Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?
- Lutz Froenicke1,9,
- Montserrat Garcia Caldés2,
- Alexander Graphodatsky3,
- Stefan Müller4,
- Leslie A. Lyons1,
- Terence J. Robinson5,
- Marianne Volleth6,
- Fengtang Yang7, and
- Johannes Wienberg4,8
- 1 Department of Population Health & Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California 95616, USA
- 2 Departament de Biologia Cellular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
- 3 ASG–Institute of Cytology and Genetics, SB Russian Academy of Sciences, Novosibirsk, 630090, Russia
- 4 Department Biology II, Human Genetics, Ludwig-Maximilians-University Munich, Martinsried, 82152, Germany
- 5 Evolutionary Genomics Group, Department of Botany & Zoology, University of Stellenbosch, 7602, South Africa
- 6 Department of Human Genetics, Otto-von-Guericke-University Magdeburg, Magdeburg, 39120, Germany
- 7 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
- 8 Institute of Human Genetics, GSF-National Research Center for Environment and Health, Neuherberg, 85764, Germany
This extract was created in the absence of an abstract.
“Excavating” ancestral genomes
The recent release of the chicken genome sequence (Hillier et al. 2004) provided exciting news for the comparative genomics community as it allows insights into the early evolution of the human genome. A bird species can now be used as an outgroup to model early mammalian genome organization and reshuffling. The genome sequence data have already been incorporated in a computational analysis of chicken, mouse, rat, and human genome sequences for the reconstruction of the ancestral genome organization of both a mammalian ancestor as well as a murid rodent ancestor (Hillier et al. 2004; Bourque et al. 2005). This bioinformatic effort joins a molecular cytogenetic model (Richard et al. 2003; Yang et al. 2003; Robinson et al. 2004; Svartman et al. 2004; Wienberg 2004; Froenicke 2005) as the second global approach to explore the architecture of the ancestral eutherian karyotype—a fundamental question in comparative genomics. Since both models use the human genome as reference, they are readily comparable. Surprisingly, however, they share few similarities. Only two small autosomes and the sex chromosomes of the hypothesized ancestral karyotypes are common to both. Unfortunately, given its significance, neither the extent of these differences nor their impact on comparative genomics have been discussed by Bourque and colleagues (2005). In an attempt to redress this, we compare the two methods of ancestral genome reconstruction, verify the resulting models, and discuss reasons for their apparent divergence.
Comparative chromosome painting
The cytogenetic model was developed over the last 10 years and is now based on comparative chromosome painting data from >80 eutherian species (including 50 primates). Comparative chromosome painting (or Zoo-FISH) allows a fast generation of large-scale comparative genome maps in Placentalia (Wienberg et al. 1990; Scherthan et al. 1994). It uses cross-species fluorescence in situ hybridization (FISH) using human or other …
