This guest post is by Paul Bilinski on his paper with coauthors Diversity and evolution of centromere repeats in the maize genome BioRxived here.
Centromeres have the potential to play a central role in speciation, yet our ability to study them has been limited because of their repetitive nature. The centromeres of many eukaryotes consist partly of large arrays of short tandem repeats, though the actual sequence of the repeat varies widely across taxa. To investigate the whether the variation found in the tandem repeats themselves could inform our understanding of their evolutionary history we made use of the reference maize genome as well as resequencing data from several lines of maize and its wild relative teosinte.
Although tandem repeats should be identical upon duplication, our analysis of CentC in maize revealed that most copies genome-wide are unique. We observed only three instances where adjacent copies were identical in sequence and length, driving home the idea that these tandem repeats have accumulated immense diversity. Given such diversity, we wanted to investigate genetic relatedness across CentC copies.
Using positional and genetic relatedness information from the fully-sequenced centromeres 2 and 5, we found high within-cluster similarity, suggesting that tandem duplications drove most CentC copy number increase. Contrary to patterns seen in Arabidopsis (Kawabe and Nasuda 2005), principle coordinate analysis of repeats found no clustering by chromosome, with groups of CentC with similar sequence distributed across all of the chromosomes.
Another surprising discovery involved the origin of the biggest arrays of CentC. As an ancient tetraploid maize originally had 20 chromosomes with 20 centromeres. Processes of fractionation and rearrangement have led to the 10 chromosomes in the extant maize genome. Schnable et al (2011) were able to identify which chromosomal segments derive from each of maize’s ancient parents, referred to as subgenomes one and two. Wang and Bennetzen (2011) built on this information, and found that about half of the modern centromeres came from each parent. Inferring subgenome of origin by flanking regions, we found that all of the CentC clusters >20kb in length derive from subgenome 1. The proportions are less skewed when looking at clusters >10kb, though in all cases we see more bp of CentC assigned to subgenome 1 than we expect based on its total bp in the genome. This is particularly interesting because subgenome 1 also shows higher overall gene expression and fewer deletions than subgenome two (Schnable et al 2011).
The diversity of CentC seen might suggest that CentC repeats were reasonably static in the genome, persisting in the same spot for a long time with occasional increases in copy number via tandem duplication. However, fluorescent in situ hybridization suggested that domestication resulted in a large loss of CentC signal across many of maize’s 10 chromosomes. We confirmed and quantified the loss of CentC using resequencing data from a set of maize and teosinte lines (Chia et al. 2012).
Combined, our results suggest long term stability of CentC clusters with new copies arising from tandem duplication, while mutation serves to homogenize rather than separate clusters. We hope our insights into centromere repeat evolution will build toward a better understanding of their role in evolution.