RT Journal Article
SR Electronic
T1 The many evolutionary fates of a large segmental duplication in mouse
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 043687
DO 10.1101/043687
A1 Andrew P Morgan
A1 J Matthew Holt
A1 Rachel C McMullan
A1 Timothy A Bell
A1 Amelia M-F Clayshulte
A1 John P Didion
A1 Liran Yadgary
A1 David Thybert
A1 Duncan T Odom
A1 Paul Flicek
A1 Leonard McMillan
A1 Fernando Pardo-Manuel de Villena
YR 2016
UL http://biorxiv.org/content/early/2016/03/15/043687.1.abstract
AB Gene duplication and loss are major sources of genetic polymorphism in populations, and are important forces shaping the evolution of genome content and organization. We have reconstructed the origin and history of a 127 kbp segmental duplication, R2d, in the house mouse (Mus musculus). De novo assembly of both the ancestral (R2d1) and the derived (R2d2) copies reveals that they have been subject to non-allelic gene conversion events spanning tens of kilobases. R2d2 is also a hotspot for structural variation: its diploid copy number ranges from 0 in the mouse reference genome to more than 80 in wild mice sampled from around the globe. Heterozygosity for low‐ and high-copy alleles of R2d2 is associated in cis with meiotic drive, suppression of meiotic crossovers, and copy-number instability, with a mutation rate in excess of 1% per generation in laboratory populations. We identify an additional 57 loci, covering 0.8% of the mouse genome, that have characteristics similar to R2d2: segmental duplication, phylogenetic discordance and low recombination rate. Our results provide a striking example of allelic diversity generated by duplication and demonstrate the value of de novo assembly in a phylogenetic context for understanding the mutational processes affecting duplicate genes.