Centromeric tandem repeats: features common to 282 plant and animal species

Tandem Repeats at Centromeres

“It is important to have the validation (or not) of many concepts about satellite DNA evolution developed in the pre-genomic era, now testing whole genome sequences from a large survey of different species and repeat families all analysed comparatively with different sequencing strategies in a single and massive work.” writes Guto Kuhn at Universidade Federal de Minas Gerais, Belo Horizonte, Brasil, a collaborator with the molecular cytogenetics group – in pointing out an important paper from Melters et al. “In this paper, they analysed centromeric tandem repeats from 282 species (animals and plants) and included Long Pacific Biosciences reads into their analysis. I found particularly interesting the use of PacBio reads to undestand homogenization of repeat variants, including verification of higher order organization. It is important to have validation in a single work with a large survey of different species and repeat families. There is a very informative video showing a talk by Simon Chan explaining their work:

http://aa314.o1.gondor.io/webinar/what-can-long-reads-tell-us-about-centromere-evolution/ ”

Melters, D., Bradnam, K., Young, H., Telis, N., May, M., Ruby, J., Sebra, R., Peluso, P., Eid, J., Rank, D., Garcia, J. F., DeRisi, J., Smith, T., Tobias, C., Ibarra, J. R., Korf, I., & Chan, S. (2013). Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biology, 14 (1), R10+. URL http://dx.doi.org/10.1186/gb-2013-14-1-r10 or http://genomebiology.com/content/pdf/gb-2013-14-1-r10.pdf

Sadly, the last author, Simon W -L Chan, passed away in August 2012, from an autoimmune liver disease. I heard the tragic news while I was also lying is hospital two months after coming down with hepatitis and similar symptoms. Simon’s outstanding work will live on forever, and I hope our lab can build on his remarkable discoveries and experiments not only regarding repetitive DNA, but also about generation of haploid plants by chromosome elimination using mutations in CENH3 gene (Ravi, M., & Chan, S. W. L. (2010). Haploid plants produced by centromere-mediated genome elimination. Nature, 464 (7288), 615-618. URL http://dx.doi.org/10.1038/nature08842). I am honoured to have known him and been able to discuss research with him in the past.

http://genomebiology.com/content/pdf/gb-2013-14-1-r10.pdf

Local link to provisional PDF/online-first (please check if the final paginated version appears)

Abstract:

Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data.RESULTS:Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. We assumed that the most abundant tandem repeat is the centromere DNA, which was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution.CONCLUSIONS:While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animal and plant genomes. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes.

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