, Volume 125, Issue 3, pp 413–421 | Cite as

Speeding up chromosome evolution in Phaseolus: multiple rearrangements associated with a one-step descending dysploidy

  • Artur Fonsêca
  • Maria Eduarda Ferraz
  • Andrea Pedrosa-Harand
Research Article


The genus Phaseolus L. has been subject of extensive cytogenetic studies due to its global economic importance. It is considered karyotypically stable, with most of its ca. 75 species having 2n = 22 chromosomes, and only three species (Phaseolus leptostachyus, Phaseolus macvaughii, and Phaseolus micranthus), which form the Leptostachyus clade, having 2n = 20. To test whether a simple chromosomal fusion was the cause of this descending dysploidy, mitotic chromosomes of P. leptostachyus (2n = 20) were comparatively mapped by fluorescent in situ hybridization (FISH) using bacterial artificial chromosomes (BACs) and ribosomal DNA (rDNA) probes. Our results corroborated the conservation of the 5S and 45S rDNA sites on ancestral chromosomes 10 and 6, respectively. The reduction from x = 11 to x = 10 was the result of the insertion of chromosome 10 into the centromeric region of chromosome 11, supporting a nested chromosome fusion (NCF) as the main cause of this dysploidy. Additionally, the terminal region of the long arm of chromosome 6 was translocated to this larger chromosome. Surprisingly, the NCF was accompanied by several additional translocations and inversions previously unknown for the genus, suggesting that the dysploidy may have been associated to a burst of genome reorganization in this otherwise stable, diploid plant genus.


Phaseolus leptostachyus Fabaceae Nested chromosome fusion (NCF) BAC-FISH 



We thank M. Wetzel and L. Gonçalves Pereira Neto (Embrapa Recursos Genéticos e Biotecnologia) for providing the seeds, P. Gepts (University of California) for the BAC clones, and V. Geffroy (Université Paris-Sud) for the bacteriophage SJ19.12. A.F. was supported by a grant from Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco (FACEPE), Brazil. A.P.-H. and the project were supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brazil.

Conflict of interest

All the authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.


