Molecular refinement of gibbon genome rearrangements

Abstract

The gibbon karyotype is known to be extensively rearranged when compared to the human and to the ancestral primate karyotype. By combining a bioinformatics (paired-end sequence analysis) approach and a molecular cytogenetics approach, we have refined the synteny block arrangement of the white-cheeked gibbon (Nomascus leucogenys, NLE) with respect to the human genome. We provide the first detailed clone framework map of the gibbon genome and refine the location of 86 evolutionary breakpoints to <1 Mb resolution. An additional 12 breakpoints, mapping primarily to centromeric and telomeric regions, were mapped to ∼5 Mb resolution. Our combined FISH and BES analysis indicates that we have effectively subcloned 49 of these breakpoints within NLE gibbon BAC clones, mapped to a median resolution of 79.7 kb. Interestingly, many of the intervals associated with translocations were gene-rich, including some genes associated with normal skeletal development. Comparisons of NLE breakpoints with those of other gibbon species reveal variability in the position, suggesting that chromosomal rearrangement has been a longstanding property of this particular ape lineage. Our data emphasize the synergistic effect of combining computational genomics and cytogenetics and provide a framework for ultimate sequence and assembly of the gibbon genome.[Supplemental material is available online at www.genome.org.]Hominidae (humans and great apes) and, to a lesser extent, Old World monkeys, possess karyotypes closely resembling the hypothetical hominoid ancestor. Most evolutionary chromosomal rearrangements between ape lineages involve pericentric (including the centromere) or paracentric (not including the centromere) inversions (Yunis and Prakash 1982). In contrast, comparative studies of gibbons (small apes, family Hylobatidae) indicate that the karyotypes of all 12 (or more) species appear highly derived, with an unusually large number (n > 40) of chromosomal fissions and translocations (Jauch et al. 1992; Koehler et al. 1995a,b;Muller and Wienberg 2001;Murphy et al. 2001;Nie et al. 2001;Muller et al. 2002Muller et al. , 2003Ferguson-Smith et al. 2005;Froenicke 2005). Their chromosomal numbers range from 2n = 38 (hoolock gibbons) to 2n = 52 (Nomascus) and differ from other ape lineages in showing an accelerated rate of chromosomal translocation during evolution.Gibbons, then, provide a unique perspective of a highly rearranged ape genome with two major advantages: (1) neutrally evolving DNA shows a relatively short genetic distance (<0.05 substitutions/site) to the high-quality human reference sequence; and (2) the gibbon represents a phylogenetic link between the great apes and the Old World monkeys, providing a unique perspective of evolutionary change between 15 and 20 million years of species separation (Goodman 1999). The evolutionary relatedness of human and gibbon species facilitates crossspecies FISH experiments and comparative sequence analyses to provide exquisite resolution in refining evolutionary breakpoints of chromosomal ...

A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons

“…In order to better understand the organization of the karyotype of the last common ancestor of gibbons we compared the karyotypes of HLE, SSY, HLA, and NLE (Roberto et al 2007;Misceo et al 2008; present data) with the karyotype of Hominoidea ancestor ). The analysis showed that 33 rearrangements probably occurred in the gibbon ancestor after its divergence from Hominidae and before gibbon radiation.…”

“…The results for HLE and SSY are summarized in Figures 1 and 2 and below. Data on HLA and NLE have been already reported (Carbone et al 2006;Roberto et al 2007;Misceo et al 2008;Girirajan et al 2009). …”

“…In particular, we took into consideration the Hylobatidae ancestral karyotype proposed by Misceo et al (2008) and the FISH data already published on other gibbon species (Muller et al 2003;Roberto et al 2007;Misceo et al 2008;Girirajan et al 2009). …”

“…We compared the mapping position of HLE and SSY centromeres with respect to NLE, HLA, and Hominoidea ancestor (Roberto et al 2007;Misceo et al 2008;Stanyon et al 2008) in search of potential ENCs. The comparison showed that six hoolock and three siamang chromosomes harbor an ENC.…”

“…Molecular cytogenetic techniques now allow a significantly higher resolution than chromosome painting through the use of hybridization of precisely mapped BAC clones, microarrays, and selective sequencing. Using these approaches we recently defined the chromosomal changes and synteny block organization of Hylobates lar (HLA, lar gibbon) and Nomascus leucogenys (NLE, white-cheeked gibbon) (Carbone et al 2006;Roberto et al 2007;Misceo et al 2008;Girirajan et al 2009). Yet, the reconstruction of the evolutionary history of rearrangements is only as complete as the taxonomic array of relevant species.…”