Abstract
The Brassica napus is a truly great genome for the study of genome and gene family evolution, with a rich history of past whole-genome duplication (WGD) events. The genome has undergone a total of 5 rounds of duplications since the common ancestor with the basal angiosperm Amborella. This level of genetic redundancy is unparalleled by any other flowering plant genome that was sequenced prior to the release of the B. napus genome assembly. Three recent WGDs that occurred within the lineage of Brassicaceae are of significant value to polyploid research, namely the ‘alpha’ duplication event, the Brassica triplication and B. napus allotetraploidization. These events occurred at different evolutionary times and are representatives of paleo-polyploidy, meso-polyploidy, and neo-polyploidy, respectively. Studies of evolutionary changes and transcriptional regulation of duplicate genes derived from these WGD events have led to groundbreaking discoveries in the dynamics of polyploid genomes, including genome reorganization, gene fractionation (loss of duplicated genes), and genome dominance. These breakthroughs were largely facilitated by a number of innovations in computational methods, databases, and interconnected cyberinfrastructure that are devoted to plant comparative genomics research. With its genome now fully deciphered, B. napus continues to be one of the most important model organisms in post-polyploidy genome evolution research.
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References
Bekaert M, Edger PP, Pires JC, Conant GC (2011) Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative and absolute dosage constraints. Plant Cell 23:1719–1728
Blanc G, Wolfe KH (2004) Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16:1679–1691
Bowers JE, Chapman BA, Rong J, Paterson AH (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422:433–438
Chalhoub B et al (2014) Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345:950–953
Chen ZJ (2010) Molecular mechanisms of polyploidy and hybrid vigor. Trends Plant Sci 15:57–71
Force A et al (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531–1545
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
Goodstein DM et al (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40:D1178–D1186
Jaillon O et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–467
Kagale S et al (2014) The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure. Nat Commun 5:3706
Langham RJ et al (2004) Genomic duplication, fractionation and the origin of regulatory novelty. Genetics 166:935–945
Lee TH, Tang H, Wang X, Paterson AH (2013) PGDD: a database of gene and genome duplication in plants. Nucleic Acids Res 41:D1152–D1158
Liu S et al (2014) The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat Commun 5:3930
Lyons E, Freeling M (2008) How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J 53:661–673
Lyons E, Pedersen B, Kane J, Freeling M (2008) The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates the rosids. Trop Plant Biol 1:181–190
Lysak MA, Cheung K, Kitschke M, Bures P (2007) Ancestral chromosomal blocks are triplicated in Brassiceae species with varying chromosome number and genome size. Plant Physiol 145:402–410
Magallon S, Gomez-Acevedo S, Sanchez-Reyes LL, Hernandez-Hernandez T (2015) A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity. New Phytol 207:437–453
Moghe GD et al (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
Parkin IA, Sharpe AG, Lydiate DJ (2003) Patterns of genome duplication within the Brassica napus genome. Genome 46:291–303
Parkin IA et al (2005) Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics 171:765–781
Parkin IA et al (2014) Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol 15:R77
Proost S et al (2015) PLAZA 3.0: an access point for plant comparative genomics. Nucleic Acids Res 43:D974–D981
Schnable JC, Springer NM, Freeling M (2011) 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
Tang H et al (2008) Synteny and collinearity in plant genomes. Science 320:486–488
Tang H, Bowers JE, Wang X, Paterson AH (2010) Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc Natl Acad Sci U S A 107:472–477
Tang H et al (2011) Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinf 12:102
Tang H et al (2012) Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics 190:1563–1574
The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641
Thomas BC, Pedersen B, 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
Wang X et al (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet
Wolfe KH (2001) Yesterday’s polyploids and the mystery of diploidization. Nat Rev Genet 2:333–341
Woodhouse MR et al (2010) Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. PLoS Biol 8:e1000409
Woodhouse MR et al (2014) Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids. Proc Natl Acad Sci USA 111:5283–5288
Yoo MJ, Liu X, Pires JC, Soltis PS, Soltis DE (2014) Nonadditive gene expression in polyploids. Annu Rev Genet 48:485–517
Acknowledgements
We thank the Fujian provincial government for a Fujian ‘100 Talent Plan’ award to HT. EL is supported by USDA 2013-00984; NSF IOS—1339156; IOS—444490.
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The authors declare that they have no competing interests.
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Tang, H., Zhang, X., Tong, C., Chalhoub, B., Liu, S., Lyons, E. (2018). From Alpha-Duplication to Triplication and Sextuplication. In: Liu, S., Snowdon, R., Chalhoub, B. (eds) The Brassica napus Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-43694-4_5
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