The C-value paradox remains incompletely resolved after >40 yr and is exemplified by 2,350-fold variation in genome sizes of flowering plants. The carnivorous Lentibulariaceae genus Genlisea, displaying a 25-fold range of genome sizes, is a promising subject to study mechanisms and consequences of evolutionary genome size variation. Applying genomic, phylogenetic, and cytogenetic approaches, we uncovered bidirectional genome size evolution within the genus Genlisea. The Genlisea nigrocaulis Steyerm. genome (86 Mbp) has probably shrunk by retroelement silencing and deletion-biased double-strand break (DSB) repair, from an ancestral size of 400 to 800 Mbp to become one of the smallest among flowering plants. The G. hispidula Stapf genome has expanded by whole-genome duplication (WGD) and retrotransposition to 1550 Mbp. Genlisea hispidula became allotetraploid after the split from the G. nigrocaulis clade ∼29 Ma. Genlisea pygmaea A. St.-Hil. (179 Mbp), a close relative of G. nigrocaulis, proved to be a recent (auto)tetraploid. Our analyses suggest a common ancestor of the genus Genlisea with an intermediate 1C value (400-800 Mbp) and subsequent rapid genome size evolution in opposite directions. Many abundant repeats of the larger genome are absent in the smaller, casting doubt on their functionality for the organism, while recurrent WGD seems to safeguard against the loss of essential elements in the face of genome shrinkage. We cannot identify any consistent differences in habitat or life strategy that correlate with genome size changes, raising the possibility that these changes may be selectively neutral.

Biology Centre of the Academy of Sciences of the Czech Republic Institute of Plant Molecular Biology 370 05 Cˇeske Budejovicé Czech Republic

Faculty of Science and Central European Institute of Technology Masaryk Univ 61137 Brno Czech Republic

German Centre for Integrative Biodiversity Research Halle Jena Leipzig 04103 Leipzig Germany

Institute for Biodiversity and Ecosystem Research 2 Yurii Gagarin Street Sofia 1113 Bulgaria

Leibniz Institute of Plant Genetics and Crop Plant Research Corrensstrasse 3 06466 Gatersleben Germany

Max Planck Institute for Plant Breeding Research Carl von Linné Weg 10 50829 Köln Germany

MRC Lab of Molecular Biology Francis Crick Ave Cambridge Biomedical Campus Cambridge CB2 0QH UK

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Baucom, R.S., Estill, J.C., Chaparro, C., Upshaw, N., Jogi, A., Deragon, J.M., Westerman, R.P., Sanmiguel, P.J., Bennetzen, J.L.. 2009a. Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome. PLoS Genet. 5:e1000732. doi: 10.1371/journal.pgen.1000732

Baucom, R.S., Estill, J.C., Leebens-Mack, J., Bennetzen, J.L.. 2009b. Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Res. 19:243-254. doi: 10.1101/gr.083360.108http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000263132600008&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Bennett, M.D., Leitch, I.J., Price, H.J., Johnston, J.S.. 2003. Comparisons with Caenorhabditis (approximately 100 Mb) and Drosophila (approximately 175 Mb) using flow cytometry show genome size in Arabidopsis to be approximately 157 Mb and thus approximately 25% larger than the Arabidopsis genome initiative estimate of approximately 125 Mb. Ann. Bot. (Lond.) 91:547-557. doi: 10.1093/aob/mcg057

Bennetzen, J.L., Wang, H.. 2014. The contributions of transposable elements to the structure, function, and evolution of plant genomes. Annu. Rev. Plant Biol. 65:505-530. doi: 10.1146/annurev-arplant-050213-035811http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000340193000019&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Boetzer, M., Henkel, C.V., Jansen, H.J., Butler, D., Pirovano, W.. 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27:578-579. doi: 10.1093/bioinformatics/btq683http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000287246000019&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Conesa, A., Gotz, S.. 2008. Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int. J. Plant Genomics 2008:619832. doi: 10.1155/2008/619832

Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T., McVean, G., Durbin, R.. 2011. The variant call format and VCFtools. Bioinformatics 27:2156-2158. doi: 10.1093/bioinformatics/btr330http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000292778700023&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

