Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2005 Jan;15(1):98-110.
doi: 10.1101/gr.3002305. Epub 2004 Dec 8.

Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages

Guillaume Bourque  1 , Evgeny M Zdobnov, Peer Bork, Pavel A Pevzner, Glenn Tesler
Affiliations
Comparative Study

Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages

Guillaume Bourque et al. Genome Res. 2005 Jan.

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.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
(A) Dot-plots of anchors based on UCSC alignments for the mammalian X-chromosome versus chicken Chromosomes 1 and 4. The data are very noisy. Many spurious hits are visible on the plots, and there are additional spurious hits between the mammalian X-chromosome and the other chicken chromosomes (data not shown). These spurious hits were filtered out by GRIMM-Synteny because they did not congeal into a block of sufficiently large size. (B) Dot-plots of genes on the mammalian X-chromosome versus chicken Chromosomes 1 and 4. The data are more sparse but much cleaner than the alignment-based data. There were no spurious hits between the mammalian X-chromosome and the other chicken chromosomes.
Figure 2.
Figure 2.
Ancestral murid rodent ancestor (RA), ancestral mammalian ancestor (MA), and evolutionary tree recovered by MGR using the human, mouse, rat, and chicken genomes. Each genome is represented as an arrangement of 586 synteny blocks computed by GRIMM-Synteny on gene-based data in run gene7. Each synteny block is drawn as one unit, regardless of its length in nucleotides. Chromosomes with too many blocks are split into multiple lines. Each human chromosome is assigned a unique color, and a diagonal line is drawn through the whole chromosome. In other genomes, this diagonal line indicates the relative order and orientation of the rearranged blocks. Black triangles below ancestral chromosomes indicate weak adjacencies. The unrooted phylogram at the top of the figure shows the topology of the evolutionary tree; the last common ancestor of human, mouse, rat, and chicken would be somewhere on the edge between Chicken and MA. The minimum number of rearrangements required to convert between two genomes is shown on each edge of that tree.
Figure 3.
Figure 3.
(A) Four pre-ancestors (marked with *), obtained after carrying out a maximal number of initial inversions, and two putative ancestors (murid rodent ancestor, RA, and mammalian ancestor, MA) for gene-based data in run gene7. Each genome is represented by an arrangement of 311 new synteny blocks obtained after carrying out the initial inversions and condensing the 586 initial four-way blocks. (B) Arrangement of the set of 14 blocks from HSA8p and HSA13, which are contiguous in the pre-ancestors of all species but are found on four different chromosomes in chicken, mouse, and rat. The two putative ancestral arrangements of these blocks, as recovered by MGR, are also shown.
Figure 4.
Figure 4.
Ancestral murid rodent ancestor (RA), ancestral mammalian ancestor (MA), and evolutionary tree recovered by MGR using the human, mouse, rat, and chicken genomes. Each genome is represented as an arrangement of 430 synteny blocks computed by GRIMM-Synteny on sequence-based data in run 300K.
Figure 5.
Figure 5.
(A) Dot-plots of similarity anchors in a four-way synteny block with microrearrangements. The block was computed by GRIMM-Synteny on sequence-based data in run 300K. The block length is 380 kb in human, 340 kb in mouse, 364 kb in rat, and 419 kb in chicken. The anchors divide into nine groups, indicated by different colors; these groups have a different order and orientation in each genome. Within each group, the anchors have the same relative order in all genomes (or an overall flip of the whole group), but their absolute spacing is not preserved. (B) Microrearrangement history for the same block as generated by MGR. The nine colored blocks correspond to the nine groups of anchors in the dot-plots. The minimum number of inversions required to convert between synteny blocks in two genomes is shown on each edge of the tree.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402. - PMC - PubMed
    1. Bafna, V. and Pevzner, P. 1995. Sorting by reversals: Genome rearrangements in plant organelles and evolutionary history of X chromosome. Mol. Biol. Evol. 12: 239-246.
    1. Blanchette, M., Kunisawa, T., and Sankoff, D. 1999. Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol. 49: 193-203. - PubMed
    1. Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smit, A.F., Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D., et al. 2004. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14: 708-715. - PMC - PubMed
    1. Bourque, G. and Pevzner, P.A. 2002. Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Res. 12: 26-36. - PMC - PubMed

Publication types

LinkOut - more resources