Reconstruction of karyotype evolution in core Glires. I. The genome homology revealed by comparative chromosome painting Violetta R. Beklemisheva & Svetlana A. Romanenko & Larisa S. Biltueva & Vladimir A. Trifonov & Nadezhda V. Vorobieva & Natalya A. Serdukova & Nadezhda V. Rubtsova & Oleg V. Brandler & Patricia C. M. O’Brien & Fentang Yang & Roscoe Stanyon & Malcolm A. Ferguson-Smith & Alexander S. Graphodatsky Received: 16 February 2011 /Revised: 20 April 2011 /Accepted: 25 April 2011 /Published online: 11 May 2011 # Springer Science+Business Media B.V. 2011 Abstract Glires represent a eutherian clade consisting of rodents and lagomorphs (hares, rabbits, and pikas). Chromosome evolution of Glires is known to have variable rates in different groups: from slowly evolving lagomorphs and squirrels to extremely rapidly evolving muroids. Previous interordinal homology maps between slowly evolving Glires were based on comparison with humans. Here, we used sets of chromosome-specific probes from Tamias sibiricus (Sciuridae), Castor fiber (Castoridae) and humans to study karyotypes of six ground squirrels (genera Marmota and Spermophilus) and one tree squirrel (genus Sciurus), mountain hare (genus Lepus), and rabbit (genus Oryctolagus). These data supplemented with GTG banding comparisons allowed us to build comparative chromosome maps. Our data showed the absence of previously found squirrel associations HSA 1/8 and 2/17 in the Eurasian ground squirrels—sousliks and woodchucks, and dis- ruptions of squirrel HSA 10/13 and HSA 8/4/8/12/22 syntenies in the four Spermophilus species studied here. We found that the karyotypes of Sciuridae and Leporidae are highly conserved and close to the Rodentia ancestral karyotype, while Castoridae chro- mosomes underwent many more changes. We suggest that Lagomorpha and Sciuridae (in contrast to all other rodent families) should be considered as core Glires Chromosome Res (2011) 19:549–565 DOI 10.1007/s10577-011-9210-y Responsible Editor: Herbert Macgregor V. R. Beklemisheva : S. A. Romanenko (*) : L. S. Biltueva : V. A. Trifonov : N. V. Vorobieva : N. A. Serdukova : A. S. Graphodatsky Department of Molecular and Cellular Biology of the Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia e-mail: rosa@mcb.nsc.ru N. V. Rubtsova Institute of Cytology and Genetics, SB RAS, Novosibirsk 630090, Russia O. V. Brandler Koltsov Institute of Developmental Biology, RAS, Moscow 117334, Russia P. C. M. O’Brien : M. A. Ferguson-Smith Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 OES, UK F. Yang Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK R. Stanyon Department of Evolutionary Biology, University of Florence, Florence 50122, Italy