Reconstruction of Ancestral Genomes

Abstract

Comparative genomics allow hypotheses about the content of the genome of ancestral species and for many major branching points on the tree of life, hypothetical ancestral genomes can be reconstructed. Cross‐species chromosome painting over the last two decades has led the way in the reconstruction of ancestral genomes. Chromosome painting techniques allow to rapidly track chromosome translocations in evolution. A cladistic analysis of syntenies and chromosome associations allows rearrangements to be placed on the evolutionary tree. More recently, assemblies of genome sequences have allowed more far ranging comparisons of vertebrate genome evolution. The in‐situ hybridisation of the deoxyribonucleic acid (DNA) cloned into bacterial artificial chromosome overcomes the limitations of chromosome painting permitting the reconstruction of ancestral marker order along the single chromosome and has revealed that centromeres can reposition during evolution. These reconstructions provide insight into the evolutionary forces that have sculpted the genomes of extant species.

Key Concepts:

  • All forms of life on this planet are connected by descent from common ancestors.

  • Hypothetical ancestral genomes can be reconstructed at various nodes on the tree of life.

  • FISH is the major technique of comparative molecular cytogenetics.

  • Chromosome painting can detect chromosomal homologies even between distantly related mammalian orders.

  • Chromosomal syntenies may often be fragmented but it is highly unlikely that the same syntenic group can be brought together independently in different lineages.

  • Chromosome associations are segments homologous to different human chromosomes that are found contiguously in genomes of other species.

  • Chromosome painting maps are now available for about 200 mammalian species from all eutherian orders.

  • Bioinformatics provided an alternative approach to reconstructing ancestral genomes from the comparison of complete genome assemblies.

  • Integration between molecular cytogenetics, sequencing and bioinformatics will allow even more refined hypotheses about genome evolution.

Keywords: chromosome painting; comparative molecular cytogenetics; phylogenomics; bioinformatics; placental mammals; centromere repositioning; whole genome assemblies

Figure 1.

Reconstruction of the ancestral genome of all living eutherian mammals depicted as conserved and rearranged human chromosomes. Chromosomes are colour coded (lower right) according to their syntenic homology to human chromosomes; the colour code is in the lower right. The number to the right of chromosomes or chromosome segments also indicates human homology. The ancestral genome of placental mammals would have a diploid number of 2n=46. The figure is based on data presented in Graphodatsky et al. and Svartman and Stanyon .

Figure 2.

Reconstruction of the ancestral genome of all living primates depicted as conserved and rearranged human chromosomes. Chromosomes are colour coded (lower right) according to their syntenic homology to human chromosomes; the colour code is in the lower right. The number to the right of chromosomes or chromosome segments also indicates human homology. The primate ancestral genome would have a diploid number of 2n=48. This figure is based on data from Stanyon et al. .

Figure 3.

Reconstruction of the ancestral genome of all living carnivores depicted as conserved and rearranged human chromosome. Chromosomes are colour coded (lower right) according to their syntenic homology to human chromosomes; the colour code is in the upper right. The number to the right of chromosomes or chromosome segments also indicates human homology. The carnivore ancestral genome would have a diploid number of 2n=42. The figure is based on Perelman et al. .

Figure 4.

Reconstruction of the ancestral genome of all living sciurids depicted as conserved and rearranged human chromosomes. Chromosomes are colour coded (lower right) according to their syntenic homology to human chromosomes; the colour code is in the lower right. The number to the right of chromosomes or chromosome segments also indicates human homology. The ancestral genome of sciurids would have a diploid number of 2n=38. It is assumed that the genome of sciurids is very close to the ancestral rodent genome (see text). This figure is based on Li et al. and Romanenko et al. .

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Further Reading

Chauve C and Tannier E (2008) A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. PLoS Computational Biology 4: e1000234.

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How to Cite close
Stanyon, Roscoe, and Bigoni, Francesca(Apr 2013) Reconstruction of Ancestral Genomes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020752.pub2]