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

Abstract

Centromeres are composed of long arrays of satellite repeats in most multicellular eukaryotes investigated to date. The satellite repeat-based centromeres are believed to have evolved from "neocentromeres" that originally contained only single-or low-copy sequences. However, the emergence and evolution of the satellite repeats in centromeres has been elusive. Potato (Solanum tuberosum) provides a model system for studying centromere evolution because each of its 12 centromeres contains distinct DNA sequences, allowing comparative analysis of homoeologous centromeres from related species. We conducted genome-wide analysis of the centromeric sequences in Solanum verrucosum, a wild species closely related to potato. Unambiguous homoeologous centromeric sequences were detected in only a single centromere (Cen9) between the two species. Four centromeres (Cen2, Cen4, Cen7, and Cen10) in S. verrucosum contained distinct satellite repeats that were amplified from retrotransposon-related sequences. Strikingly, the same four centromeres in potato contain either different satellite repeats (Cen2 and Cen7) or exclusively single-and low-copy sequences (Cen4 and Cen10). Our sequence comparison of five homoeologous centromeres in two Solanum species reveals rapid divergence of centromeric sequences among closely related species. We propose that centromeric satellite repeats undergo boom-bust cycles before a favorable repeat is fixed in the population.

Endogenous pararetrovirus sequences associated with 24 nt small RNAs at the centromeres of Fritillaria imperialis L. (Liliaceae), a species with a giant genome

“…This has been reported for heterochromatin in maize ( Zea mays ) and centromeric repeats in other grasses (Kanizay and Dawe, ; Kanizay et al ., ). It also agrees with the theory of ‘boom–burst’ cycles in the evolution of centromere sequences (Zhang et al ., ).…”

Amplification and adaptation of centromeric repeats in polyploid switchgrass species

“…The two consensus sequences constructed using these two different methods were identical for each repeat. The cenH3 enrichment for each repeat was determined as described in previous reports (Gong et al ., ; Zhang et al ., ). The annotation of Pv1, Pv2, Pv29, Pv36, Pv45, Pv115, Pv118 and Pv156 were conducted using Repbase (Kohany et al ., ).…”

‘Satellite DNA transcripts have diverse biological roles in Drosophila’

“…Considering functional role on one hand, and the fast rate of satDNA turnover in the other (for example, Zhang et al, 2014;Gallach, 2014), it is possible that incompatibilities between satRNAs from one species and chromatin remodeling proteins or chromosome-specific targets (as those involved in centromere function or dosage compensation) from the other may cause genomic instabilities in hybrids, thus contributing for the speciation process (Henikoff et al, 2001;Ferree and Barbash, 2009;Barbash 2010;Brown and O'Neill, 2010).…”