De Storme, N., Geelen, D.. 2013. Sexual polyploidization in plants-cytological mechanisms and molecular regulation. New Phytol. 198:670-684. doi: 10.1111/nph.12184http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000317682900008&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Devos, K.M., Brown, J.K.M., Bennetzen, J.L.. 2002. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12:1075-1079. doi: 10.1101/gr.132102

Dolezel, J., Greilhuber, J., Suda, J.. 2007. Estimation of nuclear DNA content in plants using flow cytometry. Nat. Protoc. 2:2233-2244. doi: 10.1038/nprot.2007.310http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000253139600022&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Edgar, R.C. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797. doi: 10.1093/nar/gkh340

Fedoroff, N.V. 2012. Presidential address. Transposable elements, epigenetics, and genome evolution. Science 338:758-767. doi: 10.1126/science.338.6108.758http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000310839500034&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Fleischmann, A. 2012. Monograph of the genus Genlisea. Redfern Natural History Productions, Dorset, England.

Fleischmann, A., Michael, T.P., Rivadavia, F., Sousa, A., Wang, W., Temsch, E.M., Greilhuber, J., Muller, K.F., Heubl, G.. 2014. Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms. Ann. Bot. (Lond.) 114:1651-1663. doi: 10.1093/aob/mcu189http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000345825300007&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Fleischmann, A., Schaferhoff, B., Heubl, G., Rivadavia, F., Barthlott, W., Muller, K.F.. 2010. Phylogenetics and character evolution in the carnivorous plant genus Genlisea A. St.-Hil. (Lentibulariaceae). Mol. Phylogenet. Evol. 56:768-783. doi: 10.1016/j.ympev.2010.03.009http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000278890100026&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Galbraith, D.W., Harkins, K.R., Maddox, J.M., Ayres, N.M., Sharma, D.P., Firoozabady, E.. 1983. Rapid flow cytometric analysis of the cell cycle in intact plant tissues. Science 220:1049-1051. doi: 10.1126/science.220.4601.1049

Gregory, T.R. 2001. Coincidence, coevolution, or causation? DNA content, cellsize, and the C-value enigma. Biol. Rev. Camb. Philos. Soc. 76:65-101. doi: 10.1017/S1464793100005595

Greilhuber, J., Borsch, T., Müller, K., Worberg, A., Porembski, S., Barthlott, W.. 2006. Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size. Plant Biol. (Stuttg.) 8:770-777. doi: 10.1055/s-2006-924101

Gurushidze, M., Fuchs, J., Blattner, F.R.. 2012. The evolution of genome size variation in drumstick onions (Allium subgenus Melanocrommyum). Syst. Bot. 37:96-104. doi: 10.1600/036364412X616675http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000299799300013&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Hawkins, J.S., Kim, H., Nason, J.D., Wing, R.A., Wendel, J.F.. 2006. Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res. 16:1252-1261. doi: 10.1101/gr.5282906http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000240959800009&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Hegarty, M.J., Hiscock, J.S.. 2008. Genomic clues to the evolutionary success of polyploid plants. Curr. Biol. 18:R435-R444. doi: 10.1016/j.cub.2008.03.043http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000256047600020&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Hosouchi, T., Kumekawa, N., Tsuruoka, H., Kotani, H.. 2002. Physical map-based sizes of the centromeric regions of Arabidopsis thaliana chromosomes 1, 2, and 3. DNA Res. 9:117-121. doi: 10.1093/dnares/9.4.117

Houben, A., Demidov, D., Gernand, D., Meister, A., Leach, C.R., Schubert, I.. 2003. Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content. Plant J. 33:967-973. doi: 10.1046/j.1365-313X.2003.01681.x

