A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons

Abstract

Chromosome rearrangements in small apes are up to 20 times more frequent than in most mammals. Because of their complexity, the full extent of chromosome evolution in these hominoids is not yet fully documented. However, previous work with array painting, BAC-FISH, and selective sequencing in two of the four karyomorphs has shown that highresolution methods can precisely define chromosome breakpoints and map the complex flow of evolutionary chromosome rearrangements. Here we use these tools to precisely define the rearrangements that have occurred in the remaining two karyomorphs, genera Symphalangus (2n = 50) and Hoolock (2n = 38). This research provides the most comprehensive insight into the evolutionary origins of chromosome rearrangements involved in transforming small apes genome. Bioinformatics analyses of the human-gibbon synteny breakpoints revealed association with transposable elements and segmental duplications, providing some insight into the mechanisms that might have promoted rearrangements in small apes. In the near future, the comparison of gibbon genome sequences will provide novel insights to test hypotheses concerning the mechanisms of chromosome evolution. The precise definition of synteny block boundaries and orientation, chromosomal fusions, and centromere repositioning events presented here will facilitate genome sequence assembly for these close relatives of humans.

Comprehensive Analyses of White-Handed Gibbon Chromosomes Enables Access to 92 Evolutionary Conserved Breakpoints Compared to the Human Genome

“…Additionally, ∼ 98.9% of the breakpoints are localized in CNVs, while only 50% of them are colocalized with SDs. This finding is in concordance with Carbone et al [2006] who analyzed 100 ECBs in gibbons with a resolution of 200 kb and found that 46% of these breakpoints correspond to SDs with respect to the [Carbone et al, 2009;Capozzi et al, 2012]. Recent molecular data by Wilson et al [2015] further underline the correlation and colocalization of CNVs, common fragile sites (CFSs), as well as ECBs.…”

“…Even in the age of next-generation-sequencing, balanced and complex rearrangements as well as repetitive heterochromatic regions and CNVs cannot unambiguously be resolved by an exclusive use of these modern approaches. Therefore, comparative chromosome painting of HSA and HLA provides a necessary overview on the extensive diversity within this group, such as chromosome numbers, composition of syntenic blocks, and type of translocations [Capozzi et al, 2012]. CNVs and fast mapping of euchromatic breakpoints is accomplished by the here applied approach of array painting.…”

“…So far, no excessive analysis of HLA samples using aCGH has been accomplished. The higher resolution of this method should generate a more complete picture than cytogenetics or molecular cytogenetics alone and is also able to detect submicroscopic, previously hidden, rearrangements [Gribble et al, 2009;Capozzi et al, 2012;Liehr et al, 2013].…”

Novel variable number of tandem repeats of gibbon MAOA gene and its evolutionary significance

“…One of the interesting primates in terms of VNTR polymorphisms is gibbon, a small ape found in South and Southeast Asia (Matsudaira and Ishida 2010;Meyer et al 2012). Evolution of gibbon was rapid, and it diverged from humans approximately 17-23 million years ago (Capozzi et al 2012). The rate of chromosomal arrangements in gibbons is 10-20 times faster than the standard mammalian rate (Misceo et al 2008).…”

Karyotype Evolution in the Horseshoe Bat <b><i>Rhinolophus sedulus</i></b> by Whole-Arm Reciprocal Translocation (WART)

“…If we assume an all-metacentric karyotype with 32 chromosomes also for the ancestor of the trifoliatus group, the only mode of rearrangement which could change arm combinations in a single step is WART. It is a remarkable parallelism that in the Hylobatidae, one of the mammalian taxa with the highest rate of chromosomal rearrangements [Capozzi et al, 2012], the karyotypes of 2 sibling species, i.e. H. agilis from Sumatra and H. albibarbis from Borneo (a former subspecies of H. agilis ), also differ by a WART [Hirai et al, 2005].…”