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

  1. Mariano Rocchi1,3,
  2. Nicoletta Archidiacono1, and
  3. Roscoe Stanyon2,3
  1. 1 Department of Genetics and Microbiology, University of Bari, Bari 70126, Italy;
  2. 2 Department of Animal Biology and Genetics, University of Florence, Florence 50125, Italy

This extract was created in the absence of an abstract.

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 …

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