Karyotype evolution in species with identical chromosome number but belonging to distinct phylogenetic clades is a long-standing question of plant biology, intractable by conventional cytogenetic techniques. Here, we apply comparative chromosome painting (CCP) to reconstruct karyotype evolution in eight species with x=7 (2n=14, 28) chromosomes from six Brassicaceae tribes. CCP data allowed us to reconstruct an ancestral Proto-Calepineae Karyotype (PCK; n=7) shared by all x=7 species analyzed. The PCK has been preserved in the tribes Calepineae, Conringieae, and Noccaeeae, whereas karyotypes of Eutremeae, Isatideae, and Sisymbrieae are characterized by an additional translocation. The inferred chromosomal phylogeny provided compelling evidence for a monophyletic origin of the x=7 tribes. Moreover, chromosomal data along with previously published gene phylogenies strongly suggest the PCK to represent an ancestral karyotype of the tribe Brassiceae prior to its tribe-specific whole-genome triplication. As the PCK shares five chromosomes and conserved associations of genomic blocks with the putative Ancestral Crucifer Karyotype (n=8) of crucifer Lineage I, we propose that both karyotypes descended from a common ancestor. A tentative origin of the PCK via chromosome number reduction from n=8 to n=7 is outlined. Comparative chromosome maps of two important model species, Noccaea caerulescens and Thellungiella halophila, and complete karyotypes of two purported autotetraploid Calepineae species (2n=4x=28) were reconstructed by CCP.

Department of Functional Genomics and Proteomics Institute of Experimental Biology Masaryk University Brno CZ 625 00 Czech Republic

See more in PubMed

Ali, H.B.M., Lysak, M.A., and Schubert, I. (2005). Chromosomal localization of rDNA in the Brassicaceae. Genome 48 341–346. PubMed

Al-Shehbaz, I.A., Beilstein, M.A., and Kellogg, E.A. (2006). Systematics and phylogeny of the Brassicaceae (Cruciferae): An overview. Plant Syst. Evol. 259 89–120.

Bailey, C.D., Koch, M.A., Mayer, M., Mummenhoff, K., O'Kane, S.L., Jr., Warwick, S.I., Windham, M.D., and Al-Shehbaz, I.A. (2006). Toward a global phylogeny of the Brassicaceae. Mol. Biol. Evol. 23 2142–2160. PubMed

Beilstein, M.A., Al-Shehbaz, I.A., and Kellogg, E.A. (2006). Brassicaceae phylogeny and trichome evolution. Am. J. Bot. 93 607–619. PubMed

Berr, A., Pecinka, A., Meister, A., Kreth, G., Fuchs, J., Blattner, F.R., Lysak, M.A., and Schubert, I. (2006). Chromosome arrangement and nuclear architecture but not centromeric sequences are conserved between Arabidopsis thaliana and Arabidopsis lyrata. Plant J. 48 771–783. PubMed

Boivin, K., Acarkan, A., Mbulu, R.S., Clarenz, O., and Schmidt, R. (2004). The Arabidopsis genome sequence as a tool for genome analysis in Brassicaceae: A comparison of the Arabidopsis and Capsella rubella genomes. Plant Physiol. 135 735–744. PubMed PMC

Catcheside, D.G. (1937). Secondary pairing in Brassica oleracea. Cytologia Fujii Jub. 366–378.

Cloix, C., Tutois, S., and Tourmente, S. (2003). 5S rDNA and 5S RNA in higher plants. Rec. Res. Dev. Plant Mol. Biol. 1 207–221.

Devos, K.M. (2005). Updating the ‘crop circle.’ Curr. Opin. Plant Biol. 8 155–162. PubMed

Fransz, P., Armstrong, S., Alonso-Blanco, C., Fischer, T.C., Torres-Ruiz, R.A., and Jones, G.H. (1998). Cytogenetics for the model system Arabidopsis thaliana. Plant J. 13 867–876. PubMed

Fransz, P.F., Armstrong, S., de Jong, J.H., Parnell, L.D., van Drunen, G., Dean, C., Zabel, P., Bisseling, T., and Jones, G.H. (2000). Integrated cytogenetic map of chromosome arm 4S of A. thaliana: Structural organization of heterochromatic knob and centromere region. Cell 100 367–376. PubMed

Gaut, B.S., Wright, S.I., Rizzon, C., Dvorak, J., and Anderson, L.K. (2007). Recombination: An underappreciated factor in the evolution of plant genomes. Nat. Rev. Genet. 8 77–84. PubMed

German, D.A., and Al-Shehbaz, I.A. (2008). Five additional tribes (Aphragmeae, Biscutelleae, Calepineae, Conringieae, and Erysimeae) in the Brassicaceae (Cruciferae). Harv. Pap. Bot. 13 165–170.