Hu, T.T., Pattyn, P., Bakker, E.G., Cao, J., Cheng, J.F., Clark, R.M., Fahlgren, N., Fawcett, J.A., Grimwood, J., Gundlach, H., Haberer, G., Hollister, J.D., Ossowski, S., Ottilar, R.P., Salamov, A.A., Schneeberger, K., Spannagl, M., Wang, X., Yang, L., Nasrallah, M.E., Bergelson, J., Carrington, J.C., Gaut, B.S., Schmutz, J., Mayer, K.F., Van de Peer, Y., Grigoriev, I.V., Nordborg, M., Weigel, D., Guo, Y.L.. 2011. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 43:476-481. doi: 10.1038/ng.807http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000289972600020&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Hughes, A.L., Hughes, M.K.. 1995. Small genomes for better flyers. Nature 377:391. doi: 10.1038/377391a0

Ibarra-Laclette, E., Lyons, E., Hernandez-Guzman, G., Perez-Torres, C.A., Carretero-Paulet, L., Chang, T.H., Lan, T., Welch, A.J., Juarez, M.J., Simpson, J., Fernandez-Cortes, A., Arteaga-Vazquez, M., Gongora-Castillo, E., Acevedo-Hernandez, G., Schuster, S.C., Himmelbauer, H., Minoche, A.E., Xu, S., Lynch, M., Oropeza-Aburto, A., Cervantes-Perez, S.A., de Jesus Ortega-Estrada, M., Cervantes-Luevano, J.I., Michael, T.P., Mockler, T., Bryant, D., Herrera-Estrella, A., Albert, V.A., Herrera-Estrella, L.. 2013. Architecture and evolution of a minute plant genome. Nature 498:94-98. doi: 10.1038/nature12132http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000319947800040&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Kersey, P.J., Staines, D.M., Lawson, D., Kulesha, E., Derwent, P., Humphrey, J.C., Hughes, D.S., Keenan, S., Kerhornou, A., Koscielny, G., Langridge, N., McDowall, M.D., Megy, K., Maheswari, U., Nuhn, M., Paulini, M., Pedro, H., Toneva, I., Wilson, D., Yates, A., Birney, E.. 2012. Ensembl genomes: An integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res. 40:D91-D97. doi: 10.1093/nar/gkr895http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000298601300015&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Kirik, A., Salomon, S., Puchta, H.. 2000. Species-specific double-strand break repair and genome evolution in plants. EMBO J. 19:5562-5566. doi: 10.1093/emboj/19.20.5562

Kurtz, S., Narechania, A., Stein, J.C., Ware, D.. 2008. A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics 9:517. doi: 10.1186/1471-2164-9-517

Langmead, B., Salzberg, S.L.. 2012. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9:357-359. doi: 10.1038/nmeth.1923http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000302218500017&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Leitch, I.J., Hanson, L., Lim, K.Y., Kovarik, A., Chase, M.W., Clarkson, J.J., Leitch, A.R.. 2008. The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae). Ann. Bot. (Lond.) 101:805-814. doi: 10.1093/aob/mcm326http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000255150300007&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Leushkin, E.V., Sutormin, R.A., Nabieva, E.R., Penin, A.A., Kondrashov, A.S., Logacheva, M.D.. 2013. The miniature genome of a carnivorous plant Genlisea aurea contains a low number of genes and short non-coding sequences. BMC Genomics 14:476. doi: 10.1186/1471-2164-14-476

Li, J., Tang, H., Bowers, J.E., Ming, R., Paterson, A.H.. 2014. Insights into the common ancestor of eudicots. In: Paterson, A.H., editor, Advances in botanical research: Genomes of herbaceous land plants. Vol. 69. Academic Press, London. p. 137-174.10.1016/B978-0-12-417163-3.00006-8http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000333377100006&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Li, L., Stoeckert, C.J.Jr., Roos, D.S.. 2003. OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res. 13:2178-2189. doi: 10.1101/gr.1224503

Lu, F., Lipka, A.E., Glaubitz, J., Elshire, R., Cherney, J.H., Casler, M.D., Buckler, E.S., Costich, D.E.. 2013. Switchgrass genomic diversity, ploidy, and evolution: Novel insights from a network-based SNP discovery protocol. PLoS Genet. 9:e1003215. doi: 10.1371/journal.pgen.1003215

Lysak, M.A., Berr, A., Pecinka, A., Schmidt, R., McBreen, K., Schubert, I.. 2006a. Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. Proc. Natl. Acad. Sci. USA 103:5224-5229. doi: 10.1073/pnas.0510791103http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000236472500077&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Lysak, M., Fransz, P., Schubert, I.. 2006b. Cytogenetic analyses of Arabidopsis. Methods Mol. Biol. 323:173-186.

