Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments - PubMed (original) (raw)

Comparative Study

. 2004 Jan 14;23(1):234-43.

doi: 10.1038/sj.emboj.7600024. Epub 2003 Dec 18.

Affiliations

Comparative Study

Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments

Romain Koszul et al. EMBO J. 2004.

Abstract

There is growing evidence that duplications have played a major role in eucaryotic genome evolution. Sequencing data revealed the presence of large duplicated regions in the genomes of many eucaryotic organisms, and comparative studies have suggested that duplication of large DNA segments has been a continuing process during evolution. However, little experimental data have been produced regarding this issue. Using a gene dosage assay for growth recovery in Saccharomyces cerevisiae, we demonstrate that a majority of the revertant strains (58%) resulted from the spontaneous duplication of large DNA segments, either intra- or interchromosomally, ranging from 41 to 655 kb in size. These events result in the concomitant duplication of dozens of genes and in some cases in the formation of chimeric open reading frames at the junction of the duplicated blocks. The types of sequences at the breakpoints as well as their superposition with the replication map suggest that spontaneous large segmental duplications result from replication accidents. Aneuploidization events or suppressor mutations that do not involve large-scale rearrangements accounted for the rest of the reversion events (in 26 and 16% of the strains, respectively).

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Figures

Figure 1

Figure 1

Intra- and interchromosomal duplications of large DNA segments from the right arm of chromosome XV. Left panels show PFGE and hybridizations of the corresponding Southern blots with various ORFs whose names are indicated above each lane. Chromosomes XV and VII comigrate in the parental strain, resulting in a band with a double intensity on the gel. Relevant chromosome numbers are indicated, and the white arrowheads show the position of the modified or additional chromosomes in the karyotypes. Right panels represent CGH-array profiles with the _X_-axes consisting either in the ORFs from the right arm of chromosome XV ordered from YOR001w to YOR394w (A, C and D) or in all yeast ORFs ordered from the left telomere of chromosome I to the right telomere of chromosome XVI (B). The _Y_-axes correspond to the genomic ratios calculated between the revertant and the parental strains. Scale ranges from −0.5 to +1.5 (A, C and D) and from −1 to +2 (B). The position of RPL20B (YOR312c) is indicated by the dotted line. The last duplicated ORFs on each side of the blocks are mentioned (A, C and D). In (C) and (D), a schematic representation of the chromosomes involved in the interchromosomal duplication–translocation events is shown. (A) Representative revertant strains from class I. The sizes of the duplicated segments are indicated in parentheses and range from 41 to 288 kb. (B) Revertant strains from class II. Black and open circles on the _X_-axes of the array profiles symbolize single and duplicated centromeres, respectively. (C) Class III strain YKF1036. VtXV means a translocation of the right arm of chromosome XV onto chromosome V. (D) Class III strain YKF1246. IIItXV and XVtIII mean a translocation of the right arm of chromosomes XV and III onto chromosomes III and XV, respectively. The ORFs YCR027c and YCR028c flank the translocation breakpoint onto chromosome IIItXV.

Figure 2

Figure 2

Direct tandem organization of an intrachromosomal duplicated segment visualized by molecular combing. Molecular combing of the genomic DNA of the parental strain (top) and of YKF1022 (bottom) performed with fluorescent probes derived from recombinant cosmids 130, 1338, 488, 323 and 183 of chromosome XV (Tettelin et al, 1998). Red and green colors correspond to biotin- and digoxigenin-labeled probes, respectively. The succession of the colored signals reveals that the segmental duplication of approximately 100 kb (extending from YOR272w up to YOR328w as deduced from CGH) is oriented as a direct tandem. These patterns were analyzed on nine and 12 different DNA molecules for the WT and the YKF1022 strains, respectively.

Figure 3

Figure 3

Segmental duplication breakpoints: (A) microsatellites junctions; (B) microhomology junctions; and (C) transposon-related junctions. Gray boxes represent the localization of the junctions. For intrachromosomal events (Intra), the top and bottom sequences are the flanking telomere- and centromere-proximal sequences of the junctions, respectively. For interchromosomal duplications (Inter), top sequences correspond to the centromere-containing chromosomes whereas bottom sequences represent the right arm of chromosome XV. Sequences of the junctions are italicized in the middle lines. Microhomology regions flanking the junctions are underlined. The genetic elements involved in the junctions are mentioned below the coordinates, and the frame is specified when the breakpoint occurred within an ORF. Empty boxes on the schematic representations represent the sequenced left and right borders of some intrachromosomal duplicated blocks. In these sequences, no change was found compared to the corresponding WT sequences.

Figure 4

Figure 4

Mapping of duplicated segment end points relative to both the replication timing curve and the genetic elements of the region. (Top) Replication time data are from Raghuraman et al (2001). The _X_-axis represents a part of the right arm of chromosome XV, extending from YOR107w up to the telomere. Red diamonds symbolize replication origins with their prediction confidence level, ranging from 1 (poor confidence value) to 9 (strong confidence value), indicated in the right _Y_-axis. T's within shaded columns symbolize the major replication termination sites flanking RPL20B. Blue arrowheads are for LTRs, and oriented rectangles stand for full-length Ty elements. Red bars correspond to runs of A/T longer than 14 base pairs. Red void triangles represent GTT/AAC trinucleotide repeats longer than three units. (Bottom) Duplicated segments are symbolized by the colored lines according to the type of sequences found at their junctions: red for microsatellites, green for microhomology and blue for transposable elements. Arrowheads indicate that the segment extends to the telomere. Interchromosomal events are indicated by upper diagonals with chromosome names. The vertical black line indicates the position of YOR312c (RPL20B). Two segmental duplication events were respectively found four and 10 times.

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