Gong, Q., Li, P.H., Ma, S.S., Rupassara, S.I., and Bohnert, H.J. (2005). Salinity stress adaptation competence in the extremophile Thellungiella halophila in comparison with its relative Arabidopsis thaliana. Plant J. 44 826–839. PubMed

Jiang, J., and Gill, B.S. (2006). Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 49 1057–1068. PubMed

Jones, K. (1998). Robertsonian fusion and centric fission in karyotype evolution of higher plants. Bot. Rev. 64 273–289.

Kehrer-Sawatzki, H., and Cooper, D.N. (2008). Molecular mechanisms of chromosomal rearrangement during primate evolution. Chromosome Res. 16 41–56. PubMed

Koch, M., and Al-Shehbaz, I.A. (2008). Molecular systematics and evolution of “wild” crucifers (Brassicaceae or Cruciferae). In Biology and Breeding of Crucifers, P.K. Gupta, ed (London: Taylor and Francis Group).

Koch, M.A., Dobeš, C., Kiefer, C., Schmickl, R., Klimes, L., and Lysak, M.A. (2007). Supernetwork identifies multiple events of plastid trnF(GAA) pseudogene evolution in the Brassicaceae. Mol. Biol. Evol. 24 63–73. PubMed

Koch, M.A., and Kiefer, M. (2005). Genome evolution among cruciferous plants: A lecture from the comparison of the genetic maps of three diploid species—Capsella rubella, Arabidopsis lyrata subsp. petraea, and A. thaliana. Am. J. Bot. 92 761–767. PubMed

Kuittinen, H., de Haan, A.A., Vogl, C., Oikarinen, S., Leppala, J., Koch, M., Mitchell-Olds, T., Langley, C.H., and Savolainen, O. (2004). Comparing the linkage maps of the close relatives Arabidopsis lyrata and A. thaliana. Genetics 168 1575–1584. PubMed PMC

Lamb, C.J., Meyer, M.J., Corcoran, B., Kato, A., Han, F., and Birchler, A.J. (2007). Distinct chromosomal distributions of highly repetitive sequences in maize. Chromosome Res. 15 33–49. PubMed

Lim, K.B., et al. (2005). Characterization of rDNAs and tandem repeats in the heterochromatin of Brassica rapa. Mol. Cells 19 436–444. PubMed

Lukens, L.N., Quijada, P.A., Udall, J., Pires, J.C., Schranz, M.E., and Osborn, T.C. (2004). Genome redundancy and plasticity within ancient and recent Brassica crop species. Biol. J. Linn. Soc. 82 665–674.

Lysak, M., Berr, A., Pecinka, A., Schmidt, R., McBreen, K., and Schubert, I. (2006). Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. Proc. Natl. Acad. Sci. USA 103 5224–5229. PubMed PMC

Lysak, M.A., Cheung, K., Kitschke, M., and Bureš, P. (2007). Ancestral chromosomal blocks are triplicated in Brassiceae species with varying chromosome number and genome size. Plant Physiol. 145 402–410. PubMed PMC

Lysak, M.A., Koch, M.A., Pecinka, A., and Schubert, I. (2005). Chromosome triplication found across the tribe Brassiceae. Genome Res. 15 516–525. PubMed PMC

Lysak, M.A., and Lexer, C. (2006). Towards the era of comparative evolutionary genomics in Brassicaceae. Plant Syst. Evol. 259 175–198.

Lysak, M.A., Pecinka, A., and Schubert, I. (2003). Recent progress in chromosome painting of Arabidopsis and related species. Chromosome Res. 11 195–204. PubMed

Ma, X.F., and Gustafson, J.P. (2005). Genome evolution of allopolyploids: A process of cytological and genetic diploidization. Cytogenet. Genome Res. 109 236–249. PubMed

Nasuda, S., Hudakova, S., Schubert, I., Houben, A., and Endo, T.R. (2005). Stable barley chromosomes without centromeric repeats. Proc. Natl. Acad. Sci. USA 102 9842–9847. PubMed PMC

Ohmido, N., Kijima, K., Ashikawa, I., de Jong, J.H., and Fukui, K. (2001). Visualization of the terminal structure of rice chromosomes 6 and 12 with multicolor FISH to chromosomes and extended DNA fibers. Plant Mol. Biol. 47 413–421. PubMed

Parkin, I.A.P., Gulden, S.M., Sharpe, A.G., Lukens, L., Trick, M., Osborn, T.C., and Lydiate, D.J. (2005). Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics 171 765–781. PubMed PMC

Peer, W.A., Mahmoudian, M., Freeman, J.L., Lahner, B., Richards, E.L., Reeves, R.D., Murphy, A.S., and Salt, D.E. (2006). Assessment of plants from the Brassicaceae family as genetic models for the study of nickel and zinc hyperaccumulation. New Phytol 172 248–260. PubMed

Pontes, O., Neves, N., Silva, M., Lewis, M.S., Madlung, A., Comai, L., Viegas, W., and Pikaard, C.S. (2004). Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis suecica genome. Proc. Natl. Acad. Sci. USA 101 18240–18245. PubMed PMC