  1. Almeida C, Pedrosa-Harand A (2013) High macro-collinearity between lima bean (Phaseolus lunatus L.) and the common bean (P. vulgaris L.) as revealed by comparative cytogenetic mapping. Theor Appl Genet 126(7):1909–16CrossRefPubMedGoogle Scholar
  2. Bolzán AD (2012) Chromosomal aberrations involving telomeres and interstitial telomeric sequences. Mutagenesis 27:1–15CrossRefPubMedGoogle Scholar
  3. Bonifácio EM et al (2012) Comparative cytogenetic mapping between the lima bean (Phaseolus lunatus L.) and the common bean (P. vulgaris L.). Theor Appl Genet 124:1513–1520CrossRefPubMedGoogle Scholar
  4. Broughton WJ et al (2003) Beans (Phaseolus spp.)—model food legumes. Plant Soil 252:55–128CrossRefGoogle Scholar
  5. Cabral JS, Felix LP, Guerra M (2006) Heterochromatin diversity and its co-localization with 5S and 45S rDNA sites in chromosomes of four Maxillaria species (Orchidaceae). Genet Mol Biol 29:659–664CrossRefGoogle Scholar
  6. Camats N et al (2006) Genomic instability in rat: breakpoints induced by ionising radiation and interstitial telomeric-like sequences. Mutat Res-Fund Mol M 595:156–166CrossRefGoogle Scholar
  7. David P et al (2009) A nomadic subtelomeric disease resistance gene cluster in common bean. Plant Physiol 151:1048–1065CrossRefPubMedPubMedCentralGoogle Scholar
  8. Delgado-Salinas A, Bibler R, Lavin M (2006) Phylogeny of the genus Phaseolus (Leguminosae): a recent diversification in an ancient landscape. Syst Botany 31:779–791CrossRefGoogle Scholar
  9. Faria R, Navarro A (2010) Chromosomal speciation revisited: rearranging theory with pieces of evidence. Trends Ecol Evol 25:660–669CrossRefPubMedGoogle Scholar
  10. Fonsêca A, Pedrosa-Harand A (2013) Karyotype stability in the genus Phaseolus evidenced by the comparative mapping of the wild species Phaseolus microcarpus. Genome 56:335–343CrossRefPubMedGoogle Scholar
  11. Fonsêca A et al (2010) Cytogenetic map of common bean (Phaseolus vulgaris L.). Chromosome Res 18:487–502CrossRefPubMedPubMedCentralGoogle Scholar
  12. Fuchs J, Brandes A, Schubert I (1995) Telomere sequence localization and karyotype evolution in higher plants. Plant Syst Evol 196:227–241CrossRefGoogle Scholar
  13. Geffroy V et al (2000) Inheritance of partial resistance against Colletotrichum lindemuthianum in Phaseolus vulgaris and co-localization of quantitative trait loci with genes involved in specific resistance. Mol Plant–Microbe Interact 13:287–296Google Scholar
  14. Guerra M (2000) Chromosome number variation and evolution in monocots. Monocots: systematics and evolution. CSIRO, Collingwood, Australia, pp 127–136Google Scholar
  15. Heslop-Harrison JS, Harrison GE, Leitch IJ (1992) Reprobing of DNA: DNA in situ hybridization preparations. Trends Genet 8:372–373CrossRefPubMedGoogle Scholar
  16. International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–768CrossRefGoogle Scholar
  17. Kami J et al (2006) Development of four phylogenetically-arrayed BAC libraries and sequence of the APA locus in Phaseolus vulgaris. Theor Appl Genet 112:987–998CrossRefPubMedGoogle Scholar
  18. Kellogg EA, Bennetzen JL (2004) The evolution of nuclear genome structure in seed plants. Am J Bot 91:1709–1725CrossRefPubMedGoogle Scholar
  19. Khandelwal S (1990) Chromosome evolution in the genus Ophioglossum L. Bot J Linn Soc 102:205–217CrossRefGoogle Scholar
  20. Kovalskaya YM et al (2011) Karyotype reorganisation in the subtilis group of birch mice (Rodentia, Dipodidae, Sicista): unexpected taxonomic diversity within a limited distribution. Cytogenet Genome Res 132:271–288CrossRefPubMedGoogle Scholar
  21. Lagercrantz U (1998) Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Genetics 150:1217–1228PubMedPubMedCentralGoogle Scholar
  22. Luo MC et al (2009) Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae. Proc Natl Acad Sci USA 106:15780–15785CrossRefPubMedPubMedCentralGoogle Scholar
  23. Lysak MA, Schubert I (2013) Mechanisms of chromosome rearrangements. In: Plant Genome Diversity. Springer, Vienna, pp 137–147CrossRefGoogle Scholar
  24. Lysak MA et al (2006) Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. Proc Natl Acad Sci USA 103:5224–5229CrossRefPubMedPubMedCentralGoogle Scholar
  25. Mandáková T, Lysak MA (2008) Chromosomal phylogeny and karyotype evolution in x = 7 crucifer species (Brassicaceae). Plant Cell 20:2559–2570CrossRefPubMedPubMedCentralGoogle Scholar
  26. Mandáková T et al (2013) The more the merrier: recent hybridization and polyploidy in Cardamine. Plant Cell 25:3280–3295CrossRefPubMedPubMedCentralGoogle Scholar
  27. Maréchal R (1970) Données cytologiques sur les espèces de la sous-tribu des Papilionaceae-Phaseoleae-Phaseolinae. Deuxième série. Bull Jard Bot Nat Belg 40:307–348CrossRefGoogle Scholar
  28. Mercado-Ruaro P, Delgado-Salinas A (1996) Karyological studies in several Mexican species of Phaseolus L. and Vigna savi (Phaseolinae, Fabaceae). Adv Legume Syst 8:83–87Google Scholar
  29. Mercado-Ruaro P, Delgado-Salinas A (1998) Karyotypic studies on species of Phaseolus (Fabaceae: Phaseolinae). Am J Bot 85:1–9CrossRefPubMedGoogle Scholar
  30. Mlinarec J et al (2012) Cytogenetic and phylogenetic studies of diploid and polyploid members of Tribe Anemoninae (Ranunculaceae). Plant Biol 14:525–536CrossRefPubMedGoogle Scholar
  31. Murat F et al (2010) Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res 20:1545–1557CrossRefPubMedPubMedCentralGoogle Scholar
  32. Olson K, Gorelick R (2011) Chromosomal fission accounts for small-scale radiations in Zamia (Zamiaceae; Cycadales). Bot J Linn Soc 165:168–185CrossRefGoogle Scholar
  33. Pedrosa A et al (2002) Chromosomal map of the model legume Lotus japonicus. Genetics 161:1661–1672PubMedPubMedCentralGoogle Scholar
  34. Pedrosa-Harand A et al (2006) Extensive ribosomal DNA amplification during Andean common bean (Phaseolus vulgaris L.) evolution. Theor Appl Genet 112:924–933CrossRefPubMedGoogle Scholar
  35. Pedrosa-Harand A et al (2009) Cytogenetic mapping of common bean chromosomes reveals a less compartmentalized small-genome plant species. Chromosome Res 17:405–417CrossRefPubMedGoogle Scholar
  36. Richards EJ, Ausubel FM (1988) Isolation of a higher eukaryotic telomere from Arabidopsis thaliana. Cell 53:127–136CrossRefPubMedGoogle Scholar
  37. Rieseberg LH (2001) Chromosomal rearrangements and speciation. Trends Ecol Evol 16:351–358CrossRefPubMedGoogle Scholar
  38. Schubert I, Lysak MA (2011) Interpretation of karyotype evolution should consider chromosome structural constraints. Trends Genet 27:207–216CrossRefPubMedGoogle Scholar
  39. Smith-White S, Carter CR (1970) The cytology of Brachycome lineariloba. Chromosoma 30:129–153CrossRefPubMedGoogle Scholar
  40. Srinivasachary et al (2007) Comparative analyses reveal high levels of conserved colinearity between the finger millet and rice genomes. Theor Appl Genet 115:489–499CrossRefPubMedGoogle Scholar
  41. Tayalé A, Parisod C (2013) Natural pathways to polyploidy in plants and consequences for genome reorganization. Cytogenet Genome Res 140:79–96CrossRefPubMedGoogle Scholar
  42. Vanzela AL, Guerra M, Luceno M (1996) Rhynchospora tenuis Link (Cyperaceae), a species with the lowest number of holocentric chromosomes. Cytobios 88:219–228Google Scholar
  43. Wanzenböck EM et al (1997) Ribosomal transcription units integrated via T-DNA transformation associate with the nucleolus and do not require upstream repeat sequences for activity in Arabidopsis thaliana. Plant J 11:1007–1016CrossRefPubMedGoogle Scholar
  44. Wolny E et al (2011) Compact genomes and complex evolution in the genus Brachypodium. Chromosoma 120:199–212CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Artur Fonsêca
    • 1
  • Maria Eduarda Ferraz
    • 1
  • Andrea Pedrosa-Harand
    • 1
  1. 1.Laboratory of Plant Cytogenetics and Evolution, Department of BotanyFederal University of PernambucoRecifeBrazil

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