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Research Project: Genetic Foundations for Bioenergy Feedstocks

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Title: Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

Author
item Melters, Daniel - University Of California
item Bradnan, Keith - University Of California
item Young, Hugh - University Of California
item Telis, Natalie - University Of California
item May, Michael - University Of California
item Ruby, Graham - University Of California
item Sebra, Robert - Pacific Biosciences Inc
item Peluso, Paul - Pacific Biosciences Inc
item Eid, John - Pacific Biosciences Inc
item Rank, David - Pacific Biosciences Inc
item Garcia, Jose - Universidade Estadual Paulista (UNESP)
item Derisi, Joseph - University Of California
item Smith, Timothy - Tim
item Tobias, Christian
item Ross-ibarra, Jeffrey - University Of California
item Korf, Ian - University Of California
item Chan-simon, W - University Of California

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/30/2013
Publication Date: 1/30/2013
Citation: Melters, D.P., Bradnan, K., Young, H., Telis, N., May, M., Ruby, G.J., Sebra, R., Peluso, P., Eid, J., Rank, D., Garcia, J., Derisi, J., Smith, T.P., Tobias, C.M., Ross-Ibarra, J., Korf, I., Chan-Simon, W. 2013. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biology. doi:10.1186/gb-2013-14-1-r10.

Interpretive Summary: Many questions about centromere repeat evolution remain unanswered. How prevalent are high-copy tandem repeat arrays at the centromeres of different animal and plant species? Studies of centromere DNA in animals and plants have so far focused on single organisms or on small clades and few review articles have been dedicated to a broad survey of tandem repeats. No conserved motif has been found for centromere DNA except in small clades (for example, the CENP-B box found in mammalian centromeres). Are there shared properties among centromeric tandem repeats from diverse animals and plants? In Saccharomyces cerevisiae and closely related yeast species, short centromere DNA sequences evolve three times faster than other intergenic regions of its genome. How rapidly do centromere tandem repeats evolve and which molecular processes govern their evolution? We performed a survey of tandem repeats in a large and phylogenetically diverse set of animal and plant species in order to address these questions.

Technical 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. The assumption that the most abundant tandem repeat is the centromere DNA was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. 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. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and in length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond ~50 million years of divergence.