Ancestral genomes reconstruction: An integrated, multi-disciplinary approach is needed

A major tenet of Darwin’s theory of evolution, which will soon celebrate its 150 anniversary, is that all extant species share common ancestors, which are more or less distant in time. Over the last half century the ascent of genetics has given us many new tools to investigate the evolution of species. Advances in molecular cytogenetics, sequencing, and bioinformatics now allow hypotheses about the origin of the human genome. Molecular cytogenetics provided the first reconstructions of ancestral genomes (Wienberg and Stanyon 1995, 1997; Chowdhary et al. 1998). Chromosome flow sorting followed by DOP-PCR leads to reciprocal and multi-directional chromosome painting between all extant placental mammal orders. The results permitted hypotheses about the architecture and content of the ancestral placental mammalian karyotype, which have proved to be amazingly heuristic (Chowdhary et al. 1998; Glas et al. 1999; Froenike et al. 2003; Murphy et al. 2003; Richard et al. 2003; Yang et al. 2003; Svartman et al. 2004). Bioinformatics provided an alternative approach to reconstructing ancestral genomes (Bourque and Pevzner 2002). In a recent paper in Science, Murphy et al. (2005) made a systematic and comprehensive use of Bourque and Pevzner’s algorithm to reconstruct ancestral genomes essentially from data based on a Radiation Hybrids (RH) map of seven species. While confirming many of the conclusions from molecular cytogenetics about the Boreoeutherian ancestral genome, they proposed five additional syntenic associations that had apparently gone undetected by chromosome painting. These contrasting results lead to the March 2006 Forum in this journal highlighting the difference between these two approaches (Bourque et al. 2006; Froenicke et al. 2006). Now, in this issue of Genome Research, Ma et al. (2006) present a new bioinformatic algorithm for sequence analysis and reconstruct the Contiguous Ancestral Regions (CAR) of the Boreoeutherian ancestor at a 50-kb resolution. Their research takes full advantage of the “Comparative Genomics” tracks, present in the UCSC Genome Database (http://genome.ucsc.edu) and exploits the complete sequence assemblies of human, dogs, rat, and mouse, using opossum and chicken as outgroups. The Ma et al. (2006) algorithm provides an exceptionally valuable tool especially in view of the increase in the number of sequenced mammalian genomes that will become available in the near future (http://www.genome.gov). It is important to note that the reconstruction of ancestral genomes is not a mere jigsaw puzzle. Studies of phenomena affecting genome architecture such as chromosomal rearrangements, breakpoints, segmental duplications, and repositioning of centromeres are of crucial importance not only toward a full understanding of the forces that shaped our genome, but also in elucidating a growing number of pathologies directly or indirectly linked to features of genome architecture (Giglio et al. 2001; Armengol et al. 2003; Ventura et al. 2003; Bailey et al. 2004a; Lupski and Stankiewicz 2005; Murphy et al. 2005; Bailey and Eichler 2006; Kato et al. 2006). In this context, the Ma et al. (2006) work represents an important methodological improvement toward the reconstruction of the ancestral chromosomal architecture of Boreoeutherian mammals and understanding the origin of the human genome. From the Forum discussion it was clear that cytogenetics and bioinformatics, unfortunately, do not communicate well with each other. It is our contention that the point is not which approach is better, but how a closer collaboration could be highly productive. Indeed, the Ma et al. (2006) results have removed many of the apparent differences between the two approaches and show a significant convergence with the chromosome painting for the ancestral syntenies present in the Boreoeutherian ancestor. The advantages of the Ma et al. (2006) approach is that it presents a view of intrachromosomal genome architecture lacking chromosome painting. It has a higher resolution for ancestral genome reconstruction and mitigates the potential inaccuracy of RH maps for close markers (Matise et al. 2002). However, it should be noted that three of the four species used by Ma et al. (2006), mouse, rat, and dog, are known to have the most rapidly evolving genomes of all mammals. These species are not optimal for phylogenomic reconstruction because high evolutionary rates make convergence more likely. High evolutionary rates often compound problems of discerning the ancestral states, because it is more difficult to distinguish homology from homoplasy. There are still only a small number of complete genome assemblies available, and, unfortunately, for the immediate future, the number of fully sequenced, phylogenetically appropriate genomes will continue to be limited. Another shortcoming to the Ma et al. (2006) method is that it assumes that the phylogeny is known. However, recent publications indicate that placental mammal phylogeny is still an open question. Inconsistencies in results between cytogenetics and bioinformatics point out opportunities to reciprocally test hypotheses and improve ancestral genome reconstructions. For example, the ancestral associations predicted by Murphy et al. (2005) (1/22, 5/19, 2/18, 1/10, 20/2), not found in the painting reconstructions, are now rejected by Ma et al. (2006). However, Ma et al. (2006) did not recover the ancestral association 7/16 supported both by molecular cytogenetics and Murphy et al. (2005). Instead, their results show that the synteny of human 16 was conserved in the ancestor. This conclusion is not supported by any other publication. The most likely hypothesis is that 16p and 16q were still separate in the primate ancestor and only fused in the last common ancestor of Old World monkeys, apes, and humans (Misceo et al. 2003). Indeed, their first weakly supported join on 3Corresponding authors. E-mail rocchi@biologia.uniba.it; fax 39-080-544.3371. E-mail roscoe.stanyon@unifi.it; fax 39-055-274.3017. Article published online before print. Article and publication date are at http:// www.genome.org/cgi/doi/10.1101/gr.5687906. Perspective