Identification and characterization of functional centromeres of the common bean

Abstract

SUMMARYIn 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.

Holocentromeres inRhynchosporaare associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin

“…The identified Tyba arrays were found to be rather small, varying from 3 to 16 kb. As typical for centromeric satDNAs (25,33), we found the Tyba arrays forming high-order repeat (HOR) structures. Pentamers (830-870 bp) were the most frequent HORs in all BACs analyzed, whereas dimers (∼344 bp) were found only occasionally in two BACs (8P1 and 23M1) (SI Appendix, Table S2).…”

Epigenetic Analyses and the Distribution of Repetitive DNA and Resistance Genes Reveal the Complexity of Common Bean (<b><i>Phaseolus vulgaris</i></b> L., Fabaceae) Heterochromatin

“…A similar pattern of methylation was observed in the centromeric heterochromatin of P. vulgaris which was hypomethylated and surrounded by pericentromeric heterochromatin rich in 5mC. The association with common bean centromere-specific histone H3 (PvCENH3) or maybe the absence of specific CG, CHG, and CHH sites in the centromeric satellite sequences CentPv1 and CentPv2 [Iwata et al, 2013] may be responsible for this hypomethylation.…”

“…This heterochromatin is primarily located in pericentromeric blocks composed of different types of sequences that appear to have evolved independently in the genus [Fonsêca and Pedrosa-Harand, 2013]. In addition, the satellite sequences CentPv1 and CentPv2 are located at centromeres and associated with centromeric function [Iwata et al, 2013].…”

Boom-Bust Turnovers of Megabase-Sized Centromeric DNA inSolanumSpecies: Rapid Evolution of DNA Sequences Associated with Centromeres

“…For example, all human centromeres contain the 171-bp a-satellite repeat, ranging from several hundreds of kilobases to a few megabases (Willard and Waye, 1987;Vafa and Sullivan, 1997). However, several species contain multiple satellite repeats associated with different centromeres, including chicken (Gallus gallus) (Shang et al, 2010), pea (Pisum sativum) , potato (Gong et al, 2012), and common bean (Phaseolus vulgaris) (Iwata et al, 2013). Our results from the two Solanum species are in favor of the concept that a centromeric satellite repeat may emerge initially in a single centromere and then spread to all centromeres.…”