title: High Quality Maize Centromere 10 Sequence Reveals Evidence of Frequent Recombination Events.
abstract: The ancestral centromeres of maize contain long stretches of the tandemly arranged CentC repeat. The abundance of tandem DNA repeats and centromeric retrotransposons (CR) has presented a significant challenge to completely assembling centromeres using traditional sequencing methods. Here, we report a nearly complete assembly of the 1.85 Mb maize centromere 10 from inbred B73 using PacBio technology and BACs from the reference genome project. The error rates estimated from overlapping BAC sequences are 7 × 10(-6) and 5 × 10(-5) for mismatches and indels, respectively. The number of gaps in the region covered by the reassembly was reduced from 140 in the reference genome to three. Three expressed genes are located between 92 and 477 kb from the inferred ancestral CentC cluster, which lies within the region of highest centromeric repeat density. The improved assembly increased the count of full-length CR from 5 to 55 and revealed a 22.7 kb segmental duplication that occurred approximately 121,000 years ago. Our analysis provides evidence of frequent recombination events in the form of partial retrotransposons, deletions within retrotransposons, chimeric retrotransposons, segmental duplications including higher order CentC repeats, a deleted CentC monomer, centromere-proximal inversions, and insertion of mitochondrial sequences. Double-strand DNA break (DSB) repair is the most plausible mechanism for these events and may be the major driver of centromere repeat evolution and diversity. In many cases examined here, DSB repair appears to be mediated by microhomology, suggesting that tandem repeats may have evolved to efficiently repair frequent DSBs in centromeres.
authors.affiliation: Department of Molecular Biosciences and Bioengineering, University of Hawaíi at Mānoa Honolulu, HI, USA.
authors.forename: Thomas K
authors.initials: TK
authors.lastname: Wolfgruber
authors.affiliation: Department of Molecular Biosciences and Bioengineering, University of Hawaíi at Mānoa Honolulu, HI, USA.
authors.forename: Megan M
authors.initials: MM
authors.lastname: Nakashima
authors.affiliation: Department of Molecular Biosciences and Bioengineering, University of Hawaíi at Mānoa Honolulu, HI, USA.
authors.forename: Kevin L
authors.initials: KL
authors.lastname: Schneider
authors.affiliation: Department of Molecular Biosciences and Bioengineering, University of Hawaíi at Mānoa Honolulu, HI, USA.
authors.forename: Anupma
authors.initials: A
authors.lastname: Sharma
authors.affiliation: Department of Molecular Biosciences and Bioengineering, University of Hawaíi at Mānoa Honolulu, HI, USA.
authors.forename: Zidian
authors.initials: Z
authors.lastname: Xie
authors.affiliation: Division of Biological Sciences, University of Missouri Columbia, MO, USA.
authors.forename: Patrice S
authors.initials: PS
authors.lastname: Albert
authors.affiliation: Department of Molecular Biosciences and Bioengineering, University of Hawaíi at Mānoa Honolulu, HI, USA.
authors.forename: Ronghui
authors.initials: R
authors.lastname: Xu
authors.affiliation: Department of Plant Sciences, University of California Davis Davis, CA, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Bilinski
authors.affiliation: Department of Plant Biology, University of Georgia Athens, GA, USA.
authors.forename: R Kelly
authors.initials: RK
authors.lastname: Dawe
authors.affiliation: Department of Plant Sciences, University of California Davis Davis, CA, USA.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Ross-Ibarra
authors.affiliation: Division of Biological Sciences, University of Missouri Columbia, MO, USA.
authors.forename: James A
authors.initials: JA
authors.lastname: Birchler
authors.affiliation: Department of Molecular Biosciences and Bioengineering, University of Hawaíi at Mānoa Honolulu, HI, USA.
authors.forename: Gernot G
authors.initials: GG
authors.lastname: Presting
keywords: DNA damage repair; DNA loss at centromeres; centromere evolution; hemicentric inversion; illegitimate recombination