Rapid emergence of independent "chromosomal lineages" in silvered-leaf monkey triggered by Y/autosome translocation

Abstract

Sex/autosome translocations are rare events. The only known example in catarrhines is in the silvered-leaf monkey. Here the Y chromosome was reciprocally translocated with chromosome 1. The rearrangement produced an X₁X₂Y₁Y₂ sex chromosome system. At least three chromosomal variants of the intact chromosome 1 are known to exist. We characterized in high resolution the translocation products (Y₁ and Y₂) and the polymorphic forms of the intact chromosome 1 with a panel of more than 150 human BAC clones. We showed that the translocation products were extremely rearranged, in contrast to the high level of marker order conservation of the other silvered-leaf monkey chromosomes. Surprisingly, each translocation product appeared to form independent "chromosome lineages"; each having a myriad of distinct rearrangements. We reconstructed the evolutionary history of the translocation products by comparing the homologous chromosomes of two other colobine species: the African mantled guereza and the Indian langur. The results showed a massive reuse of breakpoints: only 12, out of the 40 breaks occurred in domains never reused in other rearrangements, while, strikingly, some domains were used up to four times. Such frequent breakpoint reuse if proved to be a general phenomenon has profound implications for mechanisms of chromosome evolution.

Figure 1

Examples of FISH experiments. All the BAC clones used in the FISH experiments belong to the RP11 BAC library. (a) The FISH signals of the two BACs RP11-932B11 (chr5:53,947,332-54,140,932) and RP11-815F22 (chr5:54,253,088-54,457,288) overlap in the human sequence and in SEN3 (left), but are split apart by the upper breakpoint (green arrow in Fig. 2a) of the inversion involving blocks #5, #6, and #12, separating blocks #4 and #5 in the trajectory LCA → TCR1a. The two BACs RP11-932B11 and RP11-815F22, therefore, delimit the margins facing the breakpoint of the blocks #4 and #5, respectively. The apparent different position of BAC RP11-815F22 in TCR1b with respect to TCR1a is the result of subsequent inversions occurred in the line to TCR1b. (b, c and d) Examples of duplicated signals produced by BACs belonging to the duplicated segments mapping, in humans, at 34 Mb, 168 Mb, and 174 Mb respectively, as reported in Table 1.

Figure 2

Evolutionary history of CGU2, TCR1a/b, Y₁, Y₂, and SEN3 chromosomes. The Figure shows the different synteny blocks arrangement of the chromosomes under study, generated by rearrangements occurred since their catarrhini common ancestor (CCA4). Each synteny block was drawn, for clarity, as one unit, regardless of its length in nucleotides. Some blocks were very small (few Mb) and would be difficult to illustrate in the figure otherwise. The ideogram on the right of TCR1a, TCR1b, Y₁, and Y₂, and on the left of SEN3 roughly represents the relative size of blocks (for details see Supplemental File 1). The same LCA intermediate was shown three times, at beginning of each of the three evolutionary lines (TCR1a/b, Y₁, Y₂, and SEN3). The three LCA ideograms appear different in (a), (b), and (c) because LCA^b and LCA^c were drawn to reflect the position, in LCA, of blocks composing SEN3, Y₁, and Y₂, respectively. The sequence orientation of each block with respect to CCA4 is indicated by an arrow on the right of the block. Down-pointing black arrows and up-pointing red arrows indicate concordant or reverse sequence orientation with respect to the human sequence, respectively. Inversions are represented by a red parenthesis on the right or left of the ideograms. TCR1b and Y₂ arms are represented upside down to better illustrate the flow of rearrangements and block orientation. Dots external to blocks (on left or right) and close to the upper or lower margin, indicate that the margin was reused two times (white dots), three times (blue dots), or four times (red dots). The lines connecting dots (i.e. same margins) were arbitrarily drawn in different shapes just to make them more easily distinguishable each other. Segmental duplication (SD) were annotated as small triangles adjacent to the margin where the FISH signal was detected, as indicated in the box in the upper left side. Multiple FISH signals generated by BACs mapping at 33–34, 168, and 174 Mb are represented by empty triangles, red triangles, and blue triangles, respectively. Details on these BACs are reported in Table 1. The thick blue segment between blocks 4/14 and 4/10 present in TCR1a and TCR1b respectively, indicates the localization of the extra-band lit up by the total TCR genomic DNA (see Fig. 4). The green arrow in Fig. 2a points to a breakpoint illustrated in Fig. 1a. For details see text.

Figure 3

Margins shared among synteny blocks. This Figure simplifies the data of block margins present in columns J/K/L/M of the HSA5 sheet of Supplemental File 1. It shows the reciprocal relationship of the different synteny blocks, for an easy identification of shared margins. Thick segments indicate shared margins. Actual blocks sizes (Mb) are annotated in parenthesis. The orientation is indicated by color: black for forward and red for reverse sequence orientation.

Figure 4

FISH of total TCR genomic DNA on male TCR metaphase. (a) Total genomic DNA was used as probe in high stringency FISH experiments on male TCR metaphase (signals in green). The red signal is due to BAC RP11-1115K14 used as a marker for Y₂ identification. The BAC maps, in humans, to chr5:96,675,964-96,821,846, inside block #7 of TCR1 and block “f” of Y₂ (see Fig. 3). The small arrow points to the heterochromatic block of the distal part of chromosome Y present in Y₂ (see Fig. 2c). The large arrow points to the extra-band on TCR1, absent in Y₁ and Y₂. Note the large size variations among centromeres of different chromosomes. (b) A partial metaphase showing a cohybridization experiment of total male TCR genomic DNA (green) and BAC RP11-919B20 (red) on the male metaphase, which yielded duplicated signals surrounding the extra-band. The BAC belong to the duplicated domain at 33–34 Mb (see Table 1). The DAPI banding alone is shown on the left to show that the extra-band appear pale as does the centromeric satellite DNA.