Mandakova, T., Joly, S., Krzywinski, M., Mummenhoff, K., Lysak, M.A.. 2010. Fast diploidization in close mesopolyploid relatives of Arabidopsis. Plant Cell 22:2277-2290. doi: 10.1105/tpc.110.074526http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000282432700015&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Nam, K., Ellegren, H.. 2012. Recombination drives vertebrate genome contraction. PLoS Genet. 8:e1002680. doi: 10.1371/journal.pgen.1002680

Neafsey, D.E., Palumbi, S.R.. 2003. Genome size evolution in pufferfish: A comparative analysis of diodontid and tetraodontid pufferfish genomes. Genome Res. 13:821-830. doi: 10.1101/gr.841703

Novak, P., Neumann, P., Macas, J.. 2010. Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics 11:378. doi: 10.1186/1471-2105-11-378

Novak, P., Neumann, P., Pech, J., Steinhaisl, J., Macas, J.. 2013. RepeatExplorer: A Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics 29:792-793. doi: 10.1093/bioinformatics/btt054http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000316270400017&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Ohri, D., Pistrick, K.. 2001. Phenology and genome size variation in Allium L.: A tight correlation? Plant Biol. (Stuttg.) 3:654-660. doi: 10.1055/s-2001-19362

Palazzo, A.F., Gregory, T.R.. 2014. The case for junk DNA. PLoS Genet. 10:e1004351. doi: 10.1371/journal.pgen.1004351

Parra, G., Bradnam, K., Korf, I.. 2007. CEGMA: A pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:1061-1067. doi: 10.1093/bioinformatics/btm071http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000246773300003&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Paterson, A.H., Wendel, J.F., Gundlach, H., Guo, H., Jenkins, J., Jin, D., Llewellyn, D., Showmaker, K.C., Shu, S., Udall, J., Yoo, M.J., Byers, R., Chen, W., Doron-Faigenboim, A., Duke, M.V., Gong, L., Grimwood, J., Grover, C., Grupp, K., Hu, G., Lee, T.H., Li, J., Lin, L., Liu, T., Marler, B.S., Page, J.T., Roberts, A.W., Romanel, E., Sanders, W.S., Szadkowski, E., Tan, X., Tang, H., Xu, C., Wang, J., Wang, Z., Zhang, D., Zhang, L., Ashrafi, H., Bedon, F., Bowers, J.E., Brubaker, C.L., Chee, P.W., Das, S., Gingle, A.R., Haigler, C.H., Harker, D., Hoffmann, L.V., Hovav, R., Jones, D.C., Lemke, C., Mansoor, S., ur Rahman, M., Rainville, L.N., Rambani, A., Reddy, U.K., Rong, J.K., Saranga, Y., Scheffler, B.E., Scheffler, J.A., Stelly, D.M., Triplett, B.A., Van Deynze, A., Vaslin, M.F., Waghmare, V.N., Walford, S.A., Wright, R.J., Zaki, E.A., Zhang, T., Dennis, E.S., Mayer, K.F., Peterson, D.G., Rokhsar, D.S., Wang, X., Schmutz, J.. 2012. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492:423-427. doi: 10.1038/nature11798http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000312488200055&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Petrov, D.A. 2001. Evolution of genome size: New approaches to an old problem. Trends Genet. 17:23-28. doi: 10.1016/S0168-9525(00)02157-0

Petrov, D.A., Lozovskaya, E.R., Hartl, D.L.. 1996. High intrinsic rate of DNA loss in Drosophila. Nature 384:346-349. doi: 10.1038/384346a0

