The evolution of centromeric satellite repeats in maize

Abstract

Corn is an important agricultural crop and an excellent model organism for genetic studies. A better understanding of corn centromeres will help in the design of artificial chromosomes that may be used to further improve the corn germplasm in the future. The tandem repeat CentC (156 nucleotides long) has been shown by fluorescent in situ hybridization to be limited to the centromeric regions. Little is known about its function there or how CentC evolves in different maize lines. The maize inbred B73 genome has been sequenced and to date over 10,000 copies of CentC have been described in this line. I have begun to characterize the CentC repeats of the inbred Mo17 and will use the B73 reference genome to extrapolate the evolutionary history of CentC in maize. A total of 92,112 base pairs of CentC and their junctions with non-CentC sequence were cloned and sequenced. Similar to the alpha satellite repeat in primates, there were many higher order repeats found within the CentC islands. However, unlike the alpha satellite repeat, not many were homogenous within a certain island. Unlike the AtCon sequence, there were no distinct conserved regions within the repeat. And unlike CentO found in rice, there were no other CentC-like types found other than CentC. In this work, I have shown the presence of higher order repeats in CentC which provides an idea of the size by which CentC islands grow. By looking at the nucleotide differences between the CentC islands of two inbreds I was able to determine the releative age of the higher order repeats. I have also shown that a single CentC monomer can be lost in a CentC island and that retrotransposon insertions into the CentC island are rampant. I was also able to compare centromeric and non-centromeric CentC islands from the same inbred. While there were differences between the two, more study is required to come to definite conclusions about the sequence differences. While resequencing a CentC-containing BAC, confusing results revealed the possible instability of CentC-rich BAC clones.