Tracking the complex flow of chromosome rearrangements from the Hominoidea Ancestor to extant Hylobates and Nomascus Gibbons by high-resolution synteny mapping

Abstract

In this study we characterized the extension, reciprocal arrangement, and orientation of syntenic chromosomal segments in the lar gibbon (Hylobates lar, HLA) by hybridization of a panel of approximately 1000 human BAC clones. Each lar gibbon rearrangement was defined by a splitting BAC clone or by two overlapping clones flanking the breakpoint. A reconstruction of the synteny arrangement of the last common ancestor of all living lesser apes was made by combining these data with previous results in Nomascus leucogenys, Hoolock hoolock, and Symphalangus syndactylus. The definition of the ancestral synteny organization facilitated tracking the cascade of chromosomal changes from the Hominoidea ancestor to the present day karyotype of Hylobates and Nomascus. Each chromosomal rearrangement could be placed within an approximate phylogenetic and temporal framework. We identified 12 lar-specific rearrangements and five previously undescribed rearrangements that occurred in the Hylobatidae ancestor. The majority of the chromosomal differences between lar gibbons and humans are due to rearrangements that occurred in the Hylobatidae ancestor (38 events), consistent with the hypothesis that the genus Hylobates is the most recently evolved lesser ape genus. The rates of rearrangements in gibbons are 10 to 20 times higher than the mammalian default rate. Segmental duplication may be a driving force in gibbon chromosome evolution, because a consistent number of rearrangements involves pericentromeric regions (10 events) and centromere inactivation (seven events). Both phenomena can be reasonably supposed to have strongly contributed to the euchromatic dispersal of segmental duplications typical of pericentromeric regions. This hypothesis can be more fully tested when the sequence of this gibbon species becomes available. The detailed synteny map provided here will, in turn, substantially facilitate sequence assembly efforts.

Figure 1.

Examples of FISH experiments on Hylobates lar metaphases using human BAC clones as probes. (a) Three examples of inversions, occuring in Hylobatidae ancestor, in which one of the two breakpoints fall in the centromeric/pericentromeric region. The figure shows the signals of the splitting BAC defining the euchromatic breakpoint. The code, in parenthesis on the right of each BAC name, refers to Supplemental Tables ST1 and ST2, where the BAC precise position on the human sequence is also reported. (b) The two BACs RP11-380J21 (red signal) and RP11-183N22 (green signal) are located, in humans, at chr3:64,053,486–64,212,751 and chr3:4,328,222–4,493,696, respectively, suggesting a rearrangement with respect to humans. On the contrary, the rearrangement occurred in the lineage leading to humans.

Figure 2.

HLA ideogram showing the synteny block correspondence with the human genome. Internal red numbers indicate the human corresponding chromosome. Blue and red arrows indicate concordant (blue) and inverse (red) sequence polarity (orientation) with respect to humans. Black numbers (chromosome) followed by a letter (BAC), on the right, indicate specific BACs as reported in the Supplemental Table S1. Breakpoints in HLA are indicated by red bars (as in Supplemental Table S2). Breaks that occurred in HyA are represented by green bars (see Supplemental Table S1). (∷) Breakage and reunion in HLA and/or HyA, and the most proximal clones are reported. Rearrangements in HSA generate apparent breaks in HLA. These apparent breaks are indicated as clones facing each other (3M/3D, for example).

Figure 3.

Hylobatidae Ancestral karyotype (HyAK). The numbers reported to the right of each chromosome represent arbitrarily chosen landmarks useful in defining the chromosome composition and in facilitating the description of rearrangements. They indicate the extension of each chromosomal arm, according to the data reported in Supplemental Table ST4, first column.

Figure 4.

Hominoidea ancestral karyotype. The number plus letter on the right indicate specific human BACs reported in the Supplemental Table S5. Synteny arrangement differences with respect to humans are only due to peri/paracentric inversions (with the exception of the 2p–2q fusion). These breaks are indicated as clones facing each other (3M/3D, for instance). When a chromosome remained unchanged in humans, its human nomenclature is reported in italics.

Figure 5.

(a) Example of the evolutionary chromosomal changes leading, from Hominoidea ancestor (ANC7 and ANC2q), to chromosomes HyA1 and HyA25 in Hylobatidae ancestor. (b) Shows the inversion in ANC13 necessary to derive HyA8 (see text for details). Numbers followed by a letter on the right of chromosomes indicate a specific human BAC as reported in both ST1 and ST5 Supplemental Tables. The numbers on the right of the final Hylobatidae ancestor chromosome (HyA) represent arbitrarily chosen points useful in indicating its composition, as reported in the ST4 Supplemental Table. Usually, they correspond to a BAC, but when found at the borders of the synteny blocks, they identify two BACs facing each other following a rearrangement. The Hylobatidae Ancestral Kayotype (HyAK) is depicted in Fig. 3.