Drivers and dynamics of diversity in plant genomes

New Phytologist

Volumn 202, Issue 1, 2014, Pages 15-18

  Panaud, Olivier ^a   Jackson, Scott A ^b   Wendel, Jonathan F ^c  

^a UNIVERSITÉ DE PERPIGNAN   (France)

^b UNIVERSITY OF GEORGIA   (United States)

^c IOWA STATE UNIVERSITY   (United States)

Author keywords

Evolution; Genome duplication; Genome evolution; Plant genome dynamics; Polyploidy; Transposable elements

Indexed keywords

ARTICLE; EVOLUTION; GENETIC VARIABILITY; GENETICS; GENOME DUPLICATION; GENOME EVOLUTION; MOLECULAR EVOLUTION; PLANT GENOME; PLANT GENOME DYNAMICS; POLYPLOIDY; POPULATION DYNAMICS; SPECIES DIFFERENCE; TRANSPOSABLE ELEMENTS; TRANSPOSON;

EVOLUTION; GENOME DUPLICATION; GENOME EVOLUTION; PLANT GENOME DYNAMICS; POLYPLOIDY; TRANSPOSABLE ELEMENTS;

DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME, PLANT; POLYPLOIDY; POPULATION DYNAMICS; SPECIES SPECIFICITY;

EID: 84894433040     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/nph.12633     Document Type: Article

References (23)

1. Ainouche M, Chelaifa H, Ferreira de Carvalho J, Bellot S, Ainouche A, Salmon A. 2012. Polyploid evolution in Spartina: dealing with highly redundant hybrid genomes. In: Soltis PS, Soltis DE, eds. Polyploidy and genome evolution. New York, NY, USA: Springer, 225-244.
2. Bucher E, Reinders J, Mirouze M. 2012. Epigenetic control of transposon transcription and mobility in Arabidopsis. Current Opinion in Plant Biology 15: 503-510.
3. Buggs RJ, Renny-Byfield S, Chester M, Jordon-Thaden IE, Viccini LF, Chamala S, Leitch AR, Schnable PS, Barbazuk WB, Soltis PS et al. 2012. Next-generation sequencing and genome evolution in allopolyploids. American Journal of Botany 99: 372-382.
4. Cheng S, van den Bergh E, Zeng P, Zhong X, Xu J, Liu X, Hofberger J, de Bruijn S, Bhide AS, Kuelahoglu C et al. 2013. The Tarenaya hassleriana genome provides insight into reproductive trait and genome evolution of crucifers. Plant Cell 25: 2813-2830.
5. Chester M, Gallagher JP, Symonds VV, Cruz da Silva AV, Mavrodiev EV, Leitch AR, Soltis PS, Soltis DE. 2012. Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae). Proceedings of the National Academy of Sciences, USA 109: 1176-1181.
6. Chester M, Lipman MJ, Gallagher JP, Soltis PS, Soltis DE. 2013. An assessment of karyotype restructuring in the neoallotetraploid Tragopogon miscellus (Asteraceae). Chromosome Research 21: 75-85.
7. Choulet F, Wicker T, Rustenholz C, Paux E, Salse J, Leroy P, Schlub S, Le Paslier MC, Magdelenat G, Gonthier C et al. 2010. Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell 22: 1686-1701.
8. Ferreira de Carvalho J, Poulain J, Da Silva C, Wincker P, Michon-Coudouel S, Dheilly A, Naquin D, Boutte J, Salmon A, Ainouche M. 2013. Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae). Heredity 110: 181-193.
9. Flowers JM, Molina J, Rubinstein S, Huang P, Schaal BA, Purugganan MD. 2012. Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice. Molecular Biology and Evolution 29: 675-687.
10. Jiao Y, Leebens-Mack J, Ayyampalayam S, Bowers JE, McKain MR, McNeal J, Rolf M, Ruzicka DR, Wafula E, Wickett NJ et al. 2012. A genome triplication associated with early diversification of the core eudicots. Genome Biology 13: R3.
11. Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS et al. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature 473: 97-100.
12. Kellogg EA, Bennetzen JL. 2004. The evolution of nuclear genome structure in seed plants. American Journal of Botany 91: 1709-1725.
13. Lipman MJ, Chester M, Soltis PS, Soltis DE. 2013. Natural hybrids between Tragopogon mirus and T. miscellus (Asteraceae): a new perspective on karyotypic changes following hybridization at the polyploid level. American Journal of Botany 100: 2016-2022.
14. McKain MR, Wickett N, Zhang Y, Ayyampalayam S, McCombie WR, Chase MW, Pires JC, dePamphilis CW, Leebens-Mack J. 2012. Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae). American Journal of Botany 99: 397-406.
15. Quraishi UM, Abrouk M, Murat F, Pont C, Foucrier S, Desmaizieres G, Confolent C, Riviere N, Charmet G, Paux E et al. 2011a. Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution. Plant Journal 65: 745-756.
16. Quraishi UM, Murat F, Abrouk M, Pont C, Confolent C, Oury FX, Ward J, Boros D, Gebruers K, Delcour JA et al. 2011b. Combined meta-genomics analyses unravel candidate genes for the grain dietary fiber content in bread wheat (Triticum aestivum L.). Functional & Integrative Genomics 11: 71-83.
17. Reagon M, Thurber CS, Gross BL, Olsen KM, Jia Y, Caicedo AL. 2010. Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice. BMC Evolutionary Biology 10: 180.
18. Sarilar V, Palacios PM, Rousselet A, Ridel C, Falque M, Eber F, Chevre AM, Joets J, Brabant P, Alix K. 2013. Allopolyploidy has a moderate impact on restructuring at three contrasting transposable element insertion sites in resynthesized Brassica napus allotetraploids. New Phytologist 198: 593-604.
19. Schranz ME, Mohammadin S, Edger PP. 2012. Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model. Current Opinion in Plant Biology 15: 147-153.
20. Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng C, Sankoff D, Depamphilis CW, Wall PK, Soltis PS. 2009. Polyploidy and angiosperm diversification. American Journal of Botany 96: 336-348.
21. Thurber CS, Jia MH, Jia Y, Caicedo AL. 2013. Similar traits, different genes? Examining convergent evolution in related weedy rice populations. Molecular Ecology 22: 685-698.
22. Victoria Fde C, Bervald CM, da Maia LC, de Sousa RO, Panaud O, de Oliveira AC. 2012. Phylogenetic relationships and selective pressure on gene families related to iron homeostasis in land plants. Genome 55: 883-900.
23. Xiao H, Jiang N, Schaffner E, Stockinger EJ, van der Knaap E. 2008. A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319: 1527-1530.