Piegu, B., Guyot, R., Picault, N., Roulin, A., Sanyal, A., Kim, H., Collura, K., Brar, D.S., Jackson, S., Wing, R.A., Panaud, O.. 2006. Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res. 16:1262-1269. doi: 10.1101/gr.5290206http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000240959800010&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Puchta, H. 2005. The repair of double-strand breaks in plants: Mechanisms and consequences for genome evolution. J. Exp. Bot. 56:1-14. doi: 10.1093/jxb/eri123

Ramsey, J., Schemske, D.W.. 1998. Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annu. Rev. Ecol. Syst. 29:467-501. doi: 10.1146/annurev.ecolsys.29.1.467

Renny-Byfield, S., Kovarik, A., Kelly, L.J., Macas, J., Novak, P., Chase, M.W., Nichols, R.A., Pancholi, M.R., Grandbastien, M.-A., Leitch, A.R.. 2013. Diploidization and genome size change in allopolyploids is associated with differential dynamics of low- and high-copy sequences. Plant J. 74:829-839. doi: 10.1111/tpj.12168http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000319512900010&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

SanMiguel, P., Gaut, B.S., Tikhonov, A., Nakajima, Y., Bennetzen, J.L.. 1998. The paleontology of intergene retrotransposons of maize. Nat. Genet. 20:43-45. doi: 10.1038/1695

Schmidt-Lebuhn, A.N., Fuchs, J., Hertel, D., Hirsch, H., Toivonen, J., Kessler, M.. 2010. An Andean radiation: Polyploidy in the tree genus Polylepis (Rosaceae, Sanguisorbeae). Plant Biol. (Stuttg.) 12:917-926. doi: 10.1111/j.1438-8677.2009.00297.xhttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000282817700010&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Schubert, I., Lysak, M.A.. 2011. Interpretation of karyotype evolution should consider chromosome structural constraints. Trends Genet. 27:207-216. doi: 10.1016/j.tig.2011.03.004http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000291567400001&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Schubert, I., Rieger, R., Fuchs, J., Pich, U.. 1994. Sequence organization and the mechanism of interstitial deletion clustering in a plant genome (Vicia faba). Mutat. Res. 325:1-5. doi: 10.1016/0165-7992(94)90020-5

Soltis, D.E., Albert, V.A., Leebens-Mack, J., Bell, C.D., Paterson, A.H., Zheng, C., Sankoff, D., Depamphilis, C.W., Wall, P.K., Soltis, P.S.. 2009. Polyploidy and angiosperm diversification. Am. J. Bot. 96:336-348. doi: 10.3732/ajb.0800079http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000262537900021&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Soltis, D.E., Soltis, P.S.. 1999. Polyploidy: Recurrent formation and genome evolution. Trends Ecol. Evol. 14:348-352. doi: 10.1016/S0169-5347(99)01638-9

Stanke, M., Morgenstern, B.. 2005. AUGUSTUS: A web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res. 33:W465-W467. doi: 10.1093/nar/gki458

Tenaillon, M.I., Hollister, J.D., Gaut, B.S.. 2010. A triptych of the evolution of plant transposable elements. Trends Plant Sci. 15:471-478. doi: 10.1016/j.tplants.2010.05.003http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000281176900008&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815. doi: 10.1038/35048692

Thomas, C.A. 1971. The genetic organization of chromosomes. Annu. Rev. Genet. 5:237-256. doi: 10.1146/annurev.ge.05.120171.001321

Tran, T.D., Cao, H.X., Jovtchev, G., Neumann, P., Novak, P., Fojtova, M., Vu, G.T.H., Macas, J., Fajkus, J., Schubert, I., Fuchs, J.. 2015. Centromere and telomere sequence alterations reflect the rapid genome evolution within the carnivorous plant genus Genlisea. Plant J. (accepted).

