Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
- 1 Genome Institute of Singapore, Singapore 138672, Republic of Singapore
- 2 European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- 3 Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA
- 4 Department of Mathematics, University of California, San Diego, La Jolla, California 92093, USA
Abstract
Molecular evolution studies are usually based on the analysis of individual genes and thus reflect only small-range variations in genomic sequences. A complementary approach is to study the evolutionary history of rearrangements in entire genomes based on the analysis of gene orders. The progress in whole genome sequencing provides an unprecedented level of detailed sequence data to infer genome rearrangements through comparative approaches. The comparative analysis of recently sequenced rodent genomes with the human genome revealed evidence for a larger number of rearrangements than previously thought and led to the reconstruction of the putative genomic architecture of the murid rodent ancestor, while the architecture of the ancestral mammalian genome and the rate of rearrangements in the human lineage remained unknown. Sequencing the chicken genome provides an opportunity to reconstruct the architecture of the ancestral mammalian genome by using chicken as an outgroup. Our analysis reveals a very low rate of rearrangements and, in particular, interchromosomal rearrangements in chicken, in the early mammalian ancestor, or in both. The suggested number of interchromosomal rearrangements between the mammalian ancestor and chicken, during an estimated 500 million years of evolution, only slightly exceeds the number of interchromosomal rearrangements that happened in the mouse lineage, over the course of about 87 million years.
Footnotes
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[Supplemental material is available online at www.genome.org.]
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↵6 This is especially true for long edges. An alternative approach would be to use a statistical model (Larget et al. 2002), but that would require a different set of assumptions and lead to different drawbacks.
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↵7 Although these ratios depend on the level of microrearrangements tolerated, we found the ratio on the MA-chicken edge to be consistently higher in all runs as compared to the one on other edges.
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↵8 We are using estimated divergence times of 16 milion years ago (Mya) for RA and 87 Mya for MA (Springer et al. 2003) and 310 Mya for birds and mammals (Hedges and Kumar 2004; Reisz and Muller 2004).
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↵9 The “maximal number of initial inversions” is the maximum we found, but there could be an alternative sequence with the same edge length and even more initial inversions.
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↵10 This definition of pre-ancestor differs from the one in Murphy et al. (2003), because the rearrangements performed are only inversions and we use the information about the reconstructed ancestors instead of the notion of “good rearrangement” (Bourque and Pevzner 2002).
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↵11 The number of weak adjacencies that we determine is actually a lower bound because we only explore a subset of all the alternative solutions.
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↵12 The total number of adjacencies is the total number of blocks plus the total number of chromosomes. Adjacencies include both “internal adjacencies” (blocks adjacent within a chromosome) and “external adjacencies” (blocks adjacent to a chromosome end).
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↵13 A topology is said to agree with another if the sets of partitions of leaves defined by the internal edges with at least one rearrangement are the same.
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Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.3002305. Article published online before print in December 2004.
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↵5 Corresponding author. E-mail bourque{at}gis.a-star.edu.sg; fax 65 6478 9058.
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- Accepted October 4, 2004.
- Received July 14, 2004.
- Cold Spring Harbor Laboratory Press
