Abstract
Plant genomes contain many duplicated genes, some of which were produced by recursive polyploidizations. These duplicated genes may evolve interactively and even concertedly through homoeologous recombination. Here, we explored likely gene conversion in Brassica rapa and Brassica oleracea. By checking gene colinearity, we detected 4296 duplicated genes existing in both the species, which were produced by whole-genome triplication from their common ancestor. Incongruities of homologous gene tree topologies indicated that 8 % of these duplicated genes were converted by one another after the divergence of B. rapa and B. oleracea. These converted genes are more often from larger duplicated chromosomal blocks, indicating that illegitimate recombination is more likely to occur between larger homoeologous chromosomal regions. This research contributed to understanding genome stability and gene evolution after polyploidization.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abrouk M, Murat F, Pont C, Messing J, Jackson S et al (2010) Palaeogenomics of plants: synteny-based modelling of extinct ancestors. Trends Plant Sci 15:479–487
Bowers JE, Chapman BA, Rong J, Paterson AH (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422:433–438
Bowers JE, Arias MA, Asher R, Avise JA, Ball RT, et al (2005) Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses. Proc Natl Acad Sci USA 102:13206–13211
Chen JM, Cooper DN, Chuzhanova N, Ferec C, Patrinos GP (2007) Gene conversion: mechanisms, evolution and human disease. Nat Rev Genet 8:762–775
Feldman M, Levy AA, Fahima T, Korol A (2012) Genomic asymmetry in allopolyploid plants: wheat as a model. J Exp Bot 63:5045–5059
Freeling M, Woodhouse MR, Subramaniam S, Turco G, Lisch D, Schnable JC (2012) Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants. Curr Opin Plant Biol 15:131–139
Gaeta RT, Chris Pires J (2009) Homoeologous recombination in allopolyploids: the polyploid ratchet. New Phytol 186:18–28
Gaeta RT, Pires JC, Iniguez-Luy F, Leon E, Osborn TC (2007) Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell 19:3403–3417
Jacquemin J, Laudie M, Cooke R (2009) A recent duplication revisited: phylogenetic analysis reveals an ancestral duplication highly-conserved throughout the Oryza genus and beyond. BMC Plant Biol 9:146
Jaillon O, Aury JM, Noel B, Policriti A, Clepet C et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–467
Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, et al (2011) Ancestral polyploidy in seed plants and angiosperms. Nature 473:97–100
Jiao Y, Leebens-Mack J, Ayyampalayam S, Bowers JE, McKain MR et al (2012) A genome triplication associated with early diversification of the core eudicots. Genome Biol 13:R3
Liu S, Liu Y, Yang X, Tong C, Edwards D, et al (2014) The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat Commun 5:3930
Marfil CF, Masuelli RW, Davison J, Comai L (2006) Genomic instability in Solanum tuberosum × Solanum kurtzianum interspecific hybrids. Genome 49:104–113
Mazowita M, Haque L, Sankoff D (2006) Stability of rearrangement measures in the comparison of genome sequences. J Comput Biol 13:554–566
McClintock B (1984) The significance of responses of the genome to challenge. Science 226:792–801
Murat F, Xu JH, Tannier E, Abrouk M, Guilhot N et al (2010) Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res 20:1545–1557
Paterson AH (2008) Paleopolyploidy and its impact on the structure and function of modern plant genomes. Genome Dyn 4:1–12
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
Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, et al (2012) Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492:423–427
Proost S, Pattyn P, Gerats T, Van de Peer Y (2011) Journey through the past: 150 million years of plant genome evolution. Plant J 66:58–65
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 USA 108:4069–4074
Soltis PS, Soltis DE (2009) The role of hybridization in plant speciation. Annu Rev Plant Biol 60:561–588
Soltis DE, Bell CD, Kim S, Soltis PS (2008) Origin and early evolution of angiosperms. Ann N Y Acad Sci 1133:3–25
Tang H, Bowers JE, Wang X, Paterson AH (2010) Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc Natl Acad Sci USA 107:472–477
Wang XY, Paterson AH (2011) Gene conversion in angiosperm genomes with an emphasis on genes duplicated by polyploidization. Genes (Basel) 2:1–20
Wang X, Shi X, Hao B, Ge S, Luo J (2005) Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol 165:937–946
Wang X, Tang H, Bowers JE, Feltus FA, Paterson AH (2007) Extensive concerted evolution of rice paralogs and the road to regaining independence. Genetics 177:1753–1763
Wang X, Tang H, Bowers JE, Paterson AH (2009) Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization. Genome Res 19:1026–1032
Wang X, Tang H, Paterson AH (2011a) Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel, in major Poaceae lineages. Plant Cell 23:27–37
Wang X, Wang H, Wang J, Sun R, Wu J et al (2011b) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039
Wang XY, Tang HB, Paterson AH (2011c) Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel, in major poaceae lineages. Plant Cell 23:27–37
Xu S, Clark T, Zheng H, Vang S, Li R et al (2008) Gene conversion in the rice genome. BMC Genom 9:93
Yang S, Yuan Y, Wang L, Li J, Wang W, et al (2012) Great majority of recombination events in Arabidopsis are gene conversion events. Proc Natl Acad Sci USA 109:20992–20997
Zhu Q, Zheng X, Luo J, Gaut BS, Ge S (2007) Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol 24:875–888
Ziolkowski PA, Kaczmarek M, Babula D, Sadowski J (2006) Genome evolution in Arabidopsis/Brassica: conservation and divergence of ancient rearranged segments and their breakpoints. Plant J 47:63–74
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Wang, J., Guo, H., Jin, D., Wang, X., Paterson, A.H. (2015). Comparative Analysis of Gene Conversion Between Duplicated Regions in Brassica rapa and B. oleracea Genomes. In: Wang, X., Kole, C. (eds) The Brassica rapa Genome. Compendium of Plant Genomes. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-47901-8_11
Download citation
DOI: https://doi.org/10.1007/978-3-662-47901-8_11
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-662-47900-1
Online ISBN: 978-3-662-47901-8
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)