Identification and characterization of functional centromeres of the common bean

Aiko Iwata, Ahmet L. Tek, Manon M S Richard, Brian Abernathy, Artur Fonsêca, Jeremy Schmutz, Nicolas W G Chen, Vincent Thareau, Ghislaine Magdelenat, Yupeng Li, Minoru Murata, Andrea Pedrosa-Harand, Valérie Geffroy, Kiyotaka Nagaki, Scott A. Jackson

Research output: Contribution to journalArticle

31 Citations (Scopus)

Abstract

In higher eukaryotes, centromeres are typically composed of megabase-sized arrays of satellite repeats that evolve rapidly and homogenize within a species' genome. Despite the importance of centromeres, our knowledge is limited to a few model species. We conducted a comprehensive analysis of common bean (Phaseolus vulgaris) centromeric satellite DNA using genomic data, fluorescence in situ hybridization (FISH), immunofluorescence and chromatin immunoprecipitation (ChIP). Two unrelated centromere-specific satellite repeats, CentPv1 and CentPv2, and the common bean centromere-specific histone H3 (PvCENH3) were identified. FISH showed that CentPv1 and CentPv2 are predominantly located at subsets of eight and three centromeres, respectively. Immunofluorescence- and ChIP-based assays demonstrated the functional significance of CentPv1 and CentPv2 at centromeres. Genomic analysis revealed several interesting features of CentPv1 and CentPv2: (i) CentPv1 is organized into an higher-order repeat structure, named Nazca, of 528 bp, whereas CentPv2 is composed of tandemly organized monomers; (ii) CentPv1 and CentPv2 have undergone chromosome-specific homogenization; and (iii) CentPv1 and CentPv2 are not likely to be commingled in the genome. These findings suggest that two distinct sets of centromere sequences have evolved independently within the common bean genome, and provide insight into centromere satellite evolution.

Original languageEnglish
Pages (from-to)47-60
Number of pages14
JournalPlant Journal
Volume76
Issue number1
DOIs
Publication statusPublished - Oct 2013

Fingerprint

Centromere
centromeres
beans
Chromatin Immunoprecipitation
Genome
fluorescence in situ hybridization
Fluorescence In Situ Hybridization
fluorescent antibody technique
Fluorescent Antibody Technique
genome
chromatin
Satellite DNA
genomics
satellite DNA
Phaseolus
homogenization
Eukaryota
histones
Histones
Phaseolus vulgaris

Keywords

  • centromere
  • centromere evolution
  • centromere-specific histone H3
  • chromosome-specific homogenization
  • higher-order repeat structure
  • Phaseolus vulgaris
  • satellite repeats

ASJC Scopus subject areas

  • Plant Science
  • Cell Biology
  • Genetics

Cite this

Iwata, A., Tek, A. L., Richard, M. M. S., Abernathy, B., Fonsêca, A., Schmutz, J., ... Jackson, S. A. (2013). Identification and characterization of functional centromeres of the common bean. Plant Journal, 76(1), 47-60. https://doi.org/10.1111/tpj.12269

Identification and characterization of functional centromeres of the common bean. / Iwata, Aiko; Tek, Ahmet L.; Richard, Manon M S; Abernathy, Brian; Fonsêca, Artur; Schmutz, Jeremy; Chen, Nicolas W G; Thareau, Vincent; Magdelenat, Ghislaine; Li, Yupeng; Murata, Minoru; Pedrosa-Harand, Andrea; Geffroy, Valérie; Nagaki, Kiyotaka; Jackson, Scott A.

In: Plant Journal, Vol. 76, No. 1, 10.2013, p. 47-60.

Research output: Contribution to journalArticle

Iwata, A, Tek, AL, Richard, MMS, Abernathy, B, Fonsêca, A, Schmutz, J, Chen, NWG, Thareau, V, Magdelenat, G, Li, Y, Murata, M, Pedrosa-Harand, A, Geffroy, V, Nagaki, K & Jackson, SA 2013, 'Identification and characterization of functional centromeres of the common bean', Plant Journal, vol. 76, no. 1, pp. 47-60. https://doi.org/10.1111/tpj.12269
Iwata A, Tek AL, Richard MMS, Abernathy B, Fonsêca A, Schmutz J et al. Identification and characterization of functional centromeres of the common bean. Plant Journal. 2013 Oct;76(1):47-60. https://doi.org/10.1111/tpj.12269
Iwata, Aiko ; Tek, Ahmet L. ; Richard, Manon M S ; Abernathy, Brian ; Fonsêca, Artur ; Schmutz, Jeremy ; Chen, Nicolas W G ; Thareau, Vincent ; Magdelenat, Ghislaine ; Li, Yupeng ; Murata, Minoru ; Pedrosa-Harand, Andrea ; Geffroy, Valérie ; Nagaki, Kiyotaka ; Jackson, Scott A. / Identification and characterization of functional centromeres of the common bean. In: Plant Journal. 2013 ; Vol. 76, No. 1. pp. 47-60.
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