BACKGROUND AND AIMS: Most crucifer species (Brassicaceae) have small nuclear genomes (mean 1C-value 617 Mb). The species with the largest genomes occur within the monophyletic Hesperis clade (Mandáková et al., Plant Physiology174: 2062-2071; also known as Clade E or Lineage III). Whereas most chromosome numbers in the clade are 6 or 7, monoploid genome sizes vary 16-fold (256-4264 Mb). To get an insight into genome size evolution in the Hesperis clade (~350 species in ~48 genera), we aimed to identify, quantify and localize in situ the repeats from which these genomes are built. We analysed nuclear repeatomes in seven species, covering the phylogenetic and genome size breadth of the clade, by low-pass whole-genome sequencing. METHODS: Genome size was estimated by flow cytometry. Genomic DNA was sequenced on an Illumina sequencer and DNA repeats were identified and quantified using RepeatExplorer; the most abundant repeats were localized on chromosomes by fluorescence in situ hybridization. To evaluate the feasibility of bacterial artificial chromosome (BAC)-based comparative chromosome painting in Hesperis-clade species, BACs of arabidopsis were used as painting probes. KEY RESULTS: Most biennial and perennial species of the Hesperis clade possess unusually large nuclear genomes due to the proliferation of long terminal repeat retrotransposons. The prevalent genome expansion was rarely, but repeatedly, counteracted by purging of transposable elements in ephemeral and annual species. CONCLUSIONS: The most common ancestor of the Hesperis clade has experienced genome upsizing due to transposable element amplification. Further genome size increases, dominating diversification of all Hesperis-clade tribes, contrast with the overall stability of chromosome numbers. In some subclades and species genome downsizing occurred, presumably as an adaptive transition to an annual life cycle. The amplification versus purging of transposable elements and tandem repeats impacted the chromosomal architecture of the Hesperis-clade species.

CEITEC Central European Institute of Technology and Faculty of Science Masaryk University Kamenice Brno Czech Republic

Institute of Botany Czech Academy of Sciences Zámek 1 252 43 Průhonice Czech Republic

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Afgan E, Baker D, Batut B, et al. . 2018. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Research 46: W537–W544. PubMed PMC

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403–410. PubMed

Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc.

Beilstein MA, Al-Shehbaz IA, Kellogg EA. 2006. Brassicaceae phylogeny and trichome evolution. American Journal of Botany 93: 607–619. PubMed

Bennett MD. 1987. Variation in genomic form in plants and its ecological implications. New Phytologist 106: 177–200.

Bennett MD, Leitch IJ, Price HJ, Johnston JS. 2003. Comparisons with Caenorhabditis (∼100 Mb) and Drosophila (∼175 Mb) using flow cytometry show genome size in Arabidopsis to be ∼157 Mb and thus ∼25 % larger than the Arabidopsis genome initiative estimate of ∼125 Mb. Annals of Botany 91: 547–557. PubMed PMC

Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research 27: 573–580. PubMed PMC

Betekhtin A, Jenkins G, Hasterok R. 2014. Reconstructing the evolution of Brachypodium genomes using comparative chromosome painting. PLoS ONE 9: e115108. PubMed PMC

Chen H, Al-Shehbaz IA, Yue J, Sun H. 2018. New insights into the taxonomy of tribe Euclidieae (Brassicaceae), evidence from nrITS sequence data. PhytoKeys 100: 125–139. PubMed PMC

Chen YC, Liu T, Yu CH, Chiang TY, Hwang CC. 2013. Effects of GC bias in next-generation-sequencing data on de novo genome assembly. PLoS ONE 8: e62856. PubMed PMC

Cheng Z, Buell CR, Wing RA, Gu M, Jiang J. 2001. Toward a cytological characterization of the rice genome. Genome Research 11: 2133–2141. PubMed PMC

Devos KM, Brown JK, Bennetzen JL. 2002. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Research 12: 1075–1079. PubMed PMC

Dodsworth S, Jang TS, Struebig M, Chase MW, Weiss-Schneeweiss H, Leitch AR. 2017. Genome-wide repeat dynamics reflect phylogenetic distance in closely related allotetraploid Nicotiana (Solanaceae). Plant Systematics and Evolution 303: 1013–1020. PubMed PMC

Doležel J, Bartoš J, Voglmayr H, Greilhuber J. 2003. Nuclear DNA content and genome size of trout and human. Cytometry 51: 127–128. PubMed