Trapnell, C., Williams, B.A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M.J., Salzberg, S.L., Wold, B.J., Pachter, L.. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28:511-515. doi: 10.1038/nbt.1621http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000277452700032&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Veleba, A., Bures, P., Adamec, L., Smarda, P., Lipnerova, I., Horova, L.. 2014. Genome size and genomic GC content evolution in the miniature genome-sized family Lentibulariaceae. New Phytol. 203:22-28. doi: 10.1111/nph.12790http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000336970200006&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Vinogradov, A.E. 1999. Intron-genome size relationship on a large evolutionary scale. J. Mol. Evol. 49:376-384. doi: 10.1007/PL00006561

Vu, G.T., Cao, H.X., Watanabe, K., Hensel, G., Blattner, F.R., Kumlehn, J., Schubert, I.. 2014. Repair of site-specific DNA double-strand breaks in barley occurs via diverse pathways primarily involving the sister chromatid. Plant Cell 26:2156-2167. doi: 10.1105/tpc.114.126607http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000338771700030&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Wang, W., Haberer, G., Gundlach, H., Glasser, C., Nussbaumer, T., Luo, M.C., Lomsadze, A., Borodovsky, M., Kerstetter, R.A., Shanklin, J., Byrant, D.W., Mockler, T.C., Appenroth, K.J., Grimwood, J., Jenkins, J., Chow, J., Choi, C., Adam, C., Cao, X.H., Fuchs, J., Schubert, I., Rokhsar, D., Schmutz, J., Michael, T.P., Mayer, K.F., Messing, J.. 2014. The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nat. Commun. 5:3311.

Wang, X., Wang, H., Wang, J., Sun, R., Wu, J., Liu, S., Bai, Y., Mun, J.H., Bancroft, I., Cheng, F., Huang, S., Li, X., Hua, W., Freeling, M., Pires, J.C., Paterson, A.H., Chalhoub, B., Wang, B., Hayward, A., Sharpe, A.G., Park, B.S., Weisshaar, B., Liu, B., Li, B., Tong, C., Song, C., Duran, C., Peng, C., Geng, C., Koh, C., Lin, C., Edwards, D., Mu, D., Shen, D., Soumpourou, E., Li, F., Fraser, F., Conant, G., Lassalle, G., King, G.J., Bonnema, G., Tang, H., Belcram, H., Zhou, H., Hirakawa, H., Abe, H., Guo, H., Wang, H., Jin, H., Parkin, I.A.P., Batley, J., Kim, J.S., Just, J., Li, J., Xu, J., Deng, J., Kim, J.A., Yu, J., Meng, J., Min, J., Poulain, J., Hatakeyama, K., Wu, K., Wang, L., Fang, L., Trick, M., Links, M.G., Zhao, M., Jin, M., Ramchiary, N., Drou, N., Berkman, P.J., Cai, Q., Huang, Q., Li, R., Tabata, S., Cheng, S., Zhang, S., Sato, S., Sun, S., Kwon, S.J., Choi, S.R., Lee, T.H., Fan, W., Zhao, X., Tan, X., Xu, X., Wang, Y., Qiu, Y., Yin, Y., Li, Y., Du, Y., Liao, Y., Lim, Y., Narusaka, Y., Wang, Z., Li, Z., Wang, Z., Xiong, Z., Zhang, Z.. 2011. The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 43:1035-1039. doi: 10.1038/ng.919http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000295316200023&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Wendel, J.F., Cronn, R.C., Alvarez, I., Liu, B., Small, R.L., Senchina, D.S.. 2002. Intron size and genome size in plants. Mol. Biol. Evol. 19:2346-2352. doi: 10.1093/oxfordjournals.molbev.a004062

Wenke, T., Dobel, T., Sorensen, T.R., Junghans, H., Weisshaar, B., Schmidt, T.. 2011. Targeted identification of short interspersed nuclear element families shows their widespread existence and extreme heterogeneity in plant genomes. Plant Cell 23:3117-3128. doi: 10.1105/tpc.111.088682http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=Agronomy_sub&KeyUT=WOS:000296739100008&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=9992b2403adf8c36119d0b6fce39b97c

Zhang, Z., Li, J., Zhao, X.Q., Wang, J., Wong, G.K., Yu, J.. 2006. KaKs_Calculator: Calculating Ka and Ks through model selection and model averaging. Genomics, Proteomics Bioinf. 4:259-263. doi: 10.1016/S1672-0229(07)60007-2

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