Probst, A.V., Fransz, P.F., Paszkowki, J., and Mittelsten Scheid, O. (2003). Two means of transcriptional reactivation within heterochromatin. Plant J. 33 743–749. PubMed

Ranz, J.M., Maurin, D., Chan, Y.S., von Grotthuss, M., Hillier, L.W., Roote, J., Ashburner, M., and Bergman, C.M. (2007). Principles of genome evolution in the Drosophila melanogaster species group. PLoS Biol. 5 1366–1381. PubMed PMC

Raskina, O., Barber, J.C., Nevo, E., and Belyayev, A. (2008). Repetitive DNA and chromosomal rearrangements: Speciation-related events in plant genomes. Cytogenet. Genome Res. 120 351–357. PubMed

Raskina, O., Belyayev, A., and Nevo, E. (2004). Quantum speciation in Aegilops: Molecular cytogenetic evidence from rDNA cluster variability in natural populations. Proc. Natl. Acad. Sci. USA 101 14818–14823. PubMed PMC

Röbbelen, G. (1960). Beiträge zur Analyse des Brassica-Genoms. Chromosoma 11 205–228. PubMed

Santos, J.L., Alfaro, D., Sanchez-Moran, E., Armstrong, S.J., Franklin, F.C.H., and Jones, G.H. (2003). Partial diploidization of meiosis in autotetraploid Arabidopsis thaliana. Genetics 165 1533–1540. PubMed PMC

Schranz, M.E., Lysak, M.A., and Mitchell-Olds, T. (2006). The ABC's of comparative genomics in the Brassicaceae: Building blocks of crucifer genomes. Trends Plant Sci. 11 535–542. PubMed

Schranz, M.E., Windsor, A.J., Song, B., Lawton-Rauh, A., and Mitchell-Olds, T. (2007). Comparative genetic mapping in Boechera stricta, a close relative of Arabidopsis. Plant Physiol. 144 286–298. PubMed PMC

Schubert, I. (2007). Chromosome evolution. Curr. Opin. Plant Biol. 10 109–115. PubMed

Schubert, I., Fransz, P.F., Fuchs, J., and de Jong, J.H. (2001). Chromosome painting in plants. Methods Cell Sci. 23 57–69. PubMed

Srinivasachary, Dida, M.M., Gale, M.D., and Devos, K.M. (2007). Comparative analyses reveal high levels of conserved colinearity between the finger millet and rice genomes. Theor. Appl. Genet. 115 489–499. PubMed

Warwick, S.I., and Al-Shehbaz, I.A. (2006). Brassicaceae: Chromosome number index and database on CD-ROM. Plant Syst. Evol. 259 237–248.

Wei, F., et al. (2007). Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet. 3 1254–1263. PubMed PMC

Zhong, X.B., Fransz, P.F., Wennekes-van Eden, J., Ramanna, M.S., van Kammen, A., Zabel, P., and de Jong, J.H. (1998). FISH studies reveal the molecular and chromosomal organization of individual telomere domains in tomato. Plant J. 13 507–517. PubMed

Bulked Oligo-FISH for Chromosome Painting and Chromosome Barcoding

Chromosome Painting Using Chromosome-Specific BAC Clones

Genome evolution of the psammophyte Pugionium for desert adaptation and further speciation

Linked by Ancestral Bonds: Multiple Whole-Genome Duplications and Reticulate Evolution in a Brassicaceae Tribe

Limitation of current probe design for oligo-cross-FISH, exemplified by chromosome evolution studies in duckweeds

Genomic Blocks in Aethionema arabicum Support Arabideae as Next Diverging Clade in Brassicaceae

Chromosomal Evolution and Apomixis in the Cruciferous Tribe Boechereae

Genome Evolution in Arabideae Was Marked by Frequent Centromere Repositioning

Chromosome Painting Facilitates Anchoring Reference Genome Sequence to Chromosomes In Situ and Integrated Karyotyping in Banana (Musa Spp.)

The story of promiscuous crucifers: origin and genome evolution of an invasive species, Cardamine occulta (Brassicaceae), and its relatives

Telomeres in Plants and Humans: Not So Different, Not So Similar

Healthy Roots and Leaves: Comparative Genome Structure of Horseradish and Watercress

Monophyletic Origin and Evolution of the Largest Crucifer Genomes

Chromosome identification for the carnivorous plant Genlisea margaretae

Young inversion with multiple linked QTLs under selection in a hybrid zone

Variation of 45S rDNA intergenic spacers in Arabidopsis thaliana

Telomere- and Telomerase-Associated Proteins and Their Functions in the Plant Cell

Repeated Whole-Genome Duplication, Karyotype Reshuffling, and Biased Retention of Stress-Responding Genes in Buckler Mustard

Telomere binding protein TRB1 is associated with promoters of translation machinery genes in vivo

A Time-Calibrated Road Map of Brassicaceae Species Radiation and Evolutionary History