Doležel J, Greillhuber J, Suda J. 2007. Estimation of nuclear DNA content in plants using flow cytometry. Nature Protocols 2: 2233–2244. PubMed

Fransz P, Armstrong S, Alonso-Blanco C, Fischer TC, Torres-Ruiz RA, Jones G. 1998. Cytogenetics for the model system Arabidopsis thaliana. Plant Journal 13: 867–876. PubMed

Fransz P, De Jong JH, Lysak M, Castiglione MR, Schubert I. 2002. Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate. Proceedings of the National Academy of Sciences of the USA 99: 14584–14589. PubMed PMC

Gaiero P, Vaio M, Peters SA, Schranz ME, de Jong H, Speranza PR. 2018. Comparative analysis of repetitive sequences among species from the potato and the tomato clades. Annals of Botany 123: 521–532. PubMed PMC

German DA, Al-Shehbaz IA. 2017. A taxonomic note on Sterigmostemum and related genera (Anchonieae, Cruciferae). Novosti Sistematicheski Vysshikh Rasteniĭ 48: 78–83.

German DA, Al-Shehbaz IA. 2018. A reconsideration of Pseudofortuynia and Tchihatchewia as synonyms of Sisymbrium and Hesperis, respectively (Brassicaceae). Phytotaxa 334: 95–98.

German DA, Grant JR, Lysak MA, Al-Shehbaz IA. 2011. Molecular phylogeny and systematics of the tribe Chorisporeae (Brassicaceae). Plant Systematics and Evolution 294: 65–86.

Greilhuber J, Obermayer R. 1999. Cryptopolyploidy in Bunias (Brassicaceae) revisited—a flow-cytometric and densitometric study. Plant Systematics and Evolution 218: 1–4.

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 Biology 8: 770–777. PubMed

Grob S, Schmid MW, Luedtke NW, Wicker T, Grossniklaus U. 2013. Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture. Genome Biology 14: R129. PubMed PMC

Hall AE, Kettler GC, Preuss D. 2006. Dynamic evolution at pericentromeres. Genome Research 16: 355–364. PubMed PMC

Harmon LJ, Weir JT, Brock CD, Glor RE, Challenger W. 2007. GEIGER: investigating evolutionary radiations. Bioinformatics 24: 129–131. PubMed

Hawkins JS, Proulx SR, Rapp RA, Wendel JF. 2009. Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants. Proceedings of the National Academy of Sciences of the USA 106: 17811–17816. PubMed PMC

Heslop-Harrison JS, Schwarzacher T. 2011. Organisation of the plant genome in chromosomes. Plant Journal 66: 18–33. PubMed

Hohmann N, Wolf EM, Lysak MA, Koch MA. 2015. A time-calibrated road map of Brassicaceae species radiation and evolutionary history. Plant Cell 27: 2770–2784. PubMed PMC

Huang CH, Sun R, Hu Y, et al. . 2016. Resolution of Brassicaceae phylogeny using nuclear genes uncovers nested radiations and supports convergent morphological evolution. Molecular Biology and Evolution 33: 394–412. PubMed PMC

Hughes CE, Atchison GW. 2015. The ubiquity of alpine plant radiations: from the Andes to the Hengduan Mountains. New Phytologist 207: 275–282. PubMed

Jaretzky R. 1928. Untersuchungen über Chromosomen und Phylogenie bei einigen Cruciferen. Jahrbücher für Wissenschaftliche Botanik 68: 1–45.

Jiao WB, Accinelli GG, Hartwig B, et al. . 2017. Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data. Genome Research 27: 778–786. PubMed PMC

Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30: 772–780. PubMed PMC

Kearse M, Moir R, Wilson A, et al. . 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647–1649. PubMed PMC

Kejnovsky E, Leitch IJ, Leitch AR. 2009. Contrasting evolutionary dynamics between angiosperm and mammalian genomes. Trends in Ecology & Evolution 24: 572–582. PubMed

Kiefer M, Schmickl R, German DA, et al. . 2014. BrassiBase: introduction to a novel knowledge database on Brassicaceae evolution. Plant and Cell Physiology 55: e3. PubMed

Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC. 2011. Adaptive seeds tame genomic sequence comparison. Genome Research 21: 487–493. PubMed PMC

Knight CA, Molinari NA, Petrov DA. 2005. The large genome constraint hypothesis: evolution, ecology and phenotype. Annals of Botany 95: 177–190. PubMed PMC

Kohany O, Gentles AJ, Hankus L, Jurka J. 2006. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 7: 474. PubMed PMC

Koo DH, Hong CP, Batley J, et al. . 2011. Rapid divergence of repetitive DNAs in Brassica relatives. Genomics 97: 173–185. PubMed

Kubešová M, Moravcova L, Suda J, Jarošík V, Pyšek P. 2010. Naturalized plants have smaller genomes than their non-invading relatives: a flow cytometric analysis of the Czech alien flora. Preslia 82: 81–96.

Kubis S, Schmidt T, Heslop-Harrison JS. 1998. Repetitive DNA elements as a major component of plant genomes. Annals of Botany 82: 45–55.

Lim KY, Leitch IJ, Leitch AR. 1998. Genomic characterisation and the detection of raspberry chromatin in polyploid Rubus. Theoretical and Applied Genetics 97: 1027–1033.

Liu L. 2017. The epigenetic modifications of Chorispora bungeana and the function of ADH1 in cold response. Thesis retrieved from China Integrated Knowledge Resources Database. http://cdmd.cnki.com.cn/Article/CDMD-10730-1018803968.htm.

Liu XF, Tan DY. 2007. Diaspore characteristics and dispersal strategies of 24 ephemeral species of Brassicaceae in the Junggar Desert of China. Journal of Plant Ecology 31: 1019–1027.

Lu JJ, Tan DY, Baskin CC, Baskin JM. 2017. Role of indehiscent pericarp in formation of soil seed bank in five cold desert Brassicaceae species. Plant Ecology 218: 1187–1200.

Lysak MA, Lexer C. 2006. Towards the era of comparative evolutionary genomics in Brassicaceae. Plant Systematics and Evolution 259: 175–198.

Lysak MA, Mandáková T. 2013. Analysis of plant meiotic chromosomes by chromosome painting. Methods in Molecular Biology 990: 13–24. PubMed

Lysak MA, Pecinka A, Schubert I. 2003. Recent progress in chromosome painting of Arabidopsis and related species. Chromosome Research 11: 195–204. PubMed

Lysak MA, Koch MA, Beaulieu JM, Meister A, Leitch IJ. 2009. The dynamic ups and downs of genome size evolution in Brassicaceae. Molecular Biology and Evolution 26: 85–98. PubMed

Lysak MA, Mandáková T, Schranz ME. 2016. Comparative paleogenomics of crucifers: ancestral genomic blocks revisited. Current Opinion in Plant Biology 30: 108–115. PubMed

Macas J, Novak P, Pellicer J, et al. . 2015. In depth characterization of repetitive DNA in 23 plant genomes reveals sources of genome size variation in the legume tribe Fabeae. PLoS ONE 10: e0143424. PubMed PMC

Mandáaková T, Kovařík A, Zozomová-Lihová J, Shimizu-Inatsugi R, Shimizu KK, Mummenhoff K, Marhold K, Lysak MA. 2013. The more the merrier: recent hybridization and polyploidy in Cardamine. Plant Cell 25: 3280–3295. PubMed PMC

Mandáková T, Lysak MA. 2016a Chromosome preparation for cytogenetic analyses in Arabidopsis. Current Protocols in Plant Biology 1: 43–51. PubMed

Mandáková T, Lysak MA. 2016b Painting of Arabidopsis chromosomes with chromosome-specific BAC clones. Current Protocols in Plant Biology 1: 359–371. PubMed

Mandáková T, Hloušková P, German D, Lysak MA. 2017. Monophyletic origin and evolution of the largest crucifer genomes. Plant Physiology 174: 2062–2071. PubMed PMC

Manton I. 1932. Introduction to the general cytology of the Cruciferae. Annals of Botany 46: 509–556.

Morata J, Tormo M, Alexiou KG, et al. . 2018. The evolutionary consequences of transposon-related pericentromer expansion in melon. Genome Biology and Evolution 10: 1584–1595. PubMed PMC

Neumann P, Novák P, Hoštáková N, Macas J. 2019. Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification. Mobile DNA 10: 1. PubMed PMC

Novák 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. PubMed

Novák P, Ávila Robledillo L, Koblížková A, Vrbová I, Neumann P, Macas J. 2017. TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Research 45: e111. PubMed PMC

Otto F. 1990. DAPI staining of fixed cells for high-resolution flow cytometry of nuclear DNA. In: Darzynkiewicz Z, Crissman HA, eds. Methods in Cell Biology, Vol. 33 New York: Academic Press, 105–110. PubMed

Paradis E, Claude J, Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289–290. PubMed

Park M, Park J, Kim S, et al. . 2012. Evolution of the large genome in Capsicum annuum occurred through accumulation of single-type long terminal repeat retrotransposons and their derivatives. Plant Journal 69: 1018–1029. PubMed

Pearson WR, Wood T, Zhang Z, Miller W. 1997. Comparison of DNA sequences with protein sequences. Genomics 46: 24–36. PubMed

Pellicer J, Hidalgo O, Dodsworth S, Leitch I. 2018. Genome size diversity and its impact on the evolution of land plants. Genes 9: 88. PubMed PMC

R Development Core Team. 2013. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; http://www.R-project.org.

Rambaut A, Drummond A. 2009. Tracer v1.6. http://tree.bio.ed.ac.uk/software/tracer.

Ren L, Huang W, Cannon EK, Bertioli DJ, Cannon SB. 2018. A mechanism for genome size reduction following genomic rearrangements. Frontiers in Genetics 9: 454. PubMed PMC

Revell LJ. 2012. phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution 3: 217–223.

Roark LM, Hui AY, Donnelly L, Birchler JA, Newton KJ. 2010. Recent and frequent insertions of chloroplast DNA into maize nuclear chromosomes. Cytogenetic and Genome Research 129: 17–23. PubMed

Robinson JT, Thorvaldsdóttir H, Winckler W, et al. . 2011. Integrative genomics viewer. Nature Biotechnology 29: 24. PubMed PMC

Ronquist F, Teslenko M, Van Der Mark P, et al. . 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539–542. PubMed PMC

Schmidt T, Heslop-Harrison JS. 1998. Genomes, genes and junk: the large-scale organization of plant chromosomes. Trends in Plant Science 3: 195–199.

Schubert I, Lysak MA. 2011. Interpretation of karyotype evolution should consider chromosome structural constraints. Trends in Genetics 27: 207–216. PubMed

Simon L, Voisin M, Tatout C, Probst AV. 2015. Structure and function of centromeric and pericentromeric heterochromatin in Arabidopsis thaliana. Frontiers in Plant Science 6: 1049. PubMed PMC

Song Y, Liu L, Feng Y, et al. . 2015. Chilling- and freezing-induced alterations in cytosine methylation and its association with the cold tolerance of an alpine subnival plant, Chorispora bungeana. PLoS ONE 10: e0135485. PubMed PMC

Sonnhammer EL, Durbin R. 1995. A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167: GC1–GC10. PubMed

Suda J, Kyncl T, Jarolímová V. 2005. Genome size variation in Macaronesian angiosperms: forty percent of the Canarian endemic flora completed. Plant Systematics and Evolution 252: 215–238.

Suda J, Meyerson LA, Leitch IJ, Pyšek P. 2015. The hidden side of plant invasions: the role of genome size. New Phytologist 205: 994–1007. PubMed

Trávníček P, Ponert J, Urfus T, et al. . 2015. Challenges of flow-cytometric estimation of nuclear genome size in orchids, a plant group with both whole-genome and progressively partial endoreplication. Cytometry 87A: 958–966. PubMed

Underwood CJ, Henderson IR, Martienssen RA. 2017. Genetic and epigenetic variation of transposable elements in Arabidopsis. Current Opinion in Plant Biology 36: 135–141. PubMed PMC

Vu GT, Cao HX, Reiss B, Schubert I. 2017. Deletion-bias in DNA double-strand break repair differentially contributes to plant genome shrinkage. New Phytologist 214: 1712–1721. PubMed

Waterworth WM, Drury GE, Bray CM, West CE. 2011. Repairing breaks in the plant genome: the importance of keeping it together. New Phytologist 192: 805–822. PubMed

Willing E-M, Rawat V, Mandáková T, et al. . 2015. Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nature Plants 1: 14023. PubMed

Zhang H, Dawe RK. 2012. Total centromere size and genome size are strongly correlated in ten grass species. Chromosome Research 20: 403–412. PubMed PMC

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