. Proc. Natl. Acad. Sci. U. S. A. 101, 9891–9896
52) Jaillon, O., et al., 2004 Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431: 946-957.
53) Kellis, M., B. W. Birren and E. S. Lander, 2004 Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617-624.
54) Kuittinen, H. et al. 2004 Comparing the linkage maps of the close relatives Arabidopsis lyrata and A. thaliana. Genetics 168, 1575–1584
55) Langham, R. J., et al., 2004 Genomic duplication, fractionation and the origin of regulatory novelty. Genetics 166: 935-945.
56) Lukens, L.N. et al. 2004 Genome redundancy and plasticity within ancient and recent Brassica crop species. Biol. J. Linnean Soc. 82, 665–674
57) Muangprom, A. and Osborn, T.C. 2004 Characterization of a dwarf gene in Brassica rapa, including the identification of a candidate gene. Theor. Appl. Genet. 108, 1378–1384
58) Rana, D. et al. 2004 Conservation of the microstructure of genome segments in Brassica napus and its diploid relatives. Plant J. 40, 725–733
59) Bowers, J.E. et al. 2003 Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422, 433–438
60) Gu, Z. L., et al., 2003 Role of duplicate genes in genetic robustness against null mutations. Nature 421: 63-66.
61) Koch, M. et al. 2003 Molecular systematics, evolution, and population biology in the mustard family (Brassicaceae). Ann. Mo. Bot. Gard. 90, 151–171
62) Lukens, L. et al. 2003 Comparison of a Brassica oleracea genetic map with the genome of Arabidopsis thaliana. Genetics 164, 359–372
63) Lysak, M.A. et al. 2003 Recent progress in chromosome painting of Arabidopsis and related species. Chromosome Res. 11, 195–204
64) Parkin, I.A.P. et al. 2003 Patterns of genome duplication within the Brassica napus genome. Genome 46, 291–303
65) Rocha, E. P., 2003 An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction. Genome Res 13: 1123-1132.
66) Devos, K. M., J. K. BROWN and J. L. BENNETZEN, 2002 Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12: 1075-1079.
67) Feuillet, C. and Keller, B. 2002 Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Ann. Bot. (Lond.) 89, 3–10
68) Gaut, B.S. 2002 Evolutionary dynamics of grass genomes. New Phytol. 154, 15–28
69) Hall, A.E. et al. 2002 Beyond the Arabidopsis genome: opportunities for comparative genomics. Plant Physiol. 129, 1439–1447
70) Hall, J.C. et al. 2002 Phylogeny of Capparaceae and Brassicaceae based on chloroplast sequence data. Am. J. Bot. 89, 1826–1842
71) Howell, E.C. et al. 2002 Integration of the cytogenetic and genetic linkage maps of Brassica oleracea. Genetics 161, 1225–1234
72) Schranz, M.E. et al. 2002 Characterization and effects of the replicated flowering time gene FLC in Brassica rapa. Genetics 162, 1457–1468
73) Simillion, C. et al. 2002 The hidden duplication past of Arabidopsis thaliana. Proc. Natl. Acad. Sci. U. S. A. 99, 13627–13632
74) Blanc, G. et al. 2000 Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12, 1093–1101
75) Devos, K.M. and Gale, M.D. 2000 Genome relationships: the grass model in current research. Plant Cell 12, 637–646
76) Lan, T.H. et al. 2000 An EST-enriched comparative map of Brassica oleracea and Arabidopsis thaliana. Genome Res. 10, 776–788
77) Vision, T.J. et al. 2000 The origins of genomic duplications in Arabidopsis. Science 290, 2114–2117
78) Force, A., et al., 1999 Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
79) Lagercrantz, U. 1998 Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Genetics 150, 1217–1228
80) Devos, K.M. and Gale, M.D. 1997 Comparative genetics in the grasses. Plant Mol. Biol. 35, 3–15
81) Osborn, T.C. et al. 1997 Comparison of flowering time genes in Brassica rapa, B. napus and Arabidopsis thaliana. Genetics 146, 1123–1129
82) Lagercrantz, U., and D. J. LYDIATE, 1996 Comparative genome mapping in Brassica. Genetics 144: 1903-1910.
83) Truco, M.J. et al. 1996 Inter- and intra-genomic homology of the Brassica genomes: Iimplications for their origin and evolution. Theor. Appl. Genet. 93, 1225–1233
@2012 Department of Genomics and Molecular Biology, Oil Crops Research Institute.


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