Stability of Large Segmental Duplications in the Yeast Genome

Abstract

The high level of gene redundancy that characterizes eukaryotic genomes results in part from segmental duplications. Spontaneous duplications of large chromosomal segments have been experimentally demonstrated in yeast. However, the dynamics of inheritance of such structures and their eventual fixation in populations remain largely unsolved. We analyzed the stability of a vast panel of large segmental duplications in Saccharomyces cerevisiae (from 41 kb for the smallest to 268 kb for the largest). We monitored the stability of three different types of interchromosomal duplications as well as that of three intrachromosomal direct tandem duplications. In the absence of any selective advantage associated with the presence of the duplication, we show that a duplicated segment internally translocated within a natural chromosome is stably inherited both mitotically and meiotically. By contrast, large duplications carried by a supernumerary chromosome are highly unstable. Duplications translocated into subtelomeric regions are lost at variable rates depending on the location of the insertion sites. Direct tandem duplications are lost by unequal crossing over, both mitotically and meiotically, at a frequency proportional to their sizes. These results show that most of the duplicated structures present an intrinsic level of instability. However, translocation within another chromosome significantly stabilizes a duplicated segment, increasing its chance to get fixed in a population even in the absence of any immediate selective advantage conferred by the duplicated genes.

Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes

“…Junctions of segmental duplications frequently contain either microsatellites or transposable elements. The stability of these segmental duplications during meiosis and mitosis was shown to rely both on the size of the duplication and on its structure (257). Replication-based mechanisms leading to segmental duplications FIG.…”

Duplicate Retention After Small‐ and Large‐Scale Duplications

“…The most common mechanisms are believed to be unequal crossing over (leading to tandemly arranged duplicates), slippage of the DNA polymerase during replication of, and duplicative retrotransposition (Bailey et al, 2003;Kondrashov and Kondrashov, 2006), but many other mechanisms are known (Koszul et al, 2006), and some organisms (e.g., Caenorhabditis elegans) seem to harbor as yet uncharacterized duplicative processes (Katju and Lynch, 2003;Koszul et al, 2006). Most of the time, these processes result in duplication of relatively short stretches of DNA, spanning one or a few genes or only part of a gene.…”

Ancient, recurrent phage attacks and recombination shaped dynamic sequence-variable mosaics at the root of phytoplasma genome evolution

“…Spanning genome locations 357003.382562 and 398072.423447, the LSD encompasses four clustered phage remnants and contains 56 ORFs. LSDs frequently occur in eukaryotic genomes and play an important role in genome evolution (40,41). The AYWB and OYM prophage genomic islands were further distinguished from their respective host DNAs on the basis of differential dinucleotide relative abundance (DRA) ( Table 2 and Table S3), a unique signature of an organism's DNA that has been exploited in studies of genomic heterogeneity and lateral gene transfer (